diff --git a/dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml b/dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml index fcba2c4b29..e4d85bf399 100644 --- a/dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml +++ b/dhp-build/dhp-code-style/src/main/resources/eclipse/formatter_dnet.xml @@ -19,7 +19,7 @@ - + diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 0819a8bd20..1dc3208b5a 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -87,6 +87,11 @@ org.postgresql postgresql + + + com.squareup.okhttp3 + okhttp + diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/InputStreamRequestBody.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/InputStreamRequestBody.java new file mode 100644 index 0000000000..c3f3934363 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/InputStreamRequestBody.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.dhp.common.api; + +import java.io.IOException; +import java.io.InputStream; + +import okhttp3.MediaType; +import okhttp3.RequestBody; +import okhttp3.internal.Util; +import okio.BufferedSink; +import okio.Okio; +import okio.Source; + +public class InputStreamRequestBody extends RequestBody { + + private InputStream inputStream; + private MediaType mediaType; + private long lenght; + + public static RequestBody create(final MediaType mediaType, final InputStream inputStream, final long len) { + + return new InputStreamRequestBody(inputStream, mediaType, len); + } + + private InputStreamRequestBody(InputStream inputStream, MediaType mediaType, long len) { + this.inputStream = inputStream; + this.mediaType = mediaType; + this.lenght = len; + } + + @Override + public MediaType contentType() { + return mediaType; + } + + @Override + public long contentLength() { + + return lenght; + + } + + @Override + public void writeTo(BufferedSink sink) throws IOException { + Source source = null; + try { + source = Okio.source(inputStream); + sink.writeAll(source); + } finally { + Util.closeQuietly(source); + } + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java new file mode 100644 index 0000000000..b75872eb48 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java @@ -0,0 +1,8 @@ + +package eu.dnetlib.dhp.common.api; + +public class MissingConceptDoiException extends Throwable { + public MissingConceptDoiException(String message) { + super(message); + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java new file mode 100644 index 0000000000..f2dd4f0ac8 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java @@ -0,0 +1,264 @@ + +package eu.dnetlib.dhp.common.api; + +import java.io.*; +import java.io.IOException; + +import com.google.gson.Gson; + +import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel; +import eu.dnetlib.dhp.common.api.zenodo.ZenodoModelList; +import okhttp3.*; + +public class ZenodoAPIClient implements Serializable { + + String urlString; + String bucket; + + String deposition_id; + String access_token; + + public static final MediaType MEDIA_TYPE_JSON = MediaType.parse("application/json; charset=utf-8"); + + private static final MediaType MEDIA_TYPE_ZIP = MediaType.parse("application/zip"); + + public String getUrlString() { + return urlString; + } + + public void setUrlString(String urlString) { + this.urlString = urlString; + } + + public String getBucket() { + return bucket; + } + + public void setBucket(String bucket) { + this.bucket = bucket; + } + + public void setDeposition_id(String deposition_id) { + this.deposition_id = deposition_id; + } + + public ZenodoAPIClient(String urlString, String access_token) throws IOException { + + this.urlString = urlString; + this.access_token = access_token; + } + + /** + * Brand new deposition in Zenodo. It sets the deposition_id and the bucket where to store the files to upload + * @return response code + * @throws IOException + */ + public int newDeposition() throws IOException { + String json = "{}"; + OkHttpClient httpClient = new OkHttpClient(); + + RequestBody body = RequestBody.create(MEDIA_TYPE_JSON, json); + + Request request = new Request.Builder() + .url(urlString) + .addHeader("Content-Type", "application/json") // add request headers + .addHeader("Authorization", "Bearer " + access_token) + .post(body) + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + + // Get response body + json = response.body().string(); + + ZenodoModel newSubmission = new Gson().fromJson(json, ZenodoModel.class); + this.bucket = newSubmission.getLinks().getBucket(); + this.deposition_id = newSubmission.getId(); + + return response.code(); + + } + + } + + /** + * Upload files in Zenodo. + * @param is the inputStream for the file to upload + * @param file_name the name of the file as it will appear on Zenodo + * @param len the size of the file + * @return the response code + */ + public int uploadIS(InputStream is, String file_name, long len) throws IOException { + OkHttpClient httpClient = new OkHttpClient(); + + Request request = new Request.Builder() + .url(bucket + "/" + file_name) + .addHeader("Content-Type", "application/zip") // add request headers + .addHeader("Authorization", "Bearer " + access_token) + .put(InputStreamRequestBody.create(MEDIA_TYPE_ZIP, is, len)) + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + return response.code(); + } + } + + /** + * Associates metadata information to the current deposition + * @param metadata the metadata + * @return response code + * @throws IOException + */ + public int sendMretadata(String metadata) throws IOException { + + OkHttpClient httpClient = new OkHttpClient(); + + RequestBody body = RequestBody.create(MEDIA_TYPE_JSON, metadata); + + Request request = new Request.Builder() + .url(urlString + "/" + deposition_id) + .addHeader("Content-Type", "application/json") // add request headers + .addHeader("Authorization", "Bearer " + access_token) + .put(body) + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + + return response.code(); + + } + + } + + /** + * To publish the current deposition. It works for both new deposition or new version of an old deposition + * @return response code + * @throws IOException + */ + public int publish() throws IOException { + + String json = "{}"; + + OkHttpClient httpClient = new OkHttpClient(); + + Request request = new Request.Builder() + .url(urlString + "/" + deposition_id + "/actions/publish") + .addHeader("Authorization", "Bearer " + access_token) + .post(RequestBody.create(MEDIA_TYPE_JSON, json)) + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + + return response.code(); + + } + } + + /** + * To create a new version of an already published deposition. + * It sets the deposition_id and the bucket to be used for the new version. + * @param concept_rec_id the concept record id of the deposition for which to create a new version. It is + * the last part of the url for the DOI Zenodo suggests to use to cite all versions: + * DOI: 10.xxx/zenodo.656930 concept_rec_id = 656930 + * @return response code + * @throws IOException + * @throws MissingConceptDoiException + */ + public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException { + setDepositionId(concept_rec_id); + String json = "{}"; + + OkHttpClient httpClient = new OkHttpClient(); + + Request request = new Request.Builder() + .url(urlString + "/" + deposition_id + "/actions/newversion") + .addHeader("Authorization", "Bearer " + access_token) + .post(RequestBody.create(MEDIA_TYPE_JSON, json)) + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + + ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class); + String latest_draft = zenodoModel.getLinks().getLatest_draft(); + deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1); + bucket = getBucket(latest_draft); + return response.code(); + + } + } + + private void setDepositionId(String concept_rec_id) throws IOException, MissingConceptDoiException { + + ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class); + + for (ZenodoModel zm : zenodoModelList) { + if (zm.getConceptrecid().equals(concept_rec_id)) { + deposition_id = zm.getId(); + return; + } + } + + throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions"); + + } + + private String getPrevDepositions() throws IOException { + OkHttpClient httpClient = new OkHttpClient(); + + Request request = new Request.Builder() + .url(urlString) + .addHeader("Content-Type", "application/json") // add request headers + .addHeader("Authorization", "Bearer " + access_token) + .get() + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + + return response.body().string(); + + } + + } + + private String getBucket(String url) throws IOException { + OkHttpClient httpClient = new OkHttpClient(); + + Request request = new Request.Builder() + .url(url) + .addHeader("Content-Type", "application/json") // add request headers + .addHeader("Authorization", "Bearer " + access_token) + .get() + .build(); + + try (Response response = httpClient.newCall(request).execute()) { + + if (!response.isSuccessful()) + throw new IOException("Unexpected code " + response + response.body().string()); + + // Get response body + ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class); + + return zenodoModel.getLinks().getBucket(); + + } + + } + +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Community.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Community.java new file mode 100644 index 0000000000..a022243830 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Community.java @@ -0,0 +1,14 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +public class Community { + private String identifier; + + public String getIdentifier() { + return identifier; + } + + public void setIdentifier(String identifier) { + this.identifier = identifier; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java new file mode 100644 index 0000000000..c03762693b --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java @@ -0,0 +1,47 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +public class Creator { + private String affiliation; + private String name; + private String orcid; + + public String getAffiliation() { + return affiliation; + } + + public void setAffiliation(String affiliation) { + this.affiliation = affiliation; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getOrcid() { + return orcid; + } + + public void setOrcid(String orcid) { + this.orcid = orcid; + } + + public static Creator newInstance(String name, String affiliation, String orcid) { + Creator c = new Creator(); + if (!(name == null)) { + c.name = name; + } + if (!(affiliation == null)) { + c.affiliation = affiliation; + } + if (!(orcid == null)) { + c.orcid = orcid; + } + + return c; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java new file mode 100644 index 0000000000..c7428de7d4 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; + +import net.minidev.json.annotate.JsonIgnore; + +public class File implements Serializable { + private String checksum; + private String filename; + private long filesize; + private String id; + + @JsonIgnore + // private Links links; + + public String getChecksum() { + return checksum; + } + + public void setChecksum(String checksum) { + this.checksum = checksum; + } + + public String getFilename() { + return filename; + } + + public void setFilename(String filename) { + this.filename = filename; + } + + public long getFilesize() { + return filesize; + } + + public void setFilesize(long filesize) { + this.filesize = filesize; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + +// @JsonIgnore +// public Links getLinks() { +// return links; +// } +// +// @JsonIgnore +// public void setLinks(Links links) { +// this.links = links; +// } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Grant.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Grant.java new file mode 100644 index 0000000000..476f1d9d89 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Grant.java @@ -0,0 +1,23 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; + +public class Grant implements Serializable { + private String id; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public static Grant newInstance(String id) { + Grant g = new Grant(); + g.id = id; + + return g; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Links.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Links.java new file mode 100644 index 0000000000..bdf8e5d2cf --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Links.java @@ -0,0 +1,92 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; + +public class Links implements Serializable { + + private String bucket; + + private String discard; + + private String edit; + private String files; + private String html; + private String latest_draft; + private String latest_draft_html; + private String publish; + + private String self; + + public String getBucket() { + return bucket; + } + + public void setBucket(String bucket) { + this.bucket = bucket; + } + + public String getDiscard() { + return discard; + } + + public void setDiscard(String discard) { + this.discard = discard; + } + + public String getEdit() { + return edit; + } + + public void setEdit(String edit) { + this.edit = edit; + } + + public String getFiles() { + return files; + } + + public void setFiles(String files) { + this.files = files; + } + + public String getHtml() { + return html; + } + + public void setHtml(String html) { + this.html = html; + } + + public String getLatest_draft() { + return latest_draft; + } + + public void setLatest_draft(String latest_draft) { + this.latest_draft = latest_draft; + } + + public String getLatest_draft_html() { + return latest_draft_html; + } + + public void setLatest_draft_html(String latest_draft_html) { + this.latest_draft_html = latest_draft_html; + } + + public String getPublish() { + return publish; + } + + public void setPublish(String publish) { + this.publish = publish; + } + + public String getSelf() { + return self; + } + + public void setSelf(String self) { + this.self = self; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Metadata.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Metadata.java new file mode 100644 index 0000000000..b161adb9b5 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Metadata.java @@ -0,0 +1,153 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; +import java.util.List; + +public class Metadata implements Serializable { + + private String access_right; + private List communities; + private List creators; + private String description; + private String doi; + private List grants; + private List keywords; + private String language; + private String license; + private PrereserveDoi prereserve_doi; + private String publication_date; + private List references; + private List related_identifiers; + private String title; + private String upload_type; + private String version; + + public String getUpload_type() { + return upload_type; + } + + public void setUpload_type(String upload_type) { + this.upload_type = upload_type; + } + + public String getVersion() { + return version; + } + + public void setVersion(String version) { + this.version = version; + } + + public String getAccess_right() { + return access_right; + } + + public void setAccess_right(String access_right) { + this.access_right = access_right; + } + + public List getCommunities() { + return communities; + } + + public void setCommunities(List communities) { + this.communities = communities; + } + + public List getCreators() { + return creators; + } + + public void setCreators(List creators) { + this.creators = creators; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public List getGrants() { + return grants; + } + + public void setGrants(List grants) { + this.grants = grants; + } + + public List getKeywords() { + return keywords; + } + + public void setKeywords(List keywords) { + this.keywords = keywords; + } + + public String getLanguage() { + return language; + } + + public void setLanguage(String language) { + this.language = language; + } + + public String getLicense() { + return license; + } + + public void setLicense(String license) { + this.license = license; + } + + public PrereserveDoi getPrereserve_doi() { + return prereserve_doi; + } + + public void setPrereserve_doi(PrereserveDoi prereserve_doi) { + this.prereserve_doi = prereserve_doi; + } + + public String getPublication_date() { + return publication_date; + } + + public void setPublication_date(String publication_date) { + this.publication_date = publication_date; + } + + public List getReferences() { + return references; + } + + public void setReferences(List references) { + this.references = references; + } + + public List getRelated_identifiers() { + return related_identifiers; + } + + public void setRelated_identifiers(List related_identifiers) { + this.related_identifiers = related_identifiers; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/PrereserveDoi.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/PrereserveDoi.java new file mode 100644 index 0000000000..aa088ef318 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/PrereserveDoi.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; + +public class PrereserveDoi implements Serializable { + private String doi; + private String recid; + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public String getRecid() { + return recid; + } + + public void setRecid(String recid) { + this.recid = recid; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/RelatedIdentifier.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/RelatedIdentifier.java new file mode 100644 index 0000000000..15a349636a --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/RelatedIdentifier.java @@ -0,0 +1,43 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; + +public class RelatedIdentifier implements Serializable { + private String identifier; + private String relation; + private String resource_type; + private String scheme; + + public String getIdentifier() { + return identifier; + } + + public void setIdentifier(String identifier) { + this.identifier = identifier; + } + + public String getRelation() { + return relation; + } + + public void setRelation(String relation) { + this.relation = relation; + } + + public String getResource_type() { + return resource_type; + } + + public void setResource_type(String resource_type) { + this.resource_type = resource_type; + } + + public String getScheme() { + return scheme; + } + + public void setScheme(String scheme) { + this.scheme = scheme; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModel.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModel.java new file mode 100644 index 0000000000..9843ea0f99 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModel.java @@ -0,0 +1,118 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.io.Serializable; +import java.util.List; + +public class ZenodoModel implements Serializable { + + private String conceptrecid; + private String created; + + private List files; + private String id; + private Links links; + private Metadata metadata; + private String modified; + private String owner; + private String record_id; + private String state; + private boolean submitted; + private String title; + + public String getConceptrecid() { + return conceptrecid; + } + + public void setConceptrecid(String conceptrecid) { + this.conceptrecid = conceptrecid; + } + + public String getCreated() { + return created; + } + + public void setCreated(String created) { + this.created = created; + } + + public List getFiles() { + return files; + } + + public void setFiles(List files) { + this.files = files; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public Links getLinks() { + return links; + } + + public void setLinks(Links links) { + this.links = links; + } + + public Metadata getMetadata() { + return metadata; + } + + public void setMetadata(Metadata metadata) { + this.metadata = metadata; + } + + public String getModified() { + return modified; + } + + public void setModified(String modified) { + this.modified = modified; + } + + public String getOwner() { + return owner; + } + + public void setOwner(String owner) { + this.owner = owner; + } + + public String getRecord_id() { + return record_id; + } + + public void setRecord_id(String record_id) { + this.record_id = record_id; + } + + public String getState() { + return state; + } + + public void setState(String state) { + this.state = state; + } + + public boolean isSubmitted() { + return submitted; + } + + public void setSubmitted(boolean submitted) { + this.submitted = submitted; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java new file mode 100644 index 0000000000..b3b1507143 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java @@ -0,0 +1,7 @@ + +package eu.dnetlib.dhp.common.api.zenodo; + +import java.util.ArrayList; + +public class ZenodoModelList extends ArrayList { +} diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java index 97fe4b9d83..9552eb2b32 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java @@ -1,15 +1,22 @@ package eu.dnetlib.dhp.utils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; +import java.util.Map; + +import javax.xml.ws.BindingProvider; + import org.apache.cxf.jaxws.JaxWsProxyFactoryBean; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; public class ISLookupClientFactory { - private static final Log log = LogFactory.getLog(ISLookupClientFactory.class); + private static final Logger log = LoggerFactory.getLogger(ISLookupClientFactory.class); + + private static int requestTimeout = 60000 * 10; + private static int connectTimeout = 60000 * 10; public static ISLookUpService getLookUpService(final String isLookupUrl) { return getServiceStub(ISLookUpService.class, isLookupUrl); @@ -21,6 +28,25 @@ public class ISLookupClientFactory { final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean(); jaxWsProxyFactory.setServiceClass(clazz); jaxWsProxyFactory.setAddress(endpoint); - return (T) jaxWsProxyFactory.create(); + + final T service = (T) jaxWsProxyFactory.create(); + + if (service instanceof BindingProvider) { + log + .info( + "setting timeouts for {} to requestTimeout: {}, connectTimeout: {}", + BindingProvider.class.getName(), requestTimeout, connectTimeout); + + Map requestContext = ((BindingProvider) service).getRequestContext(); + + requestContext.put("com.sun.xml.internal.ws.request.timeout", requestTimeout); + requestContext.put("com.sun.xml.internal.ws.connect.timeout", connectTimeout); + requestContext.put("com.sun.xml.ws.request.timeout", requestTimeout); + requestContext.put("com.sun.xml.ws.connect.timeout", connectTimeout); + requestContext.put("javax.xml.ws.client.receiveTimeout", requestTimeout); + requestContext.put("javax.xml.ws.client.connectionTimeout", connectTimeout); + } + + return service; } } diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java new file mode 100644 index 0000000000..f961d67483 --- /dev/null +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java @@ -0,0 +1,85 @@ + +package eu.dnetlib.dhp.common.api; + +import java.io.File; +import java.io.FileInputStream; +import java.io.IOException; +import java.io.InputStream; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +@Disabled +public class ZenodoAPIClientTest { + + private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions"; + private final String ACCESS_TOKEN = ""; + + private final String CONCEPT_REC_ID = "657113"; + + @Test + public void testNewDeposition() throws IOException { + + ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, + ACCESS_TOKEN); + Assertions.assertEquals(201, client.newDeposition()); + + File file = new File(getClass() + .getResource("/eu/dnetlib/dhp/common/api/COVID-19.json.gz") + .getPath()); + + InputStream is = new FileInputStream(file); + + Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz", file.length())); + + String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json")); + + Assertions.assertEquals(200, client.sendMretadata(metadata)); + + Assertions.assertEquals(202, client.publish()); + + } + + @Test + public void testNewVersionNewName() throws IOException, MissingConceptDoiException { + + ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, + ACCESS_TOKEN); + + Assertions.assertEquals(201, client.newVersion(CONCEPT_REC_ID)); + + File file = new File(getClass() + .getResource("/eu/dnetlib/dhp/common/api/newVersion") + .getPath()); + + InputStream is = new FileInputStream(file); + + Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition", file.length())); + + Assertions.assertEquals(202, client.publish()); + + } + + @Test + public void testNewVersionOldName() throws IOException, MissingConceptDoiException { + + ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, + ACCESS_TOKEN); + + Assertions.assertEquals(201, client.newVersion(CONCEPT_REC_ID)); + + File file = new File(getClass() + .getResource("/eu/dnetlib/dhp/common/api/newVersion2") + .getPath()); + + InputStream is = new FileInputStream(file); + + Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition", file.length())); + + Assertions.assertEquals(202, client.publish()); + + } + +} diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/metadata.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/metadata.json new file mode 100644 index 0000000000..eab3ae278a --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/metadata.json @@ -0,0 +1 @@ +{"metadata":{"access_right":"open","communities":[{"identifier":"openaire-research-graph"}],"creators":[{"affiliation":"ISTI - CNR","name":"Bardi, Alessia","orcid":"0000-0002-1112-1292"},{"affiliation":"eifl", "name":"Kuchma, Iryna"},{"affiliation":"BIH", "name":"Brobov, Evgeny"},{"affiliation":"GIDIF RBM", "name":"Truccolo, Ivana"},{"affiliation":"unesp", "name":"Monteiro, Elizabete"},{"affiliation":"und", "name":"Casalegno, Carlotta"},{"affiliation":"CARL ABRC", "name":"Clary, Erin"},{"affiliation":"The University of Edimburgh", "name":"Romanowski, Andrew"},{"affiliation":"ISTI - CNR", "name":"Pavone, Gina"},{"affiliation":"ISTI - CNR", "name":"Artini, Michele"},{"affiliation":"ISTI - CNR","name":"Atzori, Claudio","orcid":"0000-0001-9613-6639"},{"affiliation":"University of Bielefeld","name":"Bäcker, Amelie","orcid":"0000-0001-6015-2063"},{"affiliation":"ISTI - CNR","name":"Baglioni, Miriam","orcid":"0000-0002-2273-9004"},{"affiliation":"University of Bielefeld","name":"Czerniak, Andreas","orcid":"0000-0003-3883-4169"},{"affiliation":"ISTI - CNR","name":"De Bonis, Michele"},{"affiliation":"Athena Research and Innovation Centre","name":"Dimitropoulos, Harry"},{"affiliation":"Athena Research and Innovation Centre","name":"Foufoulas, Ioannis"},{"affiliation":"University of Warsaw","name":"Horst, Marek"},{"affiliation":"Athena Research and Innovation Centre","name":"Iatropoulou, Katerina"},{"affiliation":"University of Warsaw","name":"Jacewicz, Przemyslaw"},{"affiliation":"Athena Research and Innovation Centre","name":"Kokogiannaki, Argiro", "orcid":"0000-0002-3880-0244"},{"affiliation":"ISTI - CNR","name":"La Bruzzo, Sandro","orcid":"0000-0003-2855-1245"},{"affiliation":"ISTI - CNR","name":"Lazzeri, Emma"},{"affiliation":"University of Bielefeld","name":"Löhden, Aenne"},{"affiliation":"ISTI - CNR","name":"Manghi, Paolo","orcid":"0000-0001-7291-3210"},{"affiliation":"ISTI - CNR","name":"Mannocci, Andrea","orcid":"0000-0002-5193-7851"},{"affiliation":"Athena Research and Innovation Center","name":"Manola, Natalia"},{"affiliation":"ISTI - CNR","name":"Ottonello, Enrico"},{"affiliation":"University of Bielefeld","name":"Shirrwagen, Jochen"}],"description":"\\u003cp\\u003eThis dump provides access to the metadata records of publications, research data, software and projects that may be relevant to the Corona Virus Disease (COVID-19) fight. The dump contains records of the OpenAIRE COVID-19 Gateway (https://covid-19.openaire.eu/), identified via full-text mining and inference techniques applied to the OpenAIRE Research Graph (https://explore.openaire.eu/). The Graph is one of the largest Open Access collections of metadata records and links between publications, datasets, software, projects, funders, and organizations, aggregating 12,000+ scientific data sources world-wide, among which the Covid-19 data sources Zenodo COVID-19 Community, WHO (World Health Organization), BIP! FInder for COVID-19, Protein Data Bank, Dimensions, scienceOpen, and RSNA. \\u003cp\\u003eThe dump consists of a gzip file containing one json per line. Each json is compliant to the schema available at https://doi.org/10.5281/zenodo.3974226\\u003c/p\\u003e ","title":"OpenAIRE Covid-19 publications, datasets, software and projects metadata.","upload_type":"dataset","version":"1.0"}} \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newDeposition b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newDeposition new file mode 100644 index 0000000000..df7dfb0415 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newDeposition @@ -0,0 +1 @@ +This is a test for a new deposition \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newVersion b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newVersion new file mode 100644 index 0000000000..eb8ec9ef2e --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newVersion @@ -0,0 +1 @@ +This is a test for a new version of an old deposition \ No newline at end of file diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newVersion2 b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newVersion2 new file mode 100644 index 0000000000..914a2442c8 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/common/api/newVersion2 @@ -0,0 +1,2 @@ +This is a test for a new version of an old deposition. This should replace the other new version. I expect to have only two +files in the deposition \ No newline at end of file diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java index bf48605d26..b27fc9267b 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java @@ -7,6 +7,7 @@ import eu.dnetlib.dhp.schema.oaf.Qualifier; public class ModelConstants { + public static final String DNET_SUBJECT_TYPOLOGIES = "dnet:subject_classification_typologies"; public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies"; public static final String DNET_PUBLICATION_RESOURCE = "dnet:publication_resource"; public static final String DNET_ACCESS_MODES = "dnet:access_modes"; diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java index 7d8be81ac9..b5bca2e93e 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java @@ -79,6 +79,15 @@ public class ModelSupport { entityIdPrefix.put("result", "50"); } + public static final Map idPrefixEntity = Maps.newHashMap(); + + static { + idPrefixEntity.put("10", "datasource"); + idPrefixEntity.put("20", "organization"); + idPrefixEntity.put("40", "project"); + idPrefixEntity.put("50", "result"); + } + public static final Map relationInverseMap = Maps.newHashMap(); static { diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/APC.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/APC.java new file mode 100644 index 0000000000..7f5dcb3976 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/APC.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +/** + * Used to refer to the Article Processing Charge information. Not dumped in this release. It contains two parameters: - + * currency of type String to store the currency of the APC - amount of type String to stores the charged amount + */ +public class APC implements Serializable { + private String currency; + private String amount; + + public String getCurrency() { + return currency; + } + + public void setCurrency(String currency) { + this.currency = currency; + } + + public String getAmount() { + return amount; + } + + public void setAmount(String amount) { + this.amount = amount; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/AccessRight.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/AccessRight.java new file mode 100644 index 0000000000..f28c544f67 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/AccessRight.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +/** + * AccessRight. Used to represent the result access rights. It extends the eu.dnet.lib.dhp.schema.dump.oaf.Qualifier + * element with a parameter scheme of type String to store the scheme. Values for this element are found against the + * COAR access right scheme. The classid of the element accessright in eu.dnetlib.dhp.schema.oaf.Result is used to get + * the COAR corresponding code whose value will be used to set the code parameter. The COAR label corresponding to the + * COAR code will be used to set the label parameter. The scheme value will always be the one referring to the COAR + * access right scheme + */ +public class AccessRight extends Qualifier { + + private String scheme; + + public String getScheme() { + return scheme; + } + + public void setScheme(String scheme) { + this.scheme = scheme; + } + + public static AccessRight newInstance(String code, String label, String scheme) { + AccessRight ar = new AccessRight(); + ar.setCode(code); + ar.setLabel(label); + ar.setScheme(scheme); + return ar; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Author.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Author.java new file mode 100644 index 0000000000..34920bcf77 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Author.java @@ -0,0 +1,73 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; +import java.util.List; + +/** + * Used to represent the generic author of the result. It has six parameters: - name of type String to store the given + * name of the author. The value for this parameter corresponds to eu.dnetlib.dhp.schema.oaf.Author name - surname of + * type String to store the family name of the author. The value for this parameter corresponds to + * eu.dnetlib.dhp.schema.oaf.Author surname - fullname of type String to store the fullname of the author. The value for + * this parameter corresponds to eu.dnetlib.dhp.schema.oaf.Author fullname - rank of type Integer to store the rank on + * the author in the result's authors list. The value for this parameter corresponds to eu.dnetlib.dhp.schema.oaf.Author + * rank - pid of type eu.dnetlib.dhp.schema.dump.oaf.Pid to store the persistent identifier for the author. For the + * moment only ORCID identifiers will be dumped. - The id element is instantiated by using the following values in the + * eu.dnetlib.dhp.schema.oaf.Result pid: * Qualifier.classid for scheme * value for value - The provenance element is + * instantiated only if the dataInfo is set for the pid in the result to be dumped. The provenance element is + * instantiated by using the following values in the eu.dnetlib.dhp.schema.oaf.Result pid: * + * dataInfo.provenanceaction.classname for provenance * dataInfo.trust for trust + */ +public class Author implements Serializable { + + private String fullname; + + private String name; + + private String surname; + + private Integer rank; + + private Pid pid; + + public String getFullname() { + return fullname; + } + + public void setFullname(String fullname) { + this.fullname = fullname; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getSurname() { + return surname; + } + + public void setSurname(String surname) { + this.surname = surname; + } + + public Integer getRank() { + return rank; + } + + public void setRank(Integer rank) { + this.rank = rank; + } + + public Pid getPid() { + return pid; + } + + public void setPid(Pid pid) { + this.pid = pid; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Container.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Container.java new file mode 100644 index 0000000000..8699528ca4 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Container.java @@ -0,0 +1,136 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; +import java.util.Objects; + +/** + * To store information about the conference or journal where the result has been presented or published. It contains + * eleven parameters: - name of type String to store the name of the journal or conference. It corresponds to the + * parameter name of eu.dnetlib.dhp.schema.oaf.Journal - issnPrinted ot type String to store the journal printed issn. + * It corresponds to the parameter issnPrinted of eu.dnetlib.dhp.schema.oaf.Journal - issnOnline of type String to store + * the journal online issn. It corresponds to the parameter issnOnline of eu.dnetlib.dhp.schema.oaf.Journal - + * issnLinking of type String to store the journal linking issn. It corresponds to the parameter issnLinking of + * eu.dnetlib.dhp.schema.oaf.Journal - ep of type String to store the end page. It corresponds to the parameter ep of + * eu.dnetlib.dhp.schema.oaf.Journal - iss of type String to store the journal issue. It corresponds to the parameter + * iss of eu.dnetlib.dhp.schema.oaf.Journal - sp of type String to store the start page. It corresponds to the parameter + * sp of eu.dnetlib.dhp.schema.oaf.Journal - vol of type String to store the Volume. It corresponds to the parameter vol + * of eu.dnetlib.dhp.schema.oaf.Journal - edition of type String to store the edition of the journal or conference + * proceeding. It corresponds to the parameter edition of eu.dnetlib.dhp.schema.oaf.Journal - conferenceplace of type + * String to store the place of the conference. It corresponds to the parameter conferenceplace of + * eu.dnetlib.dhp.schema.oaf.Journal - conferencedate of type String to store the date of the conference. It corresponds + * to the parameter conferencedate of eu.dnetlib.dhp.schema.oaf.Journal + */ +public class Container implements Serializable { + + private String name; + + private String issnPrinted; + + private String issnOnline; + + private String issnLinking; + + private String ep; + + private String iss; + + private String sp; + + private String vol; + + private String edition; + + private String conferenceplace; + + private String conferencedate; + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getIssnPrinted() { + return issnPrinted; + } + + public void setIssnPrinted(String issnPrinted) { + this.issnPrinted = issnPrinted; + } + + public String getIssnOnline() { + return issnOnline; + } + + public void setIssnOnline(String issnOnline) { + this.issnOnline = issnOnline; + } + + public String getIssnLinking() { + return issnLinking; + } + + public void setIssnLinking(String issnLinking) { + this.issnLinking = issnLinking; + } + + public String getEp() { + return ep; + } + + public void setEp(String ep) { + this.ep = ep; + } + + public String getIss() { + return iss; + } + + public void setIss(String iss) { + this.iss = iss; + } + + public String getSp() { + return sp; + } + + public void setSp(String sp) { + this.sp = sp; + } + + public String getVol() { + return vol; + } + + public void setVol(String vol) { + this.vol = vol; + } + + public String getEdition() { + return edition; + } + + public void setEdition(String edition) { + this.edition = edition; + } + + public String getConferenceplace() { + return conferenceplace; + } + + public void setConferenceplace(String conferenceplace) { + this.conferenceplace = conferenceplace; + } + + public String getConferencedate() { + return conferencedate; + } + + public void setConferencedate(String conferencedate) { + this.conferencedate = conferencedate; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/ControlledField.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/ControlledField.java new file mode 100644 index 0000000000..cad7b8b5c5 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/ControlledField.java @@ -0,0 +1,38 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +/** + * To represent the information described by a scheme and a value in that scheme (i.e. pid). It has two parameters: - + * scheme of type String to store the scheme - value of type String to store the value in that scheme + */ +public class ControlledField implements Serializable { + private String scheme; + private String value; + + public String getScheme() { + return scheme; + } + + public void setScheme(String scheme) { + this.scheme = scheme; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public static ControlledField newInstance(String scheme, String value) { + ControlledField cf = new ControlledField(); + + cf.setScheme(scheme); + cf.setValue(value); + + return cf; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Country.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Country.java new file mode 100644 index 0000000000..3ab4d90fe8 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Country.java @@ -0,0 +1,37 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +/** + * Represents the country associated to this result. It extends eu.dnetlib.dhp.schema.dump.oaf.Qualifier with a + * provenance parameter of type eu.dnetlib.dhp.schema.dumo.oaf.Provenance. The country in not mapped if its value in the + * result reprensented in the internal format is Unknown. The value for this element correspond to: - code corresponds + * to the classid of eu.dnetlib.dhp.schema.oaf.Country - label corresponds to the classname of + * eu.dnetlib.dhp.schema.oaf.Country - provenance set only if the dataInfo associated to the Country of the result to be + * dumped is not null. In this case : - provenance corresponds to dataInfo.provenanceaction.classid (to be modified with + * datainfo.provenanceaction.classname) - trust corresponds to dataInfo.trust + */ +public class Country extends Qualifier { + + private Provenance provenance; + + public Provenance getProvenance() { + return provenance; + } + + public void setProvenance(Provenance provenance) { + this.provenance = provenance; + } + + public static Country newInstance(String code, String label, Provenance provenance) { + Country c = new Country(); + c.setProvenance(provenance); + c.setCode(code); + c.setLabel(label); + return c; + } + + public static Country newInstance(String code, String label, String provenance, String trust) { + return newInstance(code, label, Provenance.newInstance(provenance, trust)); + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Funder.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Funder.java new file mode 100644 index 0000000000..16cab22cc5 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Funder.java @@ -0,0 +1,36 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +public class Funder implements Serializable { + private String shortName; + + private String name; + + private String jurisdiction; + + public String getJurisdiction() { + return jurisdiction; + } + + public void setJurisdiction(String jurisdiction) { + this.jurisdiction = jurisdiction; + } + + public String getShortName() { + return shortName; + } + + public void setShortName(String shortName) { + this.shortName = shortName; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/GeoLocation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/GeoLocation.java new file mode 100644 index 0000000000..6bd891bbd7 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/GeoLocation.java @@ -0,0 +1,53 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +import org.apache.commons.lang3.StringUtils; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +/** + * Represents the geolocation information. It has three parameters: - point of type String to store the point + * information. It corresponds to eu.dnetlib.dhp.schema.oaf.GeoLocation point - box ot type String to store the box + * information. It corresponds to eu.dnetlib.dhp.schema.oaf.GeoLocation box - place of type String to store the place + * information. It corresponds to eu.dnetlib.dhp.schema.oaf.GeoLocation place + */ +public class GeoLocation implements Serializable { + + private String point; + + private String box; + + private String place; + + public String getPoint() { + return point; + } + + public void setPoint(String point) { + this.point = point; + } + + public String getBox() { + return box; + } + + public void setBox(String box) { + this.box = box; + } + + public String getPlace() { + return place; + } + + public void setPlace(String place) { + this.place = place; + } + + @JsonIgnore + public boolean isBlank() { + return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place); + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Instance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Instance.java new file mode 100644 index 0000000000..4a09f5a865 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Instance.java @@ -0,0 +1,107 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; +import java.util.List; + +/** + * Represents the manifestations (i.e. different versions) of the result. For example: the pre-print and the published + * versions are two manifestations of the same research result. It has the following parameters: - license of type + * String to store the license applied to the instance. It corresponds to the value of the licence in the instance to be + * dumped - accessright of type eu.dnetlib.dhp.schema.dump.oaf.AccessRight to store the accessright of the instance. - + * type of type String to store the type of the instance as defined in the corresponding dnet vocabulary + * (dnet:pubication_resource). It corresponds to the instancetype.classname of the instance to be mapped - hostedby of + * type eu.dnetlib.dhp.schema.dump.oaf.KeyValue to store the information about the source from which the instance can be + * viewed or downloaded. It is mapped against the hostedby parameter of the instance to be dumped and - key corresponds + * to hostedby.key - value corresponds to hostedby.value - url of type List list of locations where the instance + * is accessible. It corresponds to url of the instance to be dumped - collectedfrom of type + * eu.dnetlib.dhp.schema.dump.oaf.KeyValue to store the information about the source from which the instance has been + * collected. It is mapped against the collectedfrom parameter of the instance to be dumped and - key corresponds to + * collectedfrom.key - value corresponds to collectedfrom.value - publicationdate of type String to store the + * publication date of the instance ;// dateofacceptance; - refereed of type String to store information abour tthe + * review status of the instance. Possible values are 'Unknown', 'nonPeerReviewed', 'peerReviewed'. It corresponds to + * refereed.classname of the instance to be dumped + */ +public class Instance implements Serializable { + + private String license; + + private AccessRight accessright; + + private String type; + + private KeyValue hostedby; + + private List url; + + private KeyValue collectedfrom; + + private String publicationdate;// dateofacceptance; + + private String refereed; // peer-review status + + public String getLicense() { + return license; + } + + public void setLicense(String license) { + this.license = license; + } + + public AccessRight getAccessright() { + return accessright; + } + + public void setAccessright(AccessRight accessright) { + this.accessright = accessright; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public KeyValue getHostedby() { + return hostedby; + } + + public void setHostedby(KeyValue hostedby) { + this.hostedby = hostedby; + } + + public List getUrl() { + return url; + } + + public void setUrl(List url) { + this.url = url; + } + + public KeyValue getCollectedfrom() { + return collectedfrom; + } + + public void setCollectedfrom(KeyValue collectedfrom) { + this.collectedfrom = collectedfrom; + } + + public String getPublicationdate() { + return publicationdate; + } + + public void setPublicationdate(String publicationdate) { + this.publicationdate = publicationdate; + } + + public String getRefereed() { + return refereed; + } + + public void setRefereed(String refereed) { + this.refereed = refereed; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/KeyValue.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/KeyValue.java new file mode 100644 index 0000000000..849aa4d3c8 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/KeyValue.java @@ -0,0 +1,48 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +import org.apache.commons.lang3.StringUtils; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +/** + * To represent the information described by a key and a value. It has two parameters: - key to store the key (generally + * the OpenAIRE id for some entity) - value to store the value (generally the OpenAIRE name for the key) + */ +public class KeyValue implements Serializable { + + private String key; + + private String value; + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } + + public static KeyValue newInstance(String key, String value) { + KeyValue inst = new KeyValue(); + inst.key = key; + inst.value = value; + return inst; + } + + @JsonIgnore + public boolean isBlank() { + return StringUtils.isBlank(key) && StringUtils.isBlank(value); + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Pid.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Pid.java new file mode 100644 index 0000000000..786ddb1d73 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Pid.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +/** + * To represent the generic persistent identifier. It has two parameters: - id of type + * eu.dnetlib.dhp.schema.dump.oaf.ControlledField to store the scheme and value of the Persistent Identifier. - + * provenance of type eu.dnetlib.dhp.schema.dump.oaf.Provenance to store the provenance and trust of the information + */ +public class Pid implements Serializable { + private ControlledField id; + private Provenance provenance; + + public ControlledField getId() { + return id; + } + + public void setId(ControlledField pid) { + this.id = pid; + } + + public Provenance getProvenance() { + return provenance; + } + + public void setProvenance(Provenance provenance) { + this.provenance = provenance; + } + + public static Pid newInstance(ControlledField pid, Provenance provenance) { + Pid p = new Pid(); + p.id = pid; + p.provenance = provenance; + + return p; + } + + public static Pid newInstance(ControlledField pid) { + Pid p = new Pid(); + p.id = pid; + + return p; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Project.java new file mode 100644 index 0000000000..f23d5a6703 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Project.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +public class Project implements Serializable { + protected String id;// OpenAIRE id + protected String code; + + protected String acronym; + + protected String title; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Provenance.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Provenance.java new file mode 100644 index 0000000000..28fb3aaa60 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Provenance.java @@ -0,0 +1,41 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +/** + * Indicates the process that produced (or provided) the information, and the trust associated to the information. It + * has two parameters: - provenance of type String to store the provenance of the information, - trust of type String to + * store the trust associated to the information + */ +public class Provenance implements Serializable { + private String provenance; + private String trust; + + public String getProvenance() { + return provenance; + } + + public void setProvenance(String provenance) { + this.provenance = provenance; + } + + public String getTrust() { + return trust; + } + + public void setTrust(String trust) { + this.trust = trust; + } + + public static Provenance newInstance(String provenance, String trust) { + Provenance p = new Provenance(); + p.provenance = provenance; + p.trust = trust; + return p; + } + + public String toString() { + return provenance + trust; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Qualifier.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Qualifier.java new file mode 100644 index 0000000000..348c22b316 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Qualifier.java @@ -0,0 +1,42 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +import org.apache.commons.lang3.StringUtils; + +import com.fasterxml.jackson.annotation.JsonIgnore; + +/** + * To represent the information described by a code and a value It has two parameters: - code to store the code + * (generally the classid of the eu.dnetlib.dhp.schema.oaf.Qualifier element) - label to store the label (generally the + * classname of the eu.dnetlib.dhp.schema.oaf.Qualifier element + */ +public class Qualifier implements Serializable { + + private String code; // the classid in the Qualifier + private String label; // the classname in the Qualifier + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getLabel() { + return label; + } + + public void setLabel(String label) { + this.label = label; + } + + public static Qualifier newInstance(String code, String value) { + Qualifier qualifier = new Qualifier(); + qualifier.setCode(code); + qualifier.setLabel(value); + return qualifier; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Result.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Result.java new file mode 100644 index 0000000000..97ee722595 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Result.java @@ -0,0 +1,391 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + +/** + * To represent the dumped result. It will be extended in the dump for Research Communities - Research + * Initiative/Infrastructures. It has the following parameters: - author of type + * List to describe the authors of a result. For each author in the result + * represented in the internal model one author in the esternal model is produced. - type of type String to represent + * the category of the result. Possible values are publication, dataset, software, other. It corresponds to + * resulttype.classname of the dumped result - language of type eu.dnetlib.dhp.schema.dump.oaf.Qualifier to store + * information about the language of the result. It is dumped as - code corresponds to language.classid - value + * corresponds to language.classname - country of type List to store the country + * list to which the result is associated. For each country in the result respresented in the internal model one country + * in the external model is produces - subjects of type List to store the subjects for + * the result. For each subject in the result represented in the internal model one subject in the external model is + * produced - maintitle of type String to store the main title of the result. It corresponds to the value of the first + * title in the resul to be dumped having classid equals to "main title" - subtitle of type String to store the subtitle + * of the result. It corresponds to the value of the first title in the resul to be dumped having classid equals to + * "subtitle" - description of type List to store the description of the result. It corresponds to the list of + * description.value in the result represented in the internal model - publicationdate of type String to store the + * pubblication date. It corresponds to dateofacceptance.value in the result represented in the internal model - + * publisher of type String to store information about the publisher. It corresponds to publisher.value of the result + * represented in the intrenal model - embargoenddate of type String to store the embargo end date. It corresponds to + * embargoenddate.value of the result represented in the internal model - source of type List See definition of + * Dublin Core field dc:source. It corresponds to the list of source.value in the result represented in the internal + * model - format of type List It corresponds to the list of format.value in the result represented in the + * internal model - contributor of type List to represent contributors for this result. It corresponds to the + * list of contributor.value in the result represented in the internal model - coverage of type String. It corresponds + * to the list of coverage.value in the result represented in the internal model - bestaccessright of type + * eu.dnetlib.dhp.schema.dump.oaf.AccessRight to store informatin about the openest access right associated to the + * manifestations of this research results. It corresponds to the same parameter in the result represented in the + * internal model - instance of type List to store all the instances associated + * to the result. It corresponds to the same parameter in the result represented in the internal model - container of + * type eu.dnetlib.dhp.schema/dump.oaf.Container (only for result of type publication). It corresponds to the parameter + * journal of the result represented in the internal model - documentationUrl of type List (only for results of + * type software) to store the URLs to the software documentation. It corresponds to the list of documentationUrl.value + * of the result represented in the internal model - codeRepositoryUrl of type String (only for results of type + * software) to store the URL to the repository with the source code. It corresponds to codeRepositoryUrl.value of the + * result represented in the internal model - programmingLanguage of type String (only for results of type software) to + * store the programming language. It corresponds to programmingLanguaga.classid of the result represented in the + * internal model - contactperson of type List (only for results of type other) to store the contact person for + * this result. It corresponds to the list of contactperson.value of the result represented in the internal model - + * contactgroup of type List (only for results of type other) to store the information for the contact group. It + * corresponds to the list of contactgroup.value of the result represented in the internal model - tool of type + * List (only fro results of type other) to store information about tool useful for the interpretation and/or + * re-used of the research product. It corresponds to the list of tool.value in the result represented in the internal + * modelt - size of type String (only for results of type dataset) to store the size of the dataset. It corresponds to + * size.value in the result represented in the internal model - version of type String (only for results of type + * dataset) to store the version. It corresponds to version.value of the result represented in the internal model - + * geolocation fo type List (only for results of type dataset) to store + * geolocation information. For each geolocation element in the result represented in the internal model a GeoLocation + * in the external model il produced - id of type String to store the OpenAIRE id of the result. It corresponds to the + * id of the result represented in the internal model - originalId of type List to store the original ids of the + * result. It corresponds to the originalId of the result represented in the internal model - pid of type + * List to store the persistent identifiers for the result. For each pid + * in the results represented in the internal model one pid in the external model is produced. The value correspondence + * is: - scheme corresponds to pid.qualifier.classid of the result represented in the internal model - value corresponds + * to the pid.value of the result represented in the internal model - dateofcollection of type String to store + * information about the time OpenAIRE collected the record. It corresponds to dateofcollection of the result + * represented in the internal model - lasteupdatetimestamp of type String to store the timestamp of the last update of + * the record. It corresponds to lastupdatetimestamp of the resord represented in the internal model + */ +public class Result implements Serializable { + + private List author; + + // resulttype allows subclassing results into publications | datasets | software + private String type; // resulttype + + // common fields + private Qualifier language; + + private List country; + + private List subjects; + + private String maintitle; + + private String subtitle; + + private List description; + + private String publicationdate; // dateofacceptance; + + private String publisher; + + private String embargoenddate; + + private List source; + + private List format; + + private List contributor; + + private List coverage; + + private AccessRight bestaccessright; + + private List instance; + + private Container container;// Journal + + private List documentationUrl; // software + + private String codeRepositoryUrl; // software + + private String programmingLanguage; // software + + private List contactperson; // orp + + private List contactgroup; // orp + + private List tool; // orp + + private String size; // dataset + + private String version; // dataset + + private List geolocation; // dataset + + private String id; + + private List originalId; + + private List pid; + + private String dateofcollection; + + private Long lastupdatetimestamp; + + public Long getLastupdatetimestamp() { + return lastupdatetimestamp; + } + + public void setLastupdatetimestamp(Long lastupdatetimestamp) { + this.lastupdatetimestamp = lastupdatetimestamp; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getOriginalId() { + return originalId; + } + + public void setOriginalId(List originalId) { + this.originalId = originalId; + } + + public List getPid() { + return pid; + } + + public void setPid(List pid) { + this.pid = pid; + } + + public String getDateofcollection() { + return dateofcollection; + } + + public void setDateofcollection(String dateofcollection) { + this.dateofcollection = dateofcollection; + } + + public List getAuthor() { + return author; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public Container getContainer() { + return container; + } + + public void setContainer(Container container) { + this.container = container; + } + + public void setAuthor(List author) { + this.author = author; + } + + public Qualifier getLanguage() { + return language; + } + + public void setLanguage(Qualifier language) { + this.language = language; + } + + public List getCountry() { + return country; + } + + public void setCountry(List country) { + this.country = country; + } + + public List getSubjects() { + return subjects; + } + + public void setSubjects(List subjects) { + this.subjects = subjects; + } + + public String getMaintitle() { + return maintitle; + } + + public void setMaintitle(String maintitle) { + this.maintitle = maintitle; + } + + public String getSubtitle() { + return subtitle; + } + + public void setSubtitle(String subtitle) { + this.subtitle = subtitle; + } + + public List getDescription() { + return description; + } + + public void setDescription(List description) { + this.description = description; + } + + public String getPublicationdate() { + return publicationdate; + } + + public void setPublicationdate(String publicationdate) { + this.publicationdate = publicationdate; + } + + public String getPublisher() { + return publisher; + } + + public void setPublisher(String publisher) { + this.publisher = publisher; + } + + public String getEmbargoenddate() { + return embargoenddate; + } + + public void setEmbargoenddate(String embargoenddate) { + this.embargoenddate = embargoenddate; + } + + public List getSource() { + return source; + } + + public void setSource(List source) { + this.source = source; + } + + public List getFormat() { + return format; + } + + public void setFormat(List format) { + this.format = format; + } + + public List getContributor() { + return contributor; + } + + public void setContributor(List contributor) { + this.contributor = contributor; + } + + public List getCoverage() { + return coverage; + } + + public void setCoverage(List coverage) { + this.coverage = coverage; + } + + public AccessRight getBestaccessright() { + return bestaccessright; + } + + public void setBestaccessright(AccessRight bestaccessright) { + this.bestaccessright = bestaccessright; + } + + public List getInstance() { + return instance; + } + + public void setInstance(List instance) { + this.instance = instance; + } + + public List getDocumentationUrl() { + return documentationUrl; + } + + public void setDocumentationUrl(List documentationUrl) { + this.documentationUrl = documentationUrl; + } + + public String getCodeRepositoryUrl() { + return codeRepositoryUrl; + } + + public void setCodeRepositoryUrl(String codeRepositoryUrl) { + this.codeRepositoryUrl = codeRepositoryUrl; + } + + public String getProgrammingLanguage() { + return programmingLanguage; + } + + public void setProgrammingLanguage(String programmingLanguage) { + this.programmingLanguage = programmingLanguage; + } + + public List getContactperson() { + return contactperson; + } + + public void setContactperson(List contactperson) { + this.contactperson = contactperson; + } + + public List getContactgroup() { + return contactgroup; + } + + public void setContactgroup(List contactgroup) { + this.contactgroup = contactgroup; + } + + public List getTool() { + return tool; + } + + public void setTool(List tool) { + this.tool = tool; + } + + public String getSize() { + return size; + } + + public void setSize(String size) { + this.size = size; + } + + public String getVersion() { + return version; + } + + public void setVersion(String version) { + this.version = version; + } + + public List getGeolocation() { + return geolocation; + } + + public void setGeolocation(List geolocation) { + this.geolocation = geolocation; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Subject.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Subject.java new file mode 100644 index 0000000000..5c4bbef3c4 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/Subject.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.schema.dump.oaf; + +import java.io.Serializable; + +/** + * To represent keywords associated to the result. It has two parameters: - subject of type + * eu.dnetlib.dhp.schema.dump.oaf.ControlledField to describe the subject. It mapped as: - schema it corresponds to + * qualifier.classid of the dumped subject - value it corresponds to the subject value - provenance of type + * eu.dnetlib.dhp.schema.dump.oaf.Provenance to represent the provenance of the subject. It is dumped only if dataInfo + * is not null. In this case: - provenance corresponds to dataInfo.provenanceaction.classname - trust corresponds to + * dataInfo.trust + */ +public class Subject implements Serializable { + private ControlledField subject; + private Provenance provenance; + + public ControlledField getSubject() { + return subject; + } + + public void setSubject(ControlledField subject) { + this.subject = subject; + } + + public Provenance getProvenance() { + return provenance; + } + + public void setProvenance(Provenance provenance) { + this.provenance = provenance; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/CommunityResult.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/CommunityResult.java new file mode 100644 index 0000000000..8c748e103a --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/CommunityResult.java @@ -0,0 +1,51 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.community; + +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; +import eu.dnetlib.dhp.schema.dump.oaf.Result; + +/** + * extends eu.dnetlib.dhp.schema.dump.oaf.Result with the following parameters: - projects of type + * List to store the list of projects related to the result. The + * information is added after the result is mapped to the external model - context of type + * List to store information about the RC RI related to the result. + * For each context in the result represented in the internal model one context in the external model is produced - + * collectedfrom of type List to store information about the sources from which + * the record has been collected. For each collectedfrom in the result represented in the internal model one + * collectedfrom in the external model is produced + */ +public class CommunityResult extends Result { + + private List projects; + + private List context; + + protected List collectedfrom; + + public List getCollectedfrom() { + return collectedfrom; + } + + public void setCollectedfrom(List collectedfrom) { + this.collectedfrom = collectedfrom; + } + + public List getProjects() { + return projects; + } + + public void setProjects(List projects) { + this.projects = projects; + } + + public List getContext() { + return context; + } + + public void setContext(List context) { + this.context = context; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Context.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Context.java new file mode 100644 index 0000000000..3ad692b30c --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Context.java @@ -0,0 +1,40 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.community; + +import java.util.List; +import java.util.Objects; + +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; +import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; + +/** + * Reference to a relevant research infrastructure, initiative or community (RI/RC) among those collaborating with + * OpenAIRE. It extend eu.dnetlib.dhp.shema.dump.oaf.Qualifier with a parameter provenance of type + * List to store the provenances of the association between the result and + * the RC/RI. The values for this element correspond to: - code: it corresponds to the id of the context in the result + * to be mapped. If the context id refers to a RC/RI and contains '::' only the part of the id before the first "::" + * will be used as value for code - label it corresponds to the label associated to the id. The information id taken + * from the profile of the RC/RI - provenance it is set only if the dataInfo associated to the contenxt element of the + * result to be dumped is not null. For each dataInfo one instance of type eu.dnetlib.dhp.schema.dump.oaf.Provenance is + * instantiated if the element datainfo.provenanceaction is not null. In this case - provenance corresponds to + * dataInfo.provenanceaction.classname - trust corresponds to dataInfo.trust + */ +public class Context extends Qualifier { + private List provenance; + + public List getProvenance() { + return provenance; + } + + public void setProvenance(List provenance) { + this.provenance = provenance; + } + + @Override + public int hashCode() { + String provenance = new String(); + this.provenance.forEach(p -> provenance.concat(p.toString())); + return Objects.hash(getCode(), getLabel(), provenance); + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Funder.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Funder.java new file mode 100644 index 0000000000..b795fd1006 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Funder.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.community; + +import java.io.Serializable; + +/** + * To store information about the funder funding the project related to the result. It has the following parameters: - + * shortName of type String to store the funder short name (e.c. AKA). - name of type String to store the funder name + * (e.c. Akademy of Finland) - fundingStream of type String to store the funding stream - jurisdiction of type String to + * store the jurisdiction of the funder + */ +public class Funder implements Serializable { + private String shortName; + + private String name; + + private String fundingStream; + + private String jurisdiction; + + public String getJurisdiction() { + return jurisdiction; + } + + public void setJurisdiction(String jurisdiction) { + this.jurisdiction = jurisdiction; + } + + public String getShortName() { + return shortName; + } + + public void setShortName(String shortName) { + this.shortName = shortName; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getFundingStream() { + return fundingStream; + } + + public void setFundingStream(String fundingStream) { + this.fundingStream = fundingStream; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Project.java new file mode 100644 index 0000000000..7e23a13114 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/community/Project.java @@ -0,0 +1,88 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.community; + +import java.io.Serializable; + +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; + +/** + * To store information about the project related to the result. This information is not directly mapped from the result + * represented in the internal model because it is not there. The mapped result will be enriched with project + * information derived by relation between results and projects. Project class has the following parameters: - id of + * type String to store the OpenAIRE id for the Project - code of type String to store the grant agreement - acronym of + * type String to store the acronym for the project - title of type String to store the title of the project - funder of + * type eu.dnetlib.dhp.schema.dump.oaf.community.Funder to store information about the funder funding the project - + * provenance of type eu.dnetlib.dhp.schema.dump.oaf.Provenance to store information about the. provenance of the + * association between the result and the project + */ +public class Project implements Serializable { + + private String id;// OpenAIRE id + private String code; + + private String acronym; + + private String title; + + private Funder funder; + + private Provenance provenance; + + public Provenance getProvenance() { + return provenance; + } + + public void setProvenance(Provenance provenance) { + this.provenance = provenance; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public Funder getFunder() { + return funder; + } + + public void setFunder(Funder funders) { + this.funder = funders; + } + + public static Project newInstance(String id, String code, String acronym, String title, Funder funder) { + Project project = new Project(); + project.setAcronym(acronym); + project.setCode(code); + project.setFunder(funder); + project.setId(id); + project.setTitle(title); + return project; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Constants.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Constants.java new file mode 100644 index 0000000000..35cc60c1c5 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Constants.java @@ -0,0 +1,21 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +public class Constants implements Serializable { + // collectedFrom va con isProvidedBy -> becco da ModelSupport + + public static final String HOSTED_BY = "isHostedBy"; + public static final String HOSTS = "hosts"; + + // community result uso isrelatedto + + public static final String RESULT_ENTITY = "result"; + public static final String DATASOURCE_ENTITY = "datasource"; + public static final String CONTEXT_ENTITY = "context"; + + public static final String CONTEXT_ID = "60"; + public static final String CONTEXT_NS_PREFIX = "context____"; + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Datasource.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Datasource.java new file mode 100644 index 0000000000..6b2b7b1ab7 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Datasource.java @@ -0,0 +1,316 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.Container; +import eu.dnetlib.dhp.schema.dump.oaf.ControlledField; +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; + +/** + * To store information about the datasource OpenAIRE collects information from. It contains the following parameters: - + * id of type String to store the OpenAIRE id for the datasource. It corresponds to the parameter id of the datasource + * represented in the internal model - originalId of type List to store the list of original ids associated to + * the datasource. It corresponds to the parameter originalId of the datasource represented in the internal model. The + * null values are filtered out - pid of type List to store the + * persistent identifiers for the datasource. For each pid in the datasource represented in the internal model one pid + * in the external model is produced as : - schema corresponds to pid.qualifier.classid of the datasource represented in + * the internal model - value corresponds to pid.value of the datasource represented in the internal model - + * datasourceType of type eu.dnetlib.dhp.schema.dump.oaf.ControlledField to store the datasource type (e.g. + * pubsrepository::institutional, Institutional Repository) as in the dnet vocabulary dnet:datasource_typologies. It + * corresponds to datasourcetype of the datasource represented in the internal model and : - code corresponds to + * datasourcetype.classid - value corresponds to datasourcetype.classname - openairecompatibility of type String to + * store information about the OpenAIRE compatibility of the ingested results (which guidelines they are compliant to). + * It corresponds to openairecompatibility.classname of the datasource represented in the internal model - officialname + * of type Sgtring to store the official name of the datasource. It correspond to officialname.value of the datasource + * represented in the internal model - englishname of type String to store the English name of the datasource. It + * corresponds to englishname.value of the datasource represented in the internal model - websiteurl of type String to + * store the URL of the website of the datasource. It corresponds to websiteurl.value of the datasource represented in + * the internal model - logourl of type String to store the URL of the logo for the datasource. It corresponds to + * logourl.value of the datasource represented in the internal model - dateofvalidation of type String to store the data + * of validation against the guidelines for the datasource records. It corresponds to dateofvalidation.value of the + * datasource represented in the internal model - description of type String to store the description for the + * datasource. It corresponds to description.value of the datasource represented in the internal model + */ +public class Datasource implements Serializable { + + private String id; // string + + private List originalId; // list string + + private List pid; // list + + private ControlledField datasourcetype; // value + + private String openairecompatibility; // value + + private String officialname; // string + + private String englishname; // string + + private String websiteurl; // string + + private String logourl; // string + + private String dateofvalidation; // string + + private String description; // description + + private List subjects; // List + + // opendoar specific fields (od*) + + private List languages; // odlanguages List + + private List contenttypes; // odcontent types List + + // re3data fields + private String releasestartdate; // string + + private String releaseenddate; // string + + private String missionstatementurl; // string + + // {open, restricted or closed} + private String accessrights; // databaseaccesstype string + + // {open, restricted or closed} + private String uploadrights; // datauploadtype string + + // {feeRequired, registration, other} + private String databaseaccessrestriction; // string + + // {feeRequired, registration, other} + private String datauploadrestriction; // string + + private Boolean versioning; // boolean + + private String citationguidelineurl; // string + + // {yes, no, uknown} + + private String pidsystems; // string + + private String certificates; // string + + private List policies; // + + private Container journal; // issn etc del Journal + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getOriginalId() { + return originalId; + } + + public void setOriginalId(List originalId) { + this.originalId = originalId; + } + + public List getPid() { + return pid; + } + + public void setPid(List pid) { + this.pid = pid; + } + + public ControlledField getDatasourcetype() { + return datasourcetype; + } + + public void setDatasourcetype(ControlledField datasourcetype) { + this.datasourcetype = datasourcetype; + } + + public String getOpenairecompatibility() { + return openairecompatibility; + } + + public void setOpenairecompatibility(String openairecompatibility) { + this.openairecompatibility = openairecompatibility; + } + + public String getOfficialname() { + return officialname; + } + + public void setOfficialname(String officialname) { + this.officialname = officialname; + } + + public String getEnglishname() { + return englishname; + } + + public void setEnglishname(String englishname) { + this.englishname = englishname; + } + + public String getWebsiteurl() { + return websiteurl; + } + + public void setWebsiteurl(String websiteurl) { + this.websiteurl = websiteurl; + } + + public String getLogourl() { + return logourl; + } + + public void setLogourl(String logourl) { + this.logourl = logourl; + } + + public String getDateofvalidation() { + return dateofvalidation; + } + + public void setDateofvalidation(String dateofvalidation) { + this.dateofvalidation = dateofvalidation; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public List getSubjects() { + return subjects; + } + + public void setSubjects(List subjects) { + this.subjects = subjects; + } + + public List getLanguages() { + return languages; + } + + public void setLanguages(List languages) { + this.languages = languages; + } + + public List getContenttypes() { + return contenttypes; + } + + public void setContenttypes(List contenttypes) { + this.contenttypes = contenttypes; + } + + public String getReleasestartdate() { + return releasestartdate; + } + + public void setReleasestartdate(String releasestartdate) { + this.releasestartdate = releasestartdate; + } + + public String getReleaseenddate() { + return releaseenddate; + } + + public void setReleaseenddate(String releaseenddate) { + this.releaseenddate = releaseenddate; + } + + public String getMissionstatementurl() { + return missionstatementurl; + } + + public void setMissionstatementurl(String missionstatementurl) { + this.missionstatementurl = missionstatementurl; + } + + public String getAccessrights() { + return accessrights; + } + + public void setAccessrights(String accessrights) { + this.accessrights = accessrights; + } + + public String getUploadrights() { + return uploadrights; + } + + public void setUploadrights(String uploadrights) { + this.uploadrights = uploadrights; + } + + public String getDatabaseaccessrestriction() { + return databaseaccessrestriction; + } + + public void setDatabaseaccessrestriction(String databaseaccessrestriction) { + this.databaseaccessrestriction = databaseaccessrestriction; + } + + public String getDatauploadrestriction() { + return datauploadrestriction; + } + + public void setDatauploadrestriction(String datauploadrestriction) { + this.datauploadrestriction = datauploadrestriction; + } + + public Boolean getVersioning() { + return versioning; + } + + public void setVersioning(Boolean versioning) { + this.versioning = versioning; + } + + public String getCitationguidelineurl() { + return citationguidelineurl; + } + + public void setCitationguidelineurl(String citationguidelineurl) { + this.citationguidelineurl = citationguidelineurl; + } + + public String getPidsystems() { + return pidsystems; + } + + public void setPidsystems(String pidsystems) { + this.pidsystems = pidsystems; + } + + public String getCertificates() { + return certificates; + } + + public void setCertificates(String certificates) { + this.certificates = certificates; + } + + public List getPolicies() { + return policies; + } + + public void setPolicies(List policiesr3) { + this.policies = policiesr3; + } + + public Container getJournal() { + return journal; + } + + public void setJournal(Container journal) { + this.journal = journal; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Funder.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Funder.java new file mode 100644 index 0000000000..57d94f481b --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Funder.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +/** + * To store information about the funder funding the project related to the result. It has the following parameters: + * - private String shortName to store the short name of the funder (e.g. AKA) + * - private String name to store information about the name of the funder (e.g. Akademy of Finland) + * - private Fundings funding_stream to store the fundingstream + * - private String jurisdiction to store information about the jurisdiction of the funder + */ +public class Funder implements Serializable { + + private String shortName; + + private String name; + + private Fundings funding_stream; + + private String jurisdiction; + + public String getShortName() { + return shortName; + } + + public void setShortName(String shortName) { + this.shortName = shortName; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getJurisdiction() { + return jurisdiction; + } + + public void setJurisdiction(String jurisdiction) { + this.jurisdiction = jurisdiction; + } + + public Fundings getFunding_stream() { + return funding_stream; + } + + public void setFunding_stream(Fundings funding_stream) { + this.funding_stream = funding_stream; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Fundings.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Fundings.java new file mode 100644 index 0000000000..173878ef0c --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Fundings.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +/** + * To store inforamtion about the funding stream. It has two parameters: + * - private String id to store the id of the fundings stream. The id is created by appending the shortname of the + * funder to the name of each level in the xml representing the fundng stream. For example: if the funder is the + * European Commission, the funding level 0 name is FP7, the funding level 1 name is SP3 and the funding level 2 name is + * PEOPLE then the id will be: EC::FP7::SP3::PEOPLE + * - private String description to describe the funding stream. It is created by concatenating the description of each funding + * level so for the example above the description would be: SEVENTH FRAMEWORK PROGRAMME - SP3-People - Marie-Curie Actions + */ +public class Fundings implements Serializable { + + private String id; + private String description; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Granted.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Granted.java new file mode 100644 index 0000000000..1ac27ddf11 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Granted.java @@ -0,0 +1,56 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; +import java.util.Optional; + +/** + * To describe the funded amount. It has the following parameters: + * - private String currency to store the currency of the fund + * - private float totalcost to store the total cost of the project + * - private float fundedamount to store the funded amount by the funder + */ +public class Granted implements Serializable { + private String currency; + private float totalcost; + private float fundedamount; + + public String getCurrency() { + return currency; + } + + public void setCurrency(String currency) { + this.currency = currency; + } + + public float getTotalcost() { + return totalcost; + } + + public void setTotalcost(float totalcost) { + this.totalcost = totalcost; + } + + public float getFundedamount() { + return fundedamount; + } + + public void setFundedamount(float fundedamount) { + this.fundedamount = fundedamount; + } + + public static Granted newInstance(String currency, float totalcost, float fundedamount) { + Granted granted = new Granted(); + granted.currency = currency; + granted.totalcost = totalcost; + granted.fundedamount = fundedamount; + return granted; + } + + public static Granted newInstance(String currency, float fundedamount) { + Granted granted = new Granted(); + granted.currency = currency; + granted.fundedamount = fundedamount; + return granted; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Node.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Node.java new file mode 100644 index 0000000000..dac594451a --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Node.java @@ -0,0 +1,41 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +/** + * To represent the generic node in a relation. It has the following parameters: + * - private String id the openaire id of the entity in the relation + * - private String type the type of the entity in the relation. + * + * Consider the generic relation between a Result R and a Project P, the node representing R will have + * as id the id of R and as type result, while the node representing the project will have as id the id of the project + * and as type project + */ +public class Node implements Serializable { + private String id; + private String type; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public static Node newInstance(String id, String type) { + Node node = new Node(); + node.id = id; + node.type = type; + return node; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Organization.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Organization.java new file mode 100644 index 0000000000..579245c053 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Organization.java @@ -0,0 +1,88 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.ControlledField; +import eu.dnetlib.dhp.schema.dump.oaf.Country; +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; +import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + +/** + * To represent the generic organizaiton. It has the following parameters: + * - private String legalshortname to store the legalshortname of the organizaiton + * - private String legalname to store the legal name of the organization + * - private String websiteurl to store the websiteurl of the organization + * - private List alternativenames to store the alternative names of the organization + * - private Qualifier country to store the country of the organization + * - private String id to store the id of the organization + * - private List pid to store the list of pids for the organization + */ +public class Organization implements Serializable { + private String legalshortname; + private String legalname; + private String websiteurl; + private List alternativenames; + private Qualifier country; + private String id; + private List pid; + + public String getLegalshortname() { + return legalshortname; + } + + public void setLegalshortname(String legalshortname) { + this.legalshortname = legalshortname; + } + + public String getLegalname() { + return legalname; + } + + public void setLegalname(String legalname) { + this.legalname = legalname; + } + + public String getWebsiteurl() { + return websiteurl; + } + + public void setWebsiteurl(String websiteurl) { + this.websiteurl = websiteurl; + } + + public List getAlternativenames() { + return alternativenames; + } + + public void setAlternativenames(List alternativenames) { + this.alternativenames = alternativenames; + } + + public Qualifier getCountry() { + return country; + } + + public void setCountry(Qualifier country) { + this.country = country; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getPid() { + return pid; + } + + public void setPid(List pid) { + this.pid = pid; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Programme.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Programme.java new file mode 100644 index 0000000000..663ca25bc4 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Programme.java @@ -0,0 +1,37 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +/** + * To store information about the ec programme for the project. It has the following parameters: + * - private String code to store the code of the programme + * - private String description to store the description of the programme + */ +public class Programme implements Serializable { + private String code; + private String description; + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public static Programme newInstance(String code, String description) { + Programme p = new Programme(); + p.code = code; + p.description = description; + return p; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Project.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Project.java new file mode 100644 index 0000000000..25f106da52 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Project.java @@ -0,0 +1,195 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; + +/** + * This is the class representing the Project in the model used for the dumps of the whole graph. At the moment the dump + * of the Projects differs from the other dumps because we do not create relations between Funders (Organization) and + * Projects but we put the information about the Funder within the Project representation. We also removed the + * collected from element from the Project. No relation between the Project and the Datasource entity from which it is + * collected will be created. We will never create relations between Project and Datasource. In case some relation will + * be extracted from the Project they will refer the Funder and will be of type ( organization -> funds -> project, + * project -> isFundedBy -> organization) We also removed the duration parameter because the most of times it is set to + * 0. It has the following parameters: + * - private String id to store the id of the project (OpenAIRE id) + * - private String websiteurl to store the websiteurl of the project + * - private String code to store the grant agreement of the project + * - private String acronym to store the acronym of the project + * - private String title to store the tile of the project + * - private String startdate to store the start date + * - private String enddate to store the end date + * - private String callidentifier to store the call indentifier + * - private String keywords to store the keywords + * - private boolean openaccessmandateforpublications to store if the project must accomplish to the open access mandate + * for publications. This value will be set to true if one of the field in the project represented in the internal model + * is set to true + * - private boolean openaccessmandatefordataset to store if the project must accomplish to the open access mandate for + * dataset. It is set to the value in the corresponding filed of the project represented in the internal model + * - private List subject to store the list of subjects of the project + * - private List funding to store the list of funder of the project + * - private String summary to store the summary of the project + * - private Granted granted to store the granted amount + * - private List programme to store the list of programmes the project is related to + */ + +public class Project implements Serializable { + private String id; + + private String websiteurl; + private String code; + private String acronym; + private String title; + private String startdate; + + private String enddate; + + private String callidentifier; + + private String keywords; + + private boolean openaccessmandateforpublications; + + private boolean openaccessmandatefordataset; + private List subject; + + private List funding; + + private String summary; + + private Granted granted; + + private List programme; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getWebsiteurl() { + return websiteurl; + } + + public void setWebsiteurl(String websiteurl) { + this.websiteurl = websiteurl; + } + + public String getCode() { + return code; + } + + public void setCode(String code) { + this.code = code; + } + + public String getAcronym() { + return acronym; + } + + public void setAcronym(String acronym) { + this.acronym = acronym; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getStartdate() { + return startdate; + } + + public void setStartdate(String startdate) { + this.startdate = startdate; + } + + public String getEnddate() { + return enddate; + } + + public void setEnddate(String enddate) { + this.enddate = enddate; + } + + public String getCallidentifier() { + return callidentifier; + } + + public void setCallidentifier(String callidentifier) { + this.callidentifier = callidentifier; + } + + public String getKeywords() { + return keywords; + } + + public void setKeywords(String keywords) { + this.keywords = keywords; + } + + public boolean isOpenaccessmandateforpublications() { + return openaccessmandateforpublications; + } + + public void setOpenaccessmandateforpublications(boolean openaccessmandateforpublications) { + this.openaccessmandateforpublications = openaccessmandateforpublications; + } + + public boolean isOpenaccessmandatefordataset() { + return openaccessmandatefordataset; + } + + public void setOpenaccessmandatefordataset(boolean openaccessmandatefordataset) { + this.openaccessmandatefordataset = openaccessmandatefordataset; + } + + public List getSubject() { + return subject; + } + + public void setSubject(List subject) { + this.subject = subject; + } + + public List getFunding() { + return funding; + } + + public void setFunding(List funding) { + this.funding = funding; + } + + public String getSummary() { + return summary; + } + + public void setSummary(String summary) { + this.summary = summary; + } + + public Granted getGranted() { + return granted; + } + + public void setGranted(Granted granted) { + this.granted = granted; + } + + public List getProgramme() { + return programme; + } + + public void setProgramme(List programme) { + this.programme = programme; + } + +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/RelType.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/RelType.java new file mode 100644 index 0000000000..83ae2dda6f --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/RelType.java @@ -0,0 +1,40 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +/** + * To represent the semantics of the generic relation between two entities. It has the following parameters: + * - private String name to store the semantics of the relation (i.e. isAuthorInstitutionOf). It corresponds to the + * relclass parameter in the relation represented in the internal model + * represented in the internal model + * - private String type to store the type of the relation (i.e. affiliation). It corresponds to the subreltype parameter + * of the relation represented in theinternal model + */ +public class RelType implements Serializable { + private String name; // relclass + private String type; // subreltype + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public static RelType newInstance(String name, String type) { + RelType rel = new RelType(); + rel.name = name; + rel.type = type; + return rel; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Relation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Relation.java new file mode 100644 index 0000000000..4b88eb6c27 --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/Relation.java @@ -0,0 +1,68 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; +import java.util.Objects; + +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; + +/** + * To represent the gereric relation between two entities. It has the following parameters: + * - private Node source to represent the entity source of the relation + * - private Node target to represent the entity target of the relation + * - private RelType reltype to represent the semantics of the relation + * - private Provenance provenance to represent the provenance of the relation + */ +public class Relation implements Serializable { + private Node source; + private Node target; + private RelType reltype; + private Provenance provenance; + + public Node getSource() { + return source; + } + + public void setSource(Node source) { + this.source = source; + } + + public Node getTarget() { + return target; + } + + public void setTarget(Node target) { + this.target = target; + } + + public RelType getReltype() { + return reltype; + } + + public void setReltype(RelType reltype) { + this.reltype = reltype; + } + + public Provenance getProvenance() { + return provenance; + } + + public void setProvenance(Provenance provenance) { + this.provenance = provenance; + } + + @Override + public int hashCode() { + + return Objects.hash(source.getId(), target.getId(), reltype.getType() + ":" + reltype.getName()); + } + + public static Relation newInstance(Node source, Node target, RelType reltype, Provenance provenance) { + Relation relation = new Relation(); + relation.source = source; + relation.target = target; + relation.reltype = reltype; + relation.provenance = provenance; + return relation; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchCommunity.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchCommunity.java new file mode 100644 index 0000000000..026042ce9c --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchCommunity.java @@ -0,0 +1,20 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.util.List; + +/** + * To represent RC entities. It extends eu.dnetlib.dhp.dump.oaf.grap.ResearchInitiative by adding the parameter subject + * to store the list of subjects related to the community + */ +public class ResearchCommunity extends ResearchInitiative { + private List subject; + + public List getSubject() { + return subject; + } + + public void setSubject(List subject) { + this.subject = subject; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchInitiative.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchInitiative.java new file mode 100644 index 0000000000..6646fd541e --- /dev/null +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/dump/oaf/graph/ResearchInitiative.java @@ -0,0 +1,71 @@ + +package eu.dnetlib.dhp.schema.dump.oaf.graph; + +import java.io.Serializable; + +/** + * To represent entity of type RC/RI. It has the following parameters, which are mostly derived by the profile + * - private String id to store the openaire id for the entity. Is has as code 00 and will be created as + * 00|context_____::md5(originalId) + * private String originalId to store the id of the context as provided in the profile (i.e. mes) + * private String name to store the name of the context (got from the label attribute in the context definition) + * private String type to store the type of the context (i.e.: research initiative or research community) + * private String description to store the description of the context as given in the profile + * private String zenodo_community to store the zenodo community associated to the context (main zenodo community) + */ +public class ResearchInitiative implements Serializable { + private String id; // openaireId + private String originalId; // context id + private String name; // context name + private String type; // context type: research initiative or research community + private String description; + private String zenodo_community; + + public String getZenodo_community() { + return zenodo_community; + } + + public void setZenodo_community(String zenodo_community) { + this.zenodo_community = zenodo_community; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getName() { + return name; + } + + public void setName(String label) { + this.name = label; + } + + public String getOriginalId() { + return originalId; + } + + public void setOriginalId(String originalId) { + this.originalId = originalId; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } +} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java deleted file mode 100644 index ca85fa14fc..0000000000 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIRelation.java +++ /dev/null @@ -1,30 +0,0 @@ - -package eu.dnetlib.dhp.schema.scholexplorer; - -import java.util.List; - -import eu.dnetlib.dhp.schema.oaf.KeyValue; -import eu.dnetlib.dhp.schema.oaf.Relation; - -public class DLIRelation extends Relation { - - private String dateOfCollection; - - private List collectedFrom; - - public List getCollectedFrom() { - return collectedFrom; - } - - public void setCollectedFrom(List collectedFrom) { - this.collectedFrom = collectedFrom; - } - - public String getDateOfCollection() { - return dateOfCollection; - } - - public void setDateOfCollection(String dateOfCollection) { - this.dateOfCollection = dateOfCollection; - } -} diff --git a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java index e9b670d032..5da5994273 100644 --- a/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java +++ b/dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/scholexplorer/DLIUnknown.java @@ -2,10 +2,8 @@ package eu.dnetlib.dhp.schema.scholexplorer; import java.io.Serializable; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; @@ -78,6 +76,25 @@ public class DLIUnknown extends Oaf implements Serializable { if ("complete".equalsIgnoreCase(p.completionStatus)) completionStatus = "complete"; dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); + if (StringUtils.isEmpty(id) && StringUtils.isNoneEmpty(p.getId())) + id = p.getId(); + if (StringUtils.isEmpty(dateofcollection) && StringUtils.isNoneEmpty(p.getDateofcollection())) + dateofcollection = p.getDateofcollection(); + + if (StringUtils.isEmpty(dateoftransformation) && StringUtils.isNoneEmpty(p.getDateoftransformation())) + dateofcollection = p.getDateoftransformation(); + pid = mergeLists(pid, p.getPid()); + } + + protected List mergeLists(final List... lists) { + + return Arrays + .stream(lists) + .filter(Objects::nonNull) + .flatMap(List::stream) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); } private List mergeProvenance( diff --git a/dhp-workflows/dhp-broker-events/pom.xml b/dhp-workflows/dhp-broker-events/pom.xml index f98708c648..75cc0ea095 100644 --- a/dhp-workflows/dhp-broker-events/pom.xml +++ b/dhp-workflows/dhp-broker-events/pom.xml @@ -31,6 +31,10 @@ elasticsearch-hadoop + + org.apache.httpcomponents + httpclient + eu.dnetlib.dhp diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/ConditionParams.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/ConditionParams.java new file mode 100644 index 0000000000..375300c056 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/ConditionParams.java @@ -0,0 +1,31 @@ + +package eu.dnetlib.dhp.broker.model; + +import java.io.Serializable; + +public class ConditionParams implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 2719901844537516110L; + + private String value; + private String otherValue; + + public String getValue() { + return value; + } + + public void setValue(final String value) { + this.value = value; + } + + public String getOtherValue() { + return otherValue; + } + + public void setOtherValue(final String otherValue) { + this.otherValue = otherValue; + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java index 0cb0d78018..429eb7d11b 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/EventFactory.java @@ -2,7 +2,6 @@ package eu.dnetlib.dhp.broker.model; import java.text.ParseException; -import java.util.Date; import java.util.List; import java.util.stream.Collectors; @@ -19,16 +18,12 @@ public class EventFactory { private final static String PRODUCER_ID = "OpenAIRE"; - private static final int TTH_DAYS = 365; - private final static String[] DATE_PATTERNS = { "yyyy-MM-dd" }; public static Event newBrokerEvent(final UpdateInfo updateInfo) { - final long now = new Date().getTime(); - final Event res = new Event(); final MappedFields map = createMapFromResult(updateInfo); @@ -44,8 +39,8 @@ public class EventFactory { res.setPayload(updateInfo.asBrokerPayload().toJSON()); res.setMap(map); res.setTopic(updateInfo.getTopicPath()); - res.setCreationDate(now); - res.setExpiryDate(calculateExpiryDate(now)); + res.setCreationDate(0l); + res.setExpiryDate(Long.MAX_VALUE); res.setInstantMessage(false); return res; @@ -96,7 +91,9 @@ public class EventFactory { return map; } - private static String calculateEventId(final String topic, final String dsId, final String publicationId, + private static String calculateEventId(final String topic, + final String dsId, + final String publicationId, final String value) { return "event-" + DigestUtils.md5Hex(topic).substring(0, 4) + "-" @@ -105,10 +102,6 @@ public class EventFactory { + DigestUtils.md5Hex(value).substring(0, 5); } - private static long calculateExpiryDate(final long now) { - return now + TTH_DAYS * 24 * 60 * 60 * 1000; - } - private static long parseDateTolong(final String date) { if (StringUtils.isBlank(date)) { return -1; diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/MapCondition.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/MapCondition.java new file mode 100644 index 0000000000..069eee2a82 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/MapCondition.java @@ -0,0 +1,37 @@ + +package eu.dnetlib.dhp.broker.model; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; + +@JsonIgnoreProperties(ignoreUnknown = true) +public class MapCondition implements Serializable { + + /** + * + */ + private static final long serialVersionUID = -7137490975452466813L; + + private String field; + private List listParams = new ArrayList<>(); + + public String getField() { + return field; + } + + public void setField(final String field) { + this.field = field; + } + + public List getListParams() { + return listParams; + } + + public void setListParams(final List listParams) { + this.listParams = listParams; + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Notification.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Notification.java new file mode 100644 index 0000000000..4ef25bf1f4 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Notification.java @@ -0,0 +1,93 @@ + +package eu.dnetlib.dhp.broker.model; + +import java.io.Serializable; + +public class Notification implements Serializable { + + /** + * + */ + private static final long serialVersionUID = -1770420972526995727L; + + private String notificationId; + + private String subscriptionId; + + private String producerId; + + private String eventId; + + private String topic; + + private Long date; + + private String payload; + + private MappedFields map; + + public String getNotificationId() { + return notificationId; + } + + public void setNotificationId(final String notificationId) { + this.notificationId = notificationId; + } + + public String getSubscriptionId() { + return subscriptionId; + } + + public void setSubscriptionId(final String subscriptionId) { + this.subscriptionId = subscriptionId; + } + + public String getProducerId() { + return producerId; + } + + public void setProducerId(final String producerId) { + this.producerId = producerId; + } + + public String getEventId() { + return eventId; + } + + public void setEventId(final String eventId) { + this.eventId = eventId; + } + + public String getTopic() { + return topic; + } + + public void setTopic(final String topic) { + this.topic = topic; + } + + public String getPayload() { + return payload; + } + + public void setPayload(final String payload) { + this.payload = payload; + } + + public MappedFields getMap() { + return map; + } + + public void setMap(final MappedFields map) { + this.map = map; + } + + public Long getDate() { + return date; + } + + public void setDate(final Long date) { + this.date = date; + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Subscription.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Subscription.java new file mode 100644 index 0000000000..6cfd8b0a3c --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/model/Subscription.java @@ -0,0 +1,74 @@ + +package eu.dnetlib.dhp.broker.model; + +import java.io.Serializable; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +import com.fasterxml.jackson.annotation.JsonIgnoreProperties; +import com.fasterxml.jackson.databind.ObjectMapper; + +@JsonIgnoreProperties(ignoreUnknown = true) +public class Subscription implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 1051702214740830010L; + + private String subscriptionId; + + private String subscriber; + + private String topic; + + private String conditions; + + public String getSubscriptionId() { + return subscriptionId; + } + + public void setSubscriptionId(final String subscriptionId) { + this.subscriptionId = subscriptionId; + } + + public String getSubscriber() { + return subscriber; + } + + public void setSubscriber(final String subscriber) { + this.subscriber = subscriber; + } + + public String getTopic() { + return topic; + } + + public void setTopic(final String topic) { + this.topic = topic; + } + + public String getConditions() { + return conditions; + } + + public void setConditions(final String conditions) { + this.conditions = conditions; + } + + public Map> conditionsAsMap() { + final ObjectMapper mapper = new ObjectMapper(); + try { + final List list = mapper + .readValue( + getConditions(), mapper.getTypeFactory().constructCollectionType(List.class, MapCondition.class)); + return list + .stream() + .filter(mc -> !mc.getListParams().isEmpty()) + .collect(Collectors.toMap(MapCondition::getField, MapCondition::getListParams)); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index a51601cd76..8a7229b647 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -28,7 +28,7 @@ public class GenerateStatsJob { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - IndexOnESJob.class + GenerateStatsJob.class .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json"))); parser.parseArgument(args); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java new file mode 100644 index 0000000000..d3cbe0034f --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexEventSubsetJob.java @@ -0,0 +1,126 @@ + +package eu.dnetlib.dhp.broker.oa; + +import java.util.Date; +import java.util.HashMap; +import java.util.Map; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.math.NumberUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpDelete; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.sql.TypedColumn; +import org.apache.spark.util.LongAccumulator; +import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.EventGroup; +import eu.dnetlib.dhp.broker.oa.util.aggregators.subset.EventSubsetAggregator; + +public class IndexEventSubsetJob { + + private static final Logger log = LoggerFactory.getLogger(IndexEventSubsetJob.class); + + public static void main(final String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + IndexEventSubsetJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_event_subset.json"))); + parser.parseArgument(args); + + final SparkConf conf = new SparkConf(); + + final String eventsPath = parser.get("workingPath") + "/events"; + log.info("eventsPath: {}", eventsPath); + + final String index = parser.get("index"); + log.info("index: {}", index); + + final String indexHost = parser.get("esHost"); + log.info("indexHost: {}", indexHost); + + final int maxEventsForTopic = NumberUtils.toInt(parser.get("maxEventsForTopic")); + log.info("maxEventsForTopic: {}", maxEventsForTopic); + + final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl"); + log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); + + final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); + + final TypedColumn aggr = new EventSubsetAggregator(maxEventsForTopic).toColumn(); + + final LongAccumulator total = spark.sparkContext().longAccumulator("total_indexed"); + + final long now = new Date().getTime(); + + final Dataset subset = ClusterUtils + .readPath(spark, eventsPath, Event.class) + .groupByKey(e -> e.getTopic() + '@' + e.getMap().getTargetDatasourceId(), Encoders.STRING()) + .agg(aggr) + .map(t -> t._2, Encoders.bean(EventGroup.class)) + .flatMap(g -> g.getData().iterator(), Encoders.bean(Event.class)); + + final JavaRDD inputRdd = subset + .map(e -> prepareEventForIndexing(e, now, total), Encoders.STRING()) + .javaRDD(); + + final Map esCfg = new HashMap<>(); + // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); + + esCfg.put("es.index.auto.create", "false"); + esCfg.put("es.nodes", indexHost); + esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY + esCfg.put("es.batch.write.retry.count", "8"); + esCfg.put("es.batch.write.retry.wait", "60s"); + esCfg.put("es.batch.size.entries", "200"); + esCfg.put("es.nodes.wan.only", "true"); + + log.info("*** Start indexing"); + JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); + log.info("*** End indexing"); + + log.info("*** Deleting old events"); + final String message = deleteOldEvents(brokerApiBaseUrl, now - 1000); + log.info("*** Deleted events: " + message); + + } + + private static String deleteOldEvents(final String brokerApiBaseUrl, final long l) throws Exception { + final String url = brokerApiBaseUrl + "/api/events/byCreationDate/0/" + l; + final HttpDelete req = new HttpDelete(url); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + return IOUtils.toString(response.getEntity().getContent()); + } + } + + } + + private static String prepareEventForIndexing(final Event e, final long creationDate, final LongAccumulator acc) + throws JsonProcessingException { + acc.add(1); + + e.setCreationDate(creationDate); + e.setExpiryDate(Long.MAX_VALUE); + + return new ObjectMapper().writeValueAsString(e); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java new file mode 100644 index 0000000000..cb7acb46df --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexNotificationsJob.java @@ -0,0 +1,233 @@ + +package eu.dnetlib.dhp.broker.oa; + +import java.io.IOException; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +import org.apache.commons.codec.digest.DigestUtils; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpDelete; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.apache.spark.util.LongAccumulator; +import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.broker.model.ConditionParams; +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.model.MappedFields; +import eu.dnetlib.dhp.broker.model.Notification; +import eu.dnetlib.dhp.broker.model.Subscription; +import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +import eu.dnetlib.dhp.broker.oa.util.NotificationGroup; +import eu.dnetlib.dhp.broker.oa.util.SubscriptionUtils; + +public class IndexNotificationsJob { + + private static final Logger log = LoggerFactory.getLogger(IndexNotificationsJob.class); + + public static void main(final String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString(IndexNotificationsJob.class + .getResourceAsStream("/eu/dnetlib/dhp/broker/oa/index_notifications.json"))); + parser.parseArgument(args); + + final SparkConf conf = new SparkConf(); + + final String eventsPath = parser.get("workingPath") + "/events"; + log.info("eventsPath: {}", eventsPath); + + final String index = parser.get("index"); + log.info("index: {}", index); + + final String indexHost = parser.get("esHost"); + log.info("indexHost: {}", indexHost); + + final String brokerApiBaseUrl = parser.get("brokerApiBaseUrl"); + log.info("brokerApiBaseUrl: {}", brokerApiBaseUrl); + + final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); + + final LongAccumulator total = spark.sparkContext().longAccumulator("total_indexed"); + + final long startTime = new Date().getTime(); + + final List subscriptions = listSubscriptions(brokerApiBaseUrl); + + log.info("Number of subscriptions: " + subscriptions.size()); + + if (subscriptions.size() > 0) { + final Dataset notifications = ClusterUtils + .readPath(spark, eventsPath, Event.class) + .map(e -> generateNotifications(e, subscriptions, startTime), Encoders.bean(NotificationGroup.class)) + .flatMap(g -> g.getData().iterator(), Encoders.bean(Notification.class)); + + final JavaRDD inputRdd = notifications + .map(n -> prepareForIndexing(n, total), Encoders.STRING()) + .javaRDD(); + + final Map esCfg = new HashMap<>(); + // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); + + esCfg.put("es.index.auto.create", "false"); + esCfg.put("es.nodes", indexHost); + esCfg.put("es.mapping.id", "notificationId"); // THE PRIMARY KEY + esCfg.put("es.batch.write.retry.count", "8"); + esCfg.put("es.batch.write.retry.wait", "60s"); + esCfg.put("es.batch.size.entries", "200"); + esCfg.put("es.nodes.wan.only", "true"); + + log.info("*** Start indexing"); + JavaEsSpark.saveJsonToEs(inputRdd, index, esCfg); + log.info("*** End indexing"); + + log.info("*** Deleting old notifications"); + final String message = deleteOldNotifications(brokerApiBaseUrl, startTime - 1000); + log.info("*** Deleted notifications: " + message); + + log.info("*** sendNotifications (emails, ...)"); + sendNotifications(brokerApiBaseUrl, startTime - 1000); + log.info("*** ALL done."); + + } + } + + private static NotificationGroup generateNotifications(final Event e, + final List subscriptions, + final long date) { + final List list = subscriptions + .stream() + .filter(s -> StringUtils.isBlank(s.getTopic()) || s.getTopic().equals("*") || s.getTopic().equals(e.getTopic())) + .filter(s -> verifyConditions(e.getMap(), s.conditionsAsMap())) + .map(s -> generateNotification(s, e, date)) + .collect(Collectors.toList()); + + return new NotificationGroup(list); + } + + private static Notification generateNotification(final Subscription s, final Event e, final long date) { + final Notification n = new Notification(); + n.setNotificationId("ntf-" + DigestUtils.md5Hex(s.getSubscriptionId() + "@@@" + e.getEventId())); + n.setSubscriptionId(s.getSubscriptionId()); + n.setEventId(e.getEventId()); + n.setProducerId(e.getProducerId()); + n.setTopic(e.getTopic()); + n.setPayload(e.getPayload()); + n.setMap(e.getMap()); + n.setDate(date); + return n; + } + + private static boolean verifyConditions(final MappedFields map, + final Map> conditions) { + if (conditions.containsKey("targetDatasourceName") + && !SubscriptionUtils + .verifyExact(map.getTargetDatasourceName(), conditions.get("targetDatasourceName").get(0).getValue())) { + return false; + } + + if (conditions.containsKey("trust") + && !SubscriptionUtils + .verifyFloatRange(map.getTrust(), conditions.get("trust").get(0).getValue(), conditions.get("trust").get(0).getOtherValue())) { + return false; + } + + if (conditions.containsKey("targetDateofacceptance") && !conditions + .get("targetDateofacceptance") + .stream() + .anyMatch(c -> SubscriptionUtils + .verifyDateRange(map.getTargetDateofacceptance(), c.getValue(), c.getOtherValue()))) { + return false; + } + + if (conditions.containsKey("targetResultTitle") + && !conditions + .get("targetResultTitle") + .stream() + .anyMatch(c -> SubscriptionUtils.verifySimilar(map.getTargetResultTitle(), c.getValue()))) { + return false; + } + + if (conditions.containsKey("targetAuthors") + && !conditions + .get("targetAuthors") + .stream() + .allMatch(c -> SubscriptionUtils.verifyListSimilar(map.getTargetAuthors(), c.getValue()))) { + return false; + } + + if (conditions.containsKey("targetSubjects") + && !conditions + .get("targetSubjects") + .stream() + .allMatch(c -> SubscriptionUtils.verifyListExact(map.getTargetSubjects(), c.getValue()))) { + return false; + } + + return true; + + } + + private static List listSubscriptions(final String brokerApiBaseUrl) throws Exception { + final String url = brokerApiBaseUrl + "/api/subscriptions"; + final HttpGet req = new HttpGet(url); + + final ObjectMapper mapper = new ObjectMapper(); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + final String s = IOUtils.toString(response.getEntity().getContent()); + return mapper + .readValue(s, mapper.getTypeFactory().constructCollectionType(List.class, Subscription.class)); + } + } + } + + private static String deleteOldNotifications(final String brokerApiBaseUrl, final long l) throws Exception { + final String url = brokerApiBaseUrl + "/api/notifications/byDate/0/" + l; + final HttpDelete req = new HttpDelete(url); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + return IOUtils.toString(response.getEntity().getContent()); + } + } + } + + private static String sendNotifications(final String brokerApiBaseUrl, final long l) throws IOException { + final String url = brokerApiBaseUrl + "/api/openaireBroker/notifications/send/" + l; + final HttpGet req = new HttpGet(url); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + return IOUtils.toString(response.getEntity().getContent()); + } + } + } + + private static String prepareForIndexing(final Notification n, final LongAccumulator acc) + throws JsonProcessingException { + acc.add(1); + return new ObjectMapper().writeValueAsString(n); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java index 806147bdd5..762bfbb903 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/IndexOnESJob.java @@ -20,6 +20,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.broker.model.Event; import eu.dnetlib.dhp.broker.oa.util.ClusterUtils; +@Deprecated public class IndexOnESJob { private static final Logger log = LoggerFactory.getLogger(IndexOnESJob.class); @@ -48,12 +49,13 @@ public class IndexOnESJob { final JavaRDD inputRdd = ClusterUtils .readPath(spark, eventsPath, Event.class) - // .limit(10000) // TODO REMOVE .map(IndexOnESJob::eventAsJsonString, Encoders.STRING()) .javaRDD(); final Map esCfg = new HashMap<>(); // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); + + esCfg.put("es.index.auto.create", "false"); esCfg.put("es.nodes", indexHost); esCfg.put("es.mapping.id", "eventId"); // THE PRIMARY KEY esCfg.put("es.batch.write.retry.count", "8"); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/NotificationGroup.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/NotificationGroup.java new file mode 100644 index 0000000000..80cf7609b9 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/NotificationGroup.java @@ -0,0 +1,44 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; + +import eu.dnetlib.dhp.broker.model.Notification; + +public class NotificationGroup implements Serializable { + + /** + * + */ + private static final long serialVersionUID = 720996471281158977L; + + private List data = new ArrayList<>(); + + public NotificationGroup() { + } + + public NotificationGroup(final List data) { + this.data = data; + } + + public List getData() { + return data; + } + + public void setData(final List data) { + this.data = data; + } + + public NotificationGroup addElement(final Notification elem) { + data.add(elem); + return this; + } + + public NotificationGroup addGroup(final NotificationGroup group) { + data.addAll(group.getData()); + return this; + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java new file mode 100644 index 0000000000..adb1c753b1 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java @@ -0,0 +1,49 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import java.text.ParseException; +import java.util.List; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.lang3.math.NumberUtils; +import org.apache.commons.lang3.time.DateUtils; + +public class SubscriptionUtils { + + private static final long ONE_DAY = 86_400_000; + + public static boolean verifyListSimilar(final List list, final String value) { + return list.stream().anyMatch(s -> verifySimilar(s, value)); + } + + public static boolean verifyListExact(final List list, final String value) { + return list.stream().anyMatch(s -> verifyExact(s, value)); + } + + public static boolean verifySimilar(final String s1, final String s2) { + for (final String part : s2.split("\\W+")) { + if (!StringUtils.containsIgnoreCase(s1, part)) { + return false; + } + } + return true; + } + + public static boolean verifyFloatRange(final float trust, final String min, final String max) { + return trust >= NumberUtils.toFloat(min, 0) && trust <= NumberUtils.toFloat(max, 1); + } + + public static boolean verifyDateRange(final long date, final String min, final String max) { + try { + return date >= DateUtils.parseDate(min, "yyyy-MM-dd").getTime() + && date < DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY; + } catch (final ParseException e) { + return false; + } + } + + public static boolean verifyExact(final String s1, final String s2) { + return StringUtils.equalsIgnoreCase(s1, s2); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/subset/EventSubsetAggregator.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/subset/EventSubsetAggregator.java new file mode 100644 index 0000000000..cd403ade0a --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/aggregators/subset/EventSubsetAggregator.java @@ -0,0 +1,67 @@ + +package eu.dnetlib.dhp.broker.oa.util.aggregators.subset; + +import org.apache.spark.sql.Encoder; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.expressions.Aggregator; + +import eu.dnetlib.dhp.broker.model.Event; +import eu.dnetlib.dhp.broker.oa.util.EventGroup; + +public class EventSubsetAggregator extends Aggregator { + + /** + * + */ + private static final long serialVersionUID = -678071078823059805L; + + private final int maxEventsForTopic; + + public EventSubsetAggregator(final int maxEventsForTopic) { + this.maxEventsForTopic = maxEventsForTopic; + } + + @Override + public EventGroup zero() { + return new EventGroup(); + } + + @Override + public EventGroup reduce(final EventGroup g, final Event e) { + if (g.getData().size() < maxEventsForTopic) { + g.getData().add(e); + } + return g; + } + + @Override + public EventGroup merge(final EventGroup g0, final EventGroup g1) { + final int missing = maxEventsForTopic - g0.getData().size(); + + if (missing > 0) { + if (g1.getData().size() < missing) { + g0.getData().addAll(g1.getData()); + } else { + g0.getData().addAll(g1.getData().subList(0, missing)); + } + } + + return g0; + } + + @Override + public EventGroup finish(final EventGroup g) { + return g; + } + + @Override + public Encoder outputEncoder() { + return Encoders.bean(EventGroup.class); + } + + @Override + public Encoder bufferEncoder() { + return Encoders.bean(EventGroup.class); + } + +} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml index 568d5dc5a0..4184b71bd9 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml @@ -25,13 +25,25 @@ a black list (comma separeted, - for empty list) of datasource ids - esIndexName - the elasticsearch index name + esEventIndexName + the elasticsearch index name for events + + + esNotificationsIndexName + the elasticsearch index name for notifications esIndexHost the elasticsearch host + + maxIndexedEventsForDsAndTopic + the max number of events for each couple (ds/topic) + + + brokerApiBaseUrl + the url of the broker service api + sparkDriverMemory memory for driver process @@ -423,16 +435,16 @@ --datasourceTypeWhitelist${datasourceTypeWhitelist} --datasourceIdBlacklist${datasourceIdBlacklist} - + - + yarn cluster - IndexOnESJob - eu.dnetlib.dhp.broker.oa.IndexOnESJob + IndexEventSubsetOnESJob + eu.dnetlib.dhp.broker.oa.IndexEventSubsetJob dhp-broker-events-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -445,8 +457,36 @@ --conf spark.sql.shuffle.partitions=3840 --workingPath${workingPath} - --index${esIndexName} + --index${esEventIndexName} --esHost${esIndexHost} + --maxEventsForTopic${maxIndexedEventsForDsAndTopic} + --brokerApiBaseUrl${brokerApiBaseUrl} + + + + + + + + yarn + cluster + IndexNotificationsOnESJob + eu.dnetlib.dhp.broker.oa.IndexNotificationsJob + dhp-broker-events-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.dynamicAllocation.maxExecutors="8" + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=3840 + + --workingPath${workingPath} + --index${esNotificationsIndexName} + --esHost${esIndexHost} + --brokerApiBaseUrl${brokerApiBaseUrl} diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json new file mode 100644 index 0000000000..4921bc03e2 --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_event_subset.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "o", + "paramLongName": "workingPath", + "paramDescription": "the workinh path", + "paramRequired": true + }, + { + "paramName": "idx", + "paramLongName": "index", + "paramDescription": "the ES index", + "paramRequired": true + }, + { + "paramName": "es", + "paramLongName": "esHost", + "paramDescription": "the ES host", + "paramRequired": true + }, + { + "paramName": "n", + "paramLongName": "maxEventsForTopic", + "paramDescription": "the max number of events for each couple (ds/topic)", + "paramRequired": true + }, + { + "paramName": "broker", + "paramLongName": "brokerApiBaseUrl", + "paramDescription": "the url of the broker service api", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json new file mode 100644 index 0000000000..5eea894c8e --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/index_notifications.json @@ -0,0 +1,26 @@ +[ + { + "paramName": "o", + "paramLongName": "workingPath", + "paramDescription": "the workinh path", + "paramRequired": true + }, + { + "paramName": "idx", + "paramLongName": "index", + "paramDescription": "the ES index", + "paramRequired": true + }, + { + "paramName": "es", + "paramLongName": "esHost", + "paramDescription": "the ES host", + "paramRequired": true + }, + { + "paramName": "broker", + "paramLongName": "brokerApiBaseUrl", + "paramDescription": "the url of the broker service api", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml index 80505ca1ea..f629c2101e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/partial/oozie_app/workflow.xml @@ -8,6 +8,41 @@ workingPath the path where the the generated data will be stored + + + datasourceIdWhitelist + - + a white list (comma separeted, - for empty list) of datasource ids + + + datasourceTypeWhitelist + - + a white list (comma separeted, - for empty list) of datasource types + + + datasourceIdBlacklist + - + a black list (comma separeted, - for empty list) of datasource ids + + + esEventIndexName + the elasticsearch index name for events + + + esNotificationsIndexName + the elasticsearch index name for notifications + + + esIndexHost + the elasticsearch host + + + maxIndexedEventsForDsAndTopic + the max number of events for each couple (ds/topic) + + + brokerApiBaseUrl + the url of the broker service api sparkDriverMemory @@ -64,44 +99,18 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - yarn - cluster - GenerateEventsJob - eu.dnetlib.dhp.broker.oa.GenerateEventsJob - dhp-broker-events-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 - - --workingPath${workingPath} - --datasourceIdWhitelist${datasourceIdWhitelist} - --datasourceTypeWhitelist${datasourceTypeWhitelist} - --datasourceIdBlacklist${datasourceIdBlacklist} - - - - - + yarn cluster - IndexOnESJob - eu.dnetlib.dhp.broker.oa.IndexOnESJob + IndexNotificationsOnESJob + eu.dnetlib.dhp.broker.oa.IndexNotificationsJob dhp-broker-events-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} @@ -114,37 +123,15 @@ --conf spark.sql.shuffle.partitions=3840 --workingPath${workingPath} - --index${esIndexName} + --index${esNotificationsIndexName} --esHost${esIndexHost} - - - - - - - - yarn - cluster - GenerateStatsJob - eu.dnetlib.dhp.broker.oa.GenerateStatsJob - dhp-broker-events-${projectVersion}.jar - - --executor-cores=${sparkExecutorCores} - --executor-memory=${sparkExecutorMemory} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=3840 - - --graphPath${graphInputPath} - --workingPath${workingPath} + --brokerApiBaseUrl${brokerApiBaseUrl} - + + \ No newline at end of file diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java new file mode 100644 index 0000000000..b532aa9f7e --- /dev/null +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.broker.oa.util; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import java.util.Arrays; + +import org.junit.jupiter.api.Test; + +class SubscriptionUtilsTest { + + @Test + void testVerifyListSimilar() { + assertTrue(SubscriptionUtils.verifyListSimilar(Arrays.asList("Michele Artini", "Claudio Atzori"), "artini")); + assertFalse(SubscriptionUtils.verifyListSimilar(Arrays.asList("Michele Artini", "Claudio Atzori"), "bardi")); + } + + @Test + void testVerifyListExact() { + assertTrue(SubscriptionUtils.verifyListExact(Arrays.asList("Java", "Perl"), "perl")); + assertFalse(SubscriptionUtils.verifyListExact(Arrays.asList("Java", "Perl"), "C")); + } + + @Test + void testVerifySimilar() { + assertTrue(SubscriptionUtils.verifySimilar("Java Programming", "java")); + assertFalse(SubscriptionUtils.verifySimilar("Java Programming", "soap")); + } + + @Test + void testVerifyFloatRange() { + assertTrue(SubscriptionUtils.verifyFloatRange(0.5f, "0.4", "0.6")); + assertFalse(SubscriptionUtils.verifyFloatRange(0.8f, "0.4", "0.6")); + assertTrue(SubscriptionUtils.verifyFloatRange(0.5f, "", "")); + } + + @Test + void testVerifyDateRange() { + final long date = 1282738478000l; // 25 August 2010 + + assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "2011-01-01")); + assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "2021-01-01")); + } + + @Test + void testVerifyExact() { + assertTrue(SubscriptionUtils.verifyExact("Java Programming", "java programming")); + assertFalse(SubscriptionUtils.verifyExact("Java Programming", "soap programming")); + } + +} diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java index 9518efdb57..1759180d27 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java @@ -289,4 +289,12 @@ public class JsonPathTest { System.out.println("d = " + d); } + + @Test + public void testNull() throws Exception { + final Object p = null; + + System.out.println((String) p); + + } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java index d03cc25895..bba277ad67 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupRecordFactory.java @@ -6,6 +6,7 @@ import java.util.Collection; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; @@ -15,6 +16,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Lists; import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; +import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; import scala.Tuple2; @@ -30,10 +33,16 @@ public class DedupRecordFactory { final DedupConfig dedupConf) { long ts = System.currentTimeMillis(); // - final JavaPairRDD inputJsonEntities = sc - .textFile(entitiesInputPath) + final JavaPairRDD inputJsonEntities = spark + .read() + .load(entitiesInputPath) + .as(Encoders.kryo(Oaf.class)) + .map( + (MapFunction) p -> new org.codehaus.jackson.map.ObjectMapper().writeValueAsString(p), + Encoders.STRING()) + .javaRDD() .mapToPair( - (PairFunction) it -> new Tuple2( + (PairFunction) it -> new Tuple2<>( MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), it), it)); // : source is the dedup_id, target is the id of the mergedIn @@ -74,9 +83,9 @@ public class DedupRecordFactory { } } - private static Publication publicationMerger(Tuple2> e, final long ts) { + private static DLIPublication publicationMerger(Tuple2> e, final long ts) { - Publication p = new Publication(); // the result of the merge, to be returned at the end + DLIPublication p = new DLIPublication(); // the result of the merge, to be returned at the end p.setId(e._1()); @@ -91,7 +100,7 @@ public class DedupRecordFactory { .forEach( pub -> { try { - Publication publication = mapper.readValue(pub, Publication.class); + DLIPublication publication = mapper.readValue(pub, DLIPublication.class); p.mergeFrom(publication); p.setAuthor(DedupUtility.mergeAuthor(p.getAuthor(), publication.getAuthor())); @@ -110,9 +119,9 @@ public class DedupRecordFactory { return p; } - private static Dataset datasetMerger(Tuple2> e, final long ts) { + private static DLIDataset datasetMerger(Tuple2> e, final long ts) { - Dataset d = new Dataset(); // the result of the merge, to be returned at the end + DLIDataset d = new DLIDataset(); // the result of the merge, to be returned at the end d.setId(e._1()); diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java index f86410d292..8646ac7422 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateConnectedComponent.java @@ -9,18 +9,21 @@ import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.PairFunction; import org.apache.spark.graphx.Edge; import org.apache.spark.rdd.RDD; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; +import org.codehaus.jackson.map.ObjectMapper; import com.google.common.hash.Hashing; import eu.dnetlib.dedup.graph.ConnectedComponent; import eu.dnetlib.dedup.graph.GraphProcessor; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.util.MapDocumentUtil; @@ -42,7 +45,6 @@ public class SparkCreateConnectedComponent { .master(parser.get("master")) .getOrCreate(); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String inputPath = parser.get("sourcePath"); final String entity = parser.get("entity"); final String targetPath = parser.get("targetPath"); @@ -50,8 +52,12 @@ public class SparkCreateConnectedComponent { // DedupConfig.load(IOUtils.toString(SparkCreateConnectedComponent.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf2.json"))); final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); - final JavaPairRDD vertexes = sc - .textFile(inputPath + "/" + entity) + final JavaPairRDD vertexes = spark + .read() + .load(inputPath + "/" + entity) + .as(Encoders.kryo(Oaf.class)) + .map((MapFunction) p -> new ObjectMapper().writeValueAsString(p), Encoders.STRING()) + .javaRDD() .map(s -> MapDocumentUtil.getJPathString(dedupConf.getWf().getIdPath(), s)) .mapToPair( (PairFunction) s -> new Tuple2(getHashcode(s), s)); diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java index d87269f033..fa0ee1efb8 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateDedupRecord.java @@ -4,10 +4,10 @@ package eu.dnetlib.dedup; import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.pace.config.DedupConfig; @@ -41,12 +41,19 @@ public class SparkCreateDedupRecord { DedupUtility.createEntityPath(sourcePath, entity), OafEntityType.valueOf(entity), dedupConf); - dedupRecord - .map( - r -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(r); - }) - .saveAsTextFile(dedupPath + "/" + entity + "/dedup_records"); + spark + .createDataset(dedupRecord.rdd(), Encoders.kryo(OafEntity.class)) + .write() + .mode(SaveMode.Overwrite) + .save(dedupPath + "/" + entity + "/dedup_records"); +// +// +// dedupRecord +// .map( +// r -> { +// ObjectMapper mapper = new ObjectMapper(); +// return mapper.writeValueAsString(r); +// }) +// .saveAsTextFile(dedupPath + "/" + entity + "/dedup_records"); } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java index 41fe911e7e..572824e3db 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/SparkCreateSimRels.java @@ -7,10 +7,13 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.api.java.JavaPairRDD; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; +import org.codehaus.jackson.map.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; @@ -46,8 +49,13 @@ public class SparkCreateSimRels { // DedupConfig.load(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json"))); final DedupConfig dedupConf = DedupConfig.load(parser.get("dedupConf")); - JavaPairRDD mapDocument = sc - .textFile(inputPath + "/" + entity) + JavaPairRDD mapDocument = spark + .read() + .load(inputPath + "/" + entity) + .as(Encoders.kryo(Oaf.class)) + .map((MapFunction) p -> new ObjectMapper().writeValueAsString(p), Encoders.STRING()) + .javaRDD() + .repartition(1000) .mapToPair( s -> { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java index e3d4fdbe36..3134f94000 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkPropagateRelationsJob.java @@ -1,29 +1,19 @@ package eu.dnetlib.dedup.sx; -import java.io.IOException; - import org.apache.commons.io.IOUtils; -import org.apache.spark.api.java.JavaSparkContext; import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.*; - -import com.fasterxml.jackson.databind.DeserializationFeature; -import com.fasterxml.jackson.databind.ObjectMapper; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; -import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.dhp.schema.scholexplorer.OafUtils; import scala.Tuple2; public class SparkPropagateRelationsJob { - enum FieldType { - SOURCE, TARGET - } - - static final String SOURCEJSONPATH = "$.source"; - static final String TARGETJSONPATH = "$.target"; public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -39,7 +29,6 @@ public class SparkPropagateRelationsJob { .master(parser.get("master")) .getOrCreate(); - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); final String relationPath = parser.get("relationPath"); final String mergeRelPath = parser.get("mergeRelPath"); final String targetRelPath = parser.get("targetRelPath"); @@ -50,7 +39,13 @@ public class SparkPropagateRelationsJob { .as(Encoders.bean(Relation.class)) .where("relClass == 'merges'"); - final Dataset rels = spark.read().load(relationPath).as(Encoders.bean(Relation.class)); + final Dataset rels = spark + .read() + .load(relationPath) + .as(Encoders.kryo(Relation.class)) + .map( + (MapFunction) r -> r, + Encoders.bean(Relation.class)); final Dataset firstJoin = rels .joinWith(merge, merge.col("target").equalTo(rels.col("source")), "left_outer") @@ -58,9 +53,10 @@ public class SparkPropagateRelationsJob { (MapFunction, Relation>) r -> { final Relation mergeRelation = r._2(); final Relation relation = r._1(); - if (mergeRelation != null) relation.setSource(mergeRelation.getSource()); + if (relation.getDataInfo() == null) + relation.setDataInfo(OafUtils.generateDataInfo("0.9", false)); return relation; }, Encoders.bean(Relation.class)); @@ -75,38 +71,8 @@ public class SparkPropagateRelationsJob { relation.setTarget(mergeRelation.getSource()); return relation; }, - Encoders.bean(Relation.class)); + Encoders.kryo(Relation.class)); secondJoin.write().mode(SaveMode.Overwrite).save(targetRelPath); } - - private static boolean containsDedup(final String json) { - final String source = DHPUtils.getJPathString(SOURCEJSONPATH, json); - final String target = DHPUtils.getJPathString(TARGETJSONPATH, json); - - return source.toLowerCase().contains("dedup") || target.toLowerCase().contains("dedup"); - } - - private static String replaceField(final String json, final String id, final FieldType type) { - ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - try { - Relation relation = mapper.readValue(json, Relation.class); - if (relation.getDataInfo() == null) - relation.setDataInfo(new DataInfo()); - relation.getDataInfo().setDeletedbyinference(false); - switch (type) { - case SOURCE: - relation.setSource(id); - return mapper.writeValueAsString(relation); - case TARGET: - relation.setTarget(id); - return mapper.writeValueAsString(relation); - default: - throw new IllegalArgumentException(""); - } - } catch (IOException e) { - throw new RuntimeException("unable to deserialize json relation: " + json, e); - } - } } diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityWithDedupInfo.scala b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityWithDedupInfo.scala new file mode 100644 index 0000000000..ce883e2072 --- /dev/null +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/sx/SparkUpdateEntityWithDedupInfo.scala @@ -0,0 +1,75 @@ +package eu.dnetlib.dedup.sx + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown, OafUtils} +import org.apache.commons.io.IOUtils +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.LoggerFactory +import org.apache.spark.sql.functions.col + +object SparkUpdateEntityWithDedupInfo { + + def main(args: Array[String]): Unit = { + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkUpdateEntityWithDedupInfo.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/dedup/dedup_delete_by_inference_parameters.json"))) + val logger = LoggerFactory.getLogger(SparkUpdateEntityWithDedupInfo.getClass) + parser.parseArgument(args) + + val workingPath: String = parser.get("workingPath") + logger.info(s"Working dir path = $workingPath") + + implicit val oafEncoder: Encoder[OafEntity] = Encoders.kryo[OafEntity] + implicit val relEncoder: Encoder[Relation] = Encoders.bean(classOf[Relation]) + + implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication] + implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset] + implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown] + + + + val spark: SparkSession = SparkSession + .builder() + .appName(SparkUpdateEntityWithDedupInfo.getClass.getSimpleName) + .master(parser.get("master")) + .getOrCreate() + + + val entityPath = parser.get("entityPath") + val mergeRelPath = parser.get("mergeRelPath") + val dedupRecordPath = parser.get("dedupRecordPath") + val entity = parser.get("entity") + val destination = parser.get("targetPath") + + val mergedIds = spark.read.load(mergeRelPath).as[Relation] + .where("relClass == 'merges'") + .select(col("target")) + + + val entities: Dataset[(String, OafEntity)] = spark + .read + .load(entityPath).as[OafEntity] + .map(o => (o.getId, o))(Encoders.tuple(Encoders.STRING, oafEncoder)) + + + val finalDataset:Dataset[OafEntity] = entities.joinWith(mergedIds, entities("_1").equalTo(mergedIds("target")), "left") + .map(k => { + val e: OafEntity = k._1._2 + val t = k._2 + if (t != null && t.getString(0).nonEmpty) { + if (e.getDataInfo == null) { + e.setDataInfo(OafUtils.generateDataInfo()) + } + e.getDataInfo.setDeletedbyinference(true) + } + e + }) + + val dedupRecords :Dataset[OafEntity] = spark.read.load(dedupRecordPath).as[OafEntity] + + finalDataset.union(dedupRecords) + .repartition(1200).write + .mode(SaveMode.Overwrite).save(destination) + + } + +} diff --git a/dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/workflow.xml index 2f22bb764d..2214fd20ac 100644 --- a/dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/dedup/oozie_app/workflow.xml @@ -53,6 +53,7 @@ --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} + --executor-cores=${sparkExecutorCores} ${sparkExtraOPT} -mtyarn-cluster @@ -77,6 +78,7 @@ --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} + --executor-cores=${sparkExecutorCores} ${sparkExtraOPT} -mtyarn-cluster @@ -101,6 +103,7 @@ --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} + --executor-cores=${sparkExecutorCores} ${sparkExtraOPT} -mtyarn-cluster @@ -125,6 +128,7 @@ --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} + --executor-cores=${sparkExecutorCores} ${sparkExtraOPT} -mtyarn-cluster @@ -144,11 +148,12 @@ yarn-cluster cluster Update ${entity} and add DedupRecord - eu.dnetlib.dedup.sx.SparkUpdateEntityJob + eu.dnetlib.dedup.sx.SparkUpdateEntityWithDedupInfo dhp-dedup-scholexplorer-${projectVersion}.jar --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} + --executor-cores=${sparkExecutorCores} ${sparkExtraOPT} -mtyarn-cluster diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index c8eb017c71..1cc41c395e 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -109,9 +109,9 @@ public class PropagationConstant { } public static String getConstraintList(String text, List constraints) { - String ret = " and (" + text + constraints.get(0) + "'"; + String ret = " and (" + text + constraints.get(0).toLowerCase() + "'"; for (int i = 1; i < constraints.size(); i++) { - ret += " OR " + text + constraints.get(i) + "'"; + ret += " OR " + text + constraints.get(i).toLowerCase() + "'"; } ret += ")"; return ret; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java index 607315f3f8..9a24c52809 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/CommunityConfigurationFactory.java @@ -110,13 +110,6 @@ public class CommunityConfigurationFactory { } private static List parseZenodoCommunities(final Node node) { - final Node oacommunitynode = node.selectSingleNode("./oacommunity"); - String oacommunity = null; - if (oacommunitynode != null) { - String tmp = oacommunitynode.getText(); - if (StringUtils.isNotBlank(tmp)) - oacommunity = tmp; - } final List list = node.selectNodes("./zenodocommunities/zenodocommunity"); final List zenodoCommunityList = new ArrayList<>(); @@ -127,11 +120,7 @@ public class CommunityConfigurationFactory { zenodoCommunityList.add(zc); } - if (oacommunity != null) { - ZenodoCommunity zc = new ZenodoCommunity(); - zc.setZenodoCommunityId(oacommunity); - zenodoCommunityList.add(zc); - } + log.info("size of the zenodo community list " + zenodoCommunityList.size()); return zenodoCommunityList; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Provider.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Provider.java index b9c37f4dcc..a9427b5941 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Provider.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Provider.java @@ -44,7 +44,7 @@ public class Provider implements Serializable { } private void setSelCriteria(String json, VerbResolver resolver) { - log.info("Selection constraints for datasource = " + json); + log.debug("Selection constraints for datasource = " + json); selectionConstraints = new Gson().fromJson(json, SelectionConstraints.class); selectionConstraints.setSelection(resolver); @@ -54,7 +54,7 @@ public class Provider implements Serializable { try { setSelCriteria(n.getText(), resolver); } catch (Exception e) { - log.info("not set selection criteria... "); + log.debug("not set selection criteria... "); selectionConstraints = null; } } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java index 7ec2f916fb..993a7ef775 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/QueryInformationSystem.java @@ -17,7 +17,9 @@ public class QueryInformationSystem { + " let $datasources := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::contentproviders')]/concept " + " let $organizations := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::resultorganizations')]/concept " + " let $communities := $x//CONFIGURATION/context/category[./@id=concat($x//CONFIGURATION/context/@id,'::zenodocommunities')]/concept " - + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + + "let $zenodo := $x//param[./@name='zenodoCommunity']/text() " + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] and $x//context/param[./@name = 'status']/text() != 'hidden' " + " return " + " " + " { $x//CONFIGURATION/context/@id} " @@ -38,8 +40,15 @@ public class QueryInformationSystem { + " {$d/param[./@name='selcriteria']/text()} " + " " + " } " - + " " - + " " + + " " + + " " + + "{for $zc in $zenodo " + + "return " + + " " + + " " + + "{$zc} " + + " " + + "}" + " {for $zc in $communities " + " return " + " " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java index f5a985d15f..c9ff269631 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java @@ -20,8 +20,6 @@ import eu.dnetlib.dhp.schema.oaf.*; /** Created by miriam on 02/08/2018. */ public class ResultTagger implements Serializable { - private String trust = "0.8"; - private boolean clearContext(Result result) { int tmp = result.getContext().size(); List clist = result @@ -71,10 +69,10 @@ public class ResultTagger implements Serializable { // tagging for Subject final Set subjects = new HashSet<>(); - Optional> oresultsubj = Optional.ofNullable(result.getSubject()); - if (oresultsubj.isPresent()) { - oresultsubj - .get() + + if (Objects.nonNull(result.getSubject())) { + result + .getSubject() .stream() .map(subject -> subject.getValue()) .filter(StringUtils::isNotBlank) @@ -90,15 +88,23 @@ public class ResultTagger implements Serializable { final Set datasources = new HashSet<>(); final Set tmp = new HashSet<>(); - Optional> oresultinstance = Optional.ofNullable(result.getInstance()); - if (oresultinstance.isPresent()) { - for (Instance i : oresultinstance.get()) { - tmp.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|")); - tmp.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|")); + if (Objects.nonNull(result.getInstance())) { + for (Instance i : result.getInstance()) { + if (Objects.nonNull(i.getCollectedfrom())) { + if (Objects.nonNull(i.getCollectedfrom().getKey())) { + tmp.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|")); + } + } + if (Objects.nonNull(i.getHostedby())) { + if (Objects.nonNull(i.getHostedby().getKey())) { + tmp.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|")); + } + } + } - oresultinstance - .get() + result + .getInstance() .stream() .map(i -> new Pair<>(i.getCollectedfrom().getKey(), i.getHostedby().getKey())) .flatMap(p -> Stream.of(p.getFst(), p.getSnd())) @@ -163,21 +169,24 @@ public class ResultTagger implements Serializable { getDataInfo( BULKTAG_DATA_INFO_TYPE, CLASS_ID_SUBJECT, - CLASS_NAME_BULKTAG_SUBJECT)); + CLASS_NAME_BULKTAG_SUBJECT, + TAGGING_TRUST)); if (datasources.contains(c.getId())) dataInfoList .add( getDataInfo( BULKTAG_DATA_INFO_TYPE, CLASS_ID_DATASOURCE, - CLASS_NAME_BULKTAG_DATASOURCE)); + CLASS_NAME_BULKTAG_DATASOURCE, + TAGGING_TRUST)); if (czenodo.contains(c.getId())) dataInfoList .add( getDataInfo( BULKTAG_DATA_INFO_TYPE, CLASS_ID_CZENODO, - CLASS_NAME_BULKTAG_ZENODO)); + CLASS_NAME_BULKTAG_ZENODO, + TAGGING_TRUST)); } return c; }) @@ -203,21 +212,24 @@ public class ResultTagger implements Serializable { getDataInfo( BULKTAG_DATA_INFO_TYPE, CLASS_ID_SUBJECT, - CLASS_NAME_BULKTAG_SUBJECT)); + CLASS_NAME_BULKTAG_SUBJECT, + TAGGING_TRUST)); if (datasources.contains(c)) dataInfoList .add( getDataInfo( BULKTAG_DATA_INFO_TYPE, CLASS_ID_DATASOURCE, - CLASS_NAME_BULKTAG_DATASOURCE)); + CLASS_NAME_BULKTAG_DATASOURCE, + TAGGING_TRUST)); if (czenodo.contains(c)) dataInfoList .add( getDataInfo( BULKTAG_DATA_INFO_TYPE, CLASS_ID_CZENODO, - CLASS_NAME_BULKTAG_ZENODO)); + CLASS_NAME_BULKTAG_ZENODO, + TAGGING_TRUST)); context.setDataInfo(dataInfoList); return context; }) @@ -228,11 +240,12 @@ public class ResultTagger implements Serializable { } public static DataInfo getDataInfo( - String inference_provenance, String inference_class_id, String inference_class_name) { + String inference_provenance, String inference_class_id, String inference_class_name, String trust) { DataInfo di = new DataInfo(); di.setInferred(true); di.setInferenceprovenance(inference_provenance); di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name)); + di.setTrust(trust); return di; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java index 3cdc7c9411..80d98bb1a6 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java @@ -14,4 +14,6 @@ public class TaggingConstants { public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject"; public static final String CLASS_NAME_BULKTAG_DATASOURCE = "Bulktagging for Community - Datasource"; public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo"; + + public static final String TAGGING_TRUST = "0.8"; } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index f28c5aa06d..04a659a1ca 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -96,27 +96,6 @@ public class PrepareDatasourceCountryAssociation { relation.createOrReplaceTempView("relation"); organization.createOrReplaceTempView("organization"); -// String query = "SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country " -// + "FROM ( SELECT id " -// + " FROM datasource " -// + " WHERE (datainfo.deletedbyinference = false " -// + whitelisted -// + ") " -// + getConstraintList("datasourcetype.classid = '", allowedtypes) -// + ") d " -// + "JOIN ( SELECT source, target " -// + " FROM relation " -// + " WHERE relclass = '" -// + ModelConstants.IS_PROVIDED_BY -// + "' " -// + " AND datainfo.deletedbyinference = false ) rel " -// + "ON d.id = rel.source " -// + "JOIN (SELECT id, country " -// + " FROM organization " -// + " WHERE datainfo.deletedbyinference = false " -// + " AND length(country.classid) > 0) o " -// + "ON o.id = rel.target"; - String query = "SELECT source dataSourceId, " + "named_struct('classid', country.classid, 'classname', country.classname) country " + "FROM datasource d " + @@ -125,7 +104,7 @@ public class PrepareDatasourceCountryAssociation { "JOIN organization o " + "ON o.id = rel.target " + "WHERE rel.datainfo.deletedbyinference = false " + - "and rel.relclass = '" + ModelConstants.IS_PROVIDED_BY + "'" + + "and lower(rel.relclass) = '" + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "'" + "and o.datainfo.deletedbyinference = false " + "and length(o.country.classid) > 0 " + "and (" + allowed + " or " + whitelisted + ")"; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java index b15f813acd..869831ba2b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java @@ -102,15 +102,17 @@ public class PrepareResultOrcidAssociationStep1 { + " FROM result " + " LATERAL VIEW EXPLODE (author) a AS MyT " + " LATERAL VIEW EXPLODE (MyT.pid) p AS MyP " - + " WHERE MyP.qualifier.classid = 'ORCID') tmp " + + " WHERE lower(MyP.qualifier.classid) = 'orcid') tmp " + " GROUP BY id) r_t " + " JOIN (" + " SELECT source, target " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " - + getConstraintList(" relclass = '", allowedsemrel) + + getConstraintList(" lower(relclass) = '", allowedsemrel) + " ) rel_rel " + " ON source = id"; + + log.info("executedQuery: {}", query); spark .sql(query) .as(Encoders.bean(ResultOrcidList.class)) diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java index 4cd7f88dff..27ff727fdf 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/PrepareProjectResultsAssociation.java @@ -85,8 +85,8 @@ public class PrepareProjectResultsAssociation { String resproj_relation_query = "SELECT source, target " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " - + " AND relClass = '" - + ModelConstants.IS_PRODUCED_BY + + " AND lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"; Dataset resproj_relation = spark.sql(resproj_relation_query); @@ -98,7 +98,7 @@ public class PrepareProjectResultsAssociation { + " FROM (SELECT source, target " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " - + getConstraintList(" relClass = '", allowedsemrel) + + getConstraintList(" lower(relClass) = '", allowedsemrel) + " ) r1" + " JOIN resproj_relation r2 " + " ON r1.source = r2.source " diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java index 750d333e53..bea0a3e54f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/PrepareResultCommunitySet.java @@ -76,14 +76,14 @@ public class PrepareResultCommunitySet { + "FROM (SELECT source, target " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " - + " AND relClass = '" - + ModelConstants.HAS_AUTHOR_INSTITUTION + + " AND lower(relClass) = '" + + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase() + "') result_organization " + "LEFT JOIN (SELECT source, collect_set(target) org_set " + " FROM relation " + " WHERE datainfo.deletedbyinference = false " - + " AND relClass = '" - + ModelConstants.MERGES + + " AND lower(relClass) = '" + + ModelConstants.MERGES.toLowerCase() + "' " + " GROUP BY source) organization_organization " + "ON result_organization.target = organization_organization.source "; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java index 4f5ac25521..0c836a3ba9 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java @@ -144,8 +144,8 @@ public class PrepareResultCommunitySetStep1 { String resultContextQuery = String .format( RESULT_CONTEXT_QUERY_TEMPLATE, - getConstraintList(" co.id = '", communityIdList), - getConstraintList(" relClass = '", allowedsemrel)); + getConstraintList(" lower(co.id) = '", communityIdList), + getConstraintList(" lower(relClass) = '", allowedsemrel)); Dataset result_context = spark.sql(resultContextQuery); result_context.createOrReplaceTempView("result_context"); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java index 84e40fa88b..fe5889c53f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/PrepareResultInstRepoAssociation.java @@ -91,8 +91,8 @@ public class PrepareResultInstRepoAssociation { + "AND datainfo.deletedbyinference = false ) d " + "JOIN ( SELECT source, target " + "FROM relation " - + "WHERE relclass = '" - + ModelConstants.IS_PROVIDED_BY + + "WHERE lower(relclass) = '" + + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "' " + "AND datainfo.deletedbyinference = false ) rel " + "ON d.id = rel.source "; @@ -111,8 +111,8 @@ public class PrepareResultInstRepoAssociation { String query = "Select source resultId, collect_set(target) organizationSet " + "from relation " + "where datainfo.deletedbyinference = false " - + "and relClass = '" - + ModelConstants.HAS_AUTHOR_INSTITUTION + + "and lower(relClass) = '" + + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase() + "' " + "group by source"; diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml index 5ddc5fedf4..5f52c16585 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromsemrel/oozie_app/workflow.xml @@ -266,7 +266,6 @@ --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication --outputPath${outputPath}/publication - --saveGraph${saveGraph} @@ -298,7 +297,6 @@ --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset --outputPath${outputPath}/dataset - --saveGraph${saveGraph} @@ -330,7 +328,6 @@ --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct --outputPath${outputPath}/otherresearchproduct - --saveGraph${saveGraph} @@ -362,7 +359,6 @@ --hive_metastore_uris${hive_metastore_uris} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software --outputPath${outputPath}/software - --saveGraph${saveGraph} diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml index e0563abae8..2fe9a4256b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml @@ -176,7 +176,6 @@ --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication @@ -206,7 +205,6 @@ --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset @@ -236,7 +234,6 @@ --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct @@ -266,7 +263,6 @@ --datasourceOrganizationPath${workingDir}/preparedInfo/datasourceOrganization --alreadyLinkedPath${workingDir}/preparedInfo/alreadyLinked --hive_metastore_uris${hive_metastore_uris} - --saveGraph${saveGraph} --resultTableNameeu.dnetlib.dhp.schema.oaf.Software diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration.xml index e2cc41063d..eac320d098 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration.xml +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/community_configuration.xml @@ -106,12 +106,6 @@ aqua sea - - - re3data_____::9633d1e8c4309c833c2c442abeb0cfeb - - - @@ -163,7 +157,11 @@ - oac_clarin + + + oac_clarin + + diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml index a44372e4de..d4c83438b0 100644 --- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf.xml @@ -257,6 +257,9 @@ bodhgaya + + oac_dh-ch + diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 5ddcda3fa0..a0a334e3c1 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -42,6 +42,12 @@ + + + org.apache.commons + commons-compress + + commons-io commons-io @@ -59,6 +65,12 @@ org.apache.spark spark-hive_2.11 test + + + org.apache.httpcomponents + httpclient + + @@ -92,14 +104,21 @@ org.postgresql postgresql + + + org.apache.httpcomponents + httpmime + + + com.github.victools + jsonschema-generator + test + org.json4s json4s-jackson_2.11 - 3.5.3 - - diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java index 7091d97403..ae1b379061 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java @@ -90,6 +90,7 @@ public class CleanGraphSparkJob { final CleaningRuleMap mapping = CleaningRuleMap.create(vocs); readTableFromPath(spark, inputPath, clazz) + .map((MapFunction) value -> fixVocabularyNames(value), Encoders.bean(clazz)) .map((MapFunction) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz)) .map((MapFunction) value -> fixDefaults(value), Encoders.bean(clazz)) .write() @@ -98,6 +99,65 @@ public class CleanGraphSparkJob { .json(outputPath); } + protected static T fixVocabularyNames(T value) { + if (value instanceof Datasource) { + // nothing to clean here + } else if (value instanceof Project) { + // nothing to clean here + } else if (value instanceof Organization) { + Organization o = (Organization) value; + if (Objects.nonNull(o.getCountry())) { + fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE); + } + } else if (value instanceof Relation) { + // nothing to clean here + } else if (value instanceof Result) { + + Result r = (Result) value; + + fixVocabName(r.getLanguage(), ModelConstants.DNET_LANGUAGES); + fixVocabName(r.getResourcetype(), ModelConstants.DNET_DATA_CITE_RESOURCE); + fixVocabName(r.getBestaccessright(), ModelConstants.DNET_ACCESS_MODES); + + if (Objects.nonNull(r.getSubject())) { + r.getSubject().forEach(s -> fixVocabName(s.getQualifier(), ModelConstants.DNET_SUBJECT_TYPOLOGIES)); + } + if (Objects.nonNull(r.getInstance())) { + for (Instance i : r.getInstance()) { + fixVocabName(i.getAccessright(), ModelConstants.DNET_ACCESS_MODES); + fixVocabName(i.getRefereed(), ModelConstants.DNET_REVIEW_LEVELS); + } + } + if (Objects.nonNull(r.getAuthor())) { + r.getAuthor().forEach(a -> { + if (Objects.nonNull(a.getPid())) { + a.getPid().forEach(p -> { + fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES); + }); + } + }); + } + if (value instanceof Publication) { + + } else if (value instanceof eu.dnetlib.dhp.schema.oaf.Dataset) { + + } else if (value instanceof OtherResearchProduct) { + + } else if (value instanceof Software) { + + } + } + + return value; + } + + private static void fixVocabName(Qualifier q, String vocabularyName) { + if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) { + q.setSchemeid(vocabularyName); + q.setSchemename(vocabularyName); + } + } + protected static T fixDefaults(T value) { if (value instanceof Datasource) { // nothing to clean here @@ -113,6 +173,9 @@ public class CleanGraphSparkJob { } else if (value instanceof Result) { Result r = (Result) value; + if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) { + r.setPublisher(null); + } if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) { r .setLanguage( diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java new file mode 100644 index 0000000000..a466cf0742 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -0,0 +1,43 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.util.Map; + +import com.google.common.collect.Maps; + +public class Constants { + + public static final Map accessRightsCoarMap = Maps.newHashMap(); + public static final Map coarCodeLabelMap = Maps.newHashMap(); + + public static final String INFERRED = "Inferred by OpenAIRE"; + + public static final String HARVESTED = "Harvested"; + public static final String DEFAULT_TRUST = "0.9"; + public static final String USER_CLAIM = "Linked by user";; + + public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + + public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + + public static String RESEARCH_COMMUNITY = "Research Community"; + + public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + + public static String ORCID = "orcid"; + + static { + accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put("RESTRICTED", "c_16ec"); + accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); + accessRightsCoarMap.put("CLOSED", "c_14cb"); + accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + } + + static { + coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put("c_16ec", "RESTRICTED"); + coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_f1cf", "EMBARGO"); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java new file mode 100644 index 0000000000..c97d2d72ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -0,0 +1,106 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Objects; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; + +import eu.dnetlib.dhp.oa.graph.dump.ResultMapper; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; +import eu.dnetlib.dhp.schema.oaf.*; + +/** + * It fires the execution of the actual dump for result entities. If the dump is for RC/RI products its checks for each + * result its belongingess to at least one RC/RI before "asking" for its mapping. + */ +public class DumpProducts implements Serializable { + + public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath, + Class inputClazz, + Class outputClazz, + boolean graph) { + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, graph); + }); + } + + public static void execDump( + SparkSession spark, + String inputPath, + String outputPath, + String communityMapPath, + Class inputClazz, + Class outputClazz, + boolean graph) { + + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + + Utils + .readPath(spark, inputPath, inputClazz) + .map(value -> execMap(value, communityMap, graph), Encoders.bean(outputClazz)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + + } + + private static O execMap(I value, + CommunityMap communityMap, + boolean graph) { + + Optional odInfo = Optional.ofNullable(value.getDataInfo()); + if (odInfo.isPresent()) { + if (odInfo.get().getDeletedbyinference()) { + return null; + } + } else { + return null; + } + + if (!graph) { + Set communities = communityMap.keySet(); + + Optional> inputContext = Optional + .ofNullable(((eu.dnetlib.dhp.schema.oaf.Result) value).getContext()); + if (!inputContext.isPresent()) { + return null; + } + List toDumpFor = inputContext.get().stream().map(c -> { + if (communities.contains(c.getId())) { + return c.getId(); + } + if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { + return c.getId().substring(0, 3); + } + return null; + }).filter(Objects::nonNull).collect(Collectors.toList()); + if (toDumpFor.size() == 0) { + return null; + } + } + return (O) ResultMapper.map(value, communityMap, graph); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java new file mode 100644 index 0000000000..1999601045 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java @@ -0,0 +1,114 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.*; + +import org.apache.commons.compress.archivers.ar.ArArchiveEntry; +import org.apache.commons.compress.archivers.ar.ArArchiveOutputStream; +import org.apache.commons.compress.archivers.tar.TarArchiveEntry; +import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; + +public class MakeTar implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(MakeTar.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + MakeTar.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + final String outputPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", outputPath); + + final String hdfsNameNode = parser.get("nameNode"); + log.info("nameNode: {}", hdfsNameNode); + + final String inputPath = parser.get("sourcePath"); + log.info("input path : {}", inputPath); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + makeTArArchive(fileSystem, inputPath, outputPath); + + } + + public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath) throws IOException { + + RemoteIterator dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); + + while (dir_iterator.hasNext()) { + LocatedFileStatus fileStatus = dir_iterator.next(); + + Path p = fileStatus.getPath(); + String p_string = p.toString(); + String entity = p_string.substring(p_string.lastIndexOf("/") + 1); + + write(fileSystem, p_string, outputPath + "/" + entity + ".tar", entity); + } + + } + + private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name) + throws IOException { + + Path hdfsWritePath = new Path(outputPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fileSystem.delete(hdfsWritePath, true); + + } + fsDataOutputStream = fileSystem.create(hdfsWritePath); + + TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream()); + + RemoteIterator fileStatusListIterator = fileSystem + .listFiles( + new Path(inputPath), true); + + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + + Path p = fileStatus.getPath(); + String p_string = p.toString(); + if (!p_string.endsWith("_SUCCESS")) { + String name = p_string.substring(p_string.lastIndexOf("/") + 1); + TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name + ".json.gz"); + entry.setSize(fileStatus.getLen()); + ar.putArchiveEntry(entry); + + InputStream is = fileSystem.open(fileStatus.getPath()); + + BufferedInputStream bis = new BufferedInputStream(is); + + int count; + byte data[] = new byte[1024]; + while ((count = bis.read(data, 0, data.length)) != -1) { + ar.write(data, 0, count); + } + bis.close(); + ar.closeArchiveEntry(); + + } + + } + + ar.close(); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java new file mode 100644 index 0000000000..d118accbae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -0,0 +1,58 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.StringReader; +import java.util.List; + +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Element; +import org.dom4j.io.SAXReader; + +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class QueryInformationSystem { + + private ISLookUpService isLookUp; + + private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + public CommunityMap getCommunityMap() + throws ISLookUpException, DocumentException { + return getMap(isLookUp.quickSearchProfile(XQUERY)); + + } + + public ISLookUpService getIsLookUp() { + return isLookUp; + } + + public void setIsLookUp(ISLookUpService isLookUpService) { + this.isLookUp = isLookUpService; + } + + private CommunityMap getMap(List communityMap) throws DocumentException { + final CommunityMap map = new CommunityMap(); + + for (String xml : communityMap) { + final Document doc; + doc = new SAXReader().read(new StringReader(xml)); + Element root = doc.getRootElement(); + map.put(root.attribute("id").getValue(), root.attribute("label").getValue()); + } + + return map; + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java new file mode 100644 index 0000000000..41142d2851 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -0,0 +1,522 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.lang3.StringUtils; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.*; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Context; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class ResultMapper implements Serializable { + + public static Result map( + I in, Map communityMap, boolean graph) { + + Result out; + if (graph) { + out = new Result(); + } else { + out = new CommunityResult(); + } + + eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; + Optional ort = Optional.ofNullable(input.getResulttype()); + if (ort.isPresent()) { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": + + eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(v -> v.getValue()) + .collect(Collectors.toList()))); + + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": + + eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + + break; + } + + Optional + .ofNullable(input.getAuthor()) + .ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList()))); + + // I do not map Access Right UNKNOWN or OTHER + + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); + out + .setBestaccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } + + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); + + // List countryList = new ArrayList<>(); + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance + .newInstance( + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); + + // out.setCountry(countryList); + + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); + + out.setDateofcollection(input.getDateofcollection()); + + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } + + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); + + final List instanceList = new ArrayList<>(); + Optional + .ofNullable(input.getInstance()) + .ifPresent( + inst -> inst + .stream() + .forEach(i -> instanceList.add(getInstance(i, graph)))); + out + .setInstance(instanceList); + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (iTitle.size() > 0) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + List pids = new ArrayList<>(); + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> value + .stream() + .forEach( + p -> pids + .add( + ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())))); + out.setPid(pids); + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + List sourceList = new ArrayList<>(); + Optional + .ofNullable(input.getSource()) + .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); + // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + } + + if (!graph) { + ((CommunityResult) out) + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + + Set communities = communityMap.keySet(); + List contextList = Optional + .ofNullable( + input + .getContext()) + .map( + value -> value + .stream() + .map(c -> { + String community_id = c.getId(); + if (community_id.indexOf("::") > 0) { + community_id = community_id.substring(0, community_id.indexOf("::")); + } + if (communities.contains(community_id)) { + Context context = new Context(); + context.setCode(community_id); + context.setLabel(communityMap.get(community_id)); + Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); + if (dataInfo.isPresent()) { + List provenance = new ArrayList<>(); + provenance + .addAll( + dataInfo + .get() + .stream() + .map( + di -> Optional + .ofNullable(di.getProvenanceaction()) + .map( + provenanceaction -> Provenance + .newInstance( + provenanceaction.getClassname(), di.getTrust())) + .orElse(null)) + .filter(Objects::nonNull) + .collect(Collectors.toSet())); + + context.setProvenance(getUniqueProvenance(provenance)); + } + return context; + } + return null; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); + + if (contextList.size() > 0) { + Set hashValue = new HashSet<>(); + List remainigContext = new ArrayList<>(); + contextList.forEach(c -> { + if (!hashValue.contains(c.hashCode())) { + remainigContext.add(c); + hashValue.add(c.hashCode()); + } + }); + ((CommunityResult) out).setContext(remainigContext); + } + } + return out; + + } + + private static Instance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i, boolean graph) { + + Instance instance = new Instance(); + + if (!graph) { + instance + .setCollectedfrom( + KeyValue + .newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue())); + instance + .setHostedby( + KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue())); + } + + Optional opAr = Optional + .ofNullable(i.getAccessright()); + if (opAr.isPresent()) { + if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + } + } + + Optional + .ofNullable(i.getLicense()) + .ifPresent(value -> instance.setLicense(value.getValue())); + Optional + .ofNullable(i.getDateofacceptance()) + .ifPresent(value -> instance.setPublicationdate(value.getValue())); + Optional + .ofNullable(i.getRefereed()) + .ifPresent(value -> instance.setRefereed(value.getClassname())); + // .ifPresent(value -> instance.setRefereed(value.getValue())); + Optional + .ofNullable(i.getInstancetype()) + .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + + return instance; + } + + private static List getUniqueProvenance(List provenance) { + Provenance iProv = new Provenance(); + // iProv.setProvenance(Constants.INFERRED); + + Provenance hProv = new Provenance(); + // hProv.setProvenance(Constants.HARVESTED); + Provenance lProv = new Provenance(); + + for (Provenance p : provenance) { + switch (p.getProvenance()) { + case Constants.HARVESTED: + hProv = getHighestTrust(hProv, p); + break; + case Constants.INFERRED: + iProv = getHighestTrust(iProv, p); + // To be removed as soon as the new beta run has been done + // this fixex issue of not set trust during bulktagging + if (StringUtils.isEmpty(iProv.getTrust())) { + iProv.setTrust(Constants.DEFAULT_TRUST); + } + break; + case Constants.USER_CLAIM: + lProv = getHighestTrust(lProv, p); + break; + } + + } + + return Arrays + .asList(iProv, hProv, lProv) + .stream() + .filter(p -> !StringUtils.isEmpty(p.getProvenance())) + .collect(Collectors.toList()); + + } + + private static Provenance getHighestTrust(Provenance hProv, Provenance p) { + if (StringUtils.isNoneEmpty(hProv.getTrust(), p.getTrust())) + return hProv.getTrust().compareTo(p.getTrust()) > 0 ? hProv : p; + + return (StringUtils.isEmpty(p.getTrust()) && !StringUtils.isEmpty(hProv.getTrust())) ? hProv : p; + + } + + private static Subject getSubject(StructuredProperty s) { + Subject subject = new Subject(); + subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue())); + Optional di = Optional.ofNullable(s.getDataInfo()); + if (di.isPresent()) { + Provenance p = new Provenance(); + p.setProvenance(di.get().getProvenanceaction().getClassname()); + p.setTrust(di.get().getTrust()); + subject.setProvenance(p); + } + + return subject; + } + + private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) { + Author a = new Author(); + a.setFullname(oa.getFullname()); + a.setName(oa.getName()); + a.setSurname(oa.getSurname()); + a.setRank(oa.getRank()); + + Optional> oPids = Optional + .ofNullable(oa.getPid()); + if (oPids.isPresent()) { + Pid pid = getOrcid(oPids.get()); + if (pid != null) { + a.setPid(pid); + } + } + + return a; + } + + private static Pid getOrcid(List p) { + for (StructuredProperty pid : p) { + if (pid.getQualifier().getClassid().equals(Constants.ORCID)) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance + .newInstance( + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) + + ); + } + + } + } + return null; + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java new file mode 100644 index 0000000000..6ac626518c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -0,0 +1,84 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.io.Serializable; +import java.nio.charset.StandardCharsets; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.dom4j.DocumentException; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; + +/** + * This class connects with the IS related to the isLookUpUrl got as parameter. It saves the information about the + * context that will guide the dump of the results. The information saved is a HashMap. The key is the id of a community + * - research infrastructure/initiative , the value is the label of the research community - research + * infrastructure/initiative. + */ + +public class SaveCommunityMap implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); + private final QueryInformationSystem queryInformationSystem; + + private final Configuration conf; + private final BufferedWriter writer; + + public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { + conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fileSystem.delete(hdfsWritePath); + } + fsDataOutputStream = fileSystem.create(hdfsWritePath); + + queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); + + writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + + } + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SaveCommunityMap.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + final String nameNode = parser.get("nameNode"); + log.info("nameNode: {}", nameNode); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String isLookUpUrl = parser.get("isLookUpUrl"); + log.info("isLookUpUrl: {}", isLookUpUrl); + + final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl); + + scm.saveCommunityMap(); + + } + + private void saveCommunityMap() throws ISLookUpException, IOException, DocumentException { + writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap())); + writer.close(); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java new file mode 100644 index 0000000000..23784cd66c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -0,0 +1,88 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.api.MissingConceptDoiException; +import eu.dnetlib.dhp.common.api.ZenodoAPIClient; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; + +public class SendToZenodoHDFS implements Serializable { + + private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class); + + public static void main(final String[] args) throws Exception, MissingConceptDoiException { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SendToZenodoHDFS.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json"))); + + parser.parseArgument(args); + + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("nameNode"); + final String access_token = parser.get("accessToken"); + final String connection_url = parser.get("connectionUrl"); + final String metadata = parser.get("metadata"); + final Boolean newDeposition = Boolean.valueOf(parser.get("newDeposition")); + final String concept_rec_id = Optional + .ofNullable(parser.get("conceptRecordId")) + .orElse(null); + final String communityMapPath = parser.get("communityMapPath"); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); + + RemoteIterator fileStatusListIterator = fileSystem + .listFiles( + new Path(hdfsPath), true); + ZenodoAPIClient zenodoApiClient = new ZenodoAPIClient(connection_url, access_token); + if (newDeposition) { + zenodoApiClient.newDeposition(); + } else { + if (concept_rec_id == null) { + throw new MissingConceptDoiException("No concept record id has been provided"); + } + zenodoApiClient.newVersion(concept_rec_id); + } + + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + + Path p = fileStatus.getPath(); + String p_string = p.toString(); + if (!p_string.endsWith("_SUCCESS")) { + // String tmp = p_string.substring(0, p_string.lastIndexOf("/")); + String name = p_string.substring(p_string.lastIndexOf("/") + 1); + log.info("Sending information for community: " + name); + if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { + name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; + } + + FSDataInputStream inputStream = fileSystem.open(p); + zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); + + } + + } + + zenodoApiClient.sendMretadata(metadata); + zenodoApiClient.publish(); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java new file mode 100644 index 0000000000..c112c5c724 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java @@ -0,0 +1,73 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; + +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; + +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.graph.Constants; +import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class Utils { + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + + public static ISLookUpService getIsLookUpService(String isLookUpUrl) { + return ISLookupClientFactory.getLookUpService(isLookUpUrl); + } + + public static String getContextId(String id) { + + return String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5(id)); + } + + public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) { + + return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class); + + } + + public static CommunityMap readCommunityMap(FileSystem fileSystem, String communityMapPath) throws IOException { + BufferedReader br = new BufferedReader(new InputStreamReader(fileSystem.open(new Path(communityMapPath)))); + StringBuffer sb = new StringBuffer(); + try { + String line; + while ((line = br.readLine()) != null) { + sb.append(line); + } + } finally { + br.close(); + + } + + return new Gson().fromJson(sb.toString(), CommunityMap.class); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java new file mode 100644 index 0000000000..d459063377 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunityMap.java @@ -0,0 +1,8 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import java.io.Serializable; +import java.util.HashMap; + +public class CommunityMap extends HashMap implements Serializable { +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java new file mode 100644 index 0000000000..6be1befce1 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -0,0 +1,83 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; +import java.util.Set; +import java.util.stream.Collectors; + +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; + +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + +/** + * This class splits the dumped results according to the research community - research initiative/infrastructure they + * are related to. The information about the community is found in the element "context.id" in the result. Since the + * context that can be found in the result can be associated not only to communities, a community Map is provided. It + * will guide the splitting process. Note: the repartition(1) just before writing the results related to a community. + * This is a choice due to uploading constraints (just one file for each community) As soon as a better solution will be + * in place remove the repartition + */ +public class CommunitySplit implements Serializable { + + public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath) { + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + execSplit(spark, inputPath, outputPath, Utils.getCommunityMap(spark, communityMapPath).keySet()); + }); + } + + private static void execSplit(SparkSession spark, String inputPath, String outputPath, + Set communities) { + + Dataset result = Utils + .readPath(spark, inputPath + "/publication", CommunityResult.class) + .union(Utils.readPath(spark, inputPath + "/dataset", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) + .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); + + communities + .stream() + .forEach(c -> printResult(c, result, outputPath)); + + } + + private static void printResult(String c, Dataset result, String outputPath) { + Dataset community_products = result + .filter(r -> containsCommunity(r, c)); + + try { + community_products.first(); + community_products + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath + "/" + c); + } catch (Exception e) { + + } + + } + + private static boolean containsCommunity(CommunityResult r, String c) { + if (Optional.ofNullable(r.getContext()).isPresent()) { + return r + .getContext() + .stream() + .filter(con -> con.getCode().equals(c)) + .collect(Collectors.toList()) + .size() > 0; + } + return false; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java new file mode 100644 index 0000000000..300af62f35 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/ResultProject.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import java.io.Serializable; +import java.util.List; + +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; + +public class ResultProject implements Serializable { + private String resultId; + private List projectsList; + + public String getResultId() { + return resultId; + } + + public void setResultId(String resultId) { + this.resultId = resultId; + } + + public List getProjectsList() { + return projectsList; + } + + public void setProjectsList(List projectsList) { + this.projectsList = projectsList; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java new file mode 100644 index 0000000000..c4b89936ff --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkDumpCommunityProducts.java @@ -0,0 +1,62 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.oaf.Result; + +/** + * Spark action to trigger the dump of results associated to research community - reseach initiative/infrasctructure The + * actual dump if performed via the class DumpProducts that is used also for the entire graph dump + */ +public class SparkDumpCommunityProducts implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkDumpCommunityProducts.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkDumpCommunityProducts.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + String communityMapPath = parser.get("communityMapPath"); + + Class inputClazz = (Class) Class.forName(resultClassName); + + DumpProducts dump = new DumpProducts(); + + dump + .run( + isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, CommunityResult.class, + false); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java new file mode 100644 index 0000000000..6e0e059f3d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -0,0 +1,185 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.io.StringReader; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Node; +import org.dom4j.io.SAXReader; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Relation; +import scala.Tuple2; + +/** + * Preparation of the Project information to be added to the dumped results. For each result associated to at least one + * Project, a serialization of an instance af ResultProject closs is done. ResultProject contains the resultId, and the + * list of Projects (as in eu.dnetlib.dhp.schema.dump.oaf.community.Project) it is associated to + */ +public class SparkPrepareResultProject implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkPrepareResultProject.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkPrepareResultProject.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + prepareResultProjectList(spark, inputPath, outputPath); + }); + } + + private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { + Dataset relation = Utils + .readPath(spark, inputPath + "/relation", Relation.class) + .filter("dataInfo.deletedbyinference = false and relClass = 'produces'"); + Dataset projects = Utils + .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); + + projects + .joinWith(relation, projects.col("id").equalTo(relation.col("source"))) + .groupByKey( + (MapFunction, String>) value -> value + ._2() + .getTarget(), + Encoders.STRING()) + .mapGroups( + (MapGroupsFunction, ResultProject>) (s, + it) -> { + Set projectSet = new HashSet<>(); + Tuple2 first = it.next(); + ResultProject rp = new ResultProject(); + rp.setResultId(first._2().getTarget()); + eu.dnetlib.dhp.schema.oaf.Project p = first._1(); + projectSet.add(p.getId()); + Project ps = getProject(p); + + List projList = new ArrayList<>(); + projList.add(ps); + rp.setProjectsList(projList); + it.forEachRemaining(c -> { + eu.dnetlib.dhp.schema.oaf.Project op = c._1(); + if (!projectSet.contains(op.getId())) { + projList + .add(getProject(op)); + + projectSet.add(op.getId()); + + } + + }); + return rp; + }, Encoders.bean(ResultProject.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op) { + Project p = Project + .newInstance( + op.getId(), + op.getCode().getValue(), + Optional + .ofNullable(op.getAcronym()) + .map(a -> a.getValue()) + .orElse(null), + Optional + .ofNullable(op.getTitle()) + .map(v -> v.getValue()) + .orElse(null), + Optional + .ofNullable(op.getFundingtree()) + .map( + value -> value + .stream() + .map(ft -> getFunder(ft.getValue())) + .collect(Collectors.toList()) + .get(0)) + .orElse(null)); + + Optional di = Optional.ofNullable(op.getDataInfo()); + Provenance provenance = new Provenance(); + if (di.isPresent()) { + provenance.setProvenance(di.get().getProvenanceaction().getClassname()); + provenance.setTrust(di.get().getTrust()); + p.setProvenance(provenance); + } + + return p; + + } + + private static Funder getFunder(String fundingtree) { + // ["nsf_________::NSFNSFNational Science + // FoundationUSnsf_________::NSF::CISE/OAD::CISE/CCFDivision + // of Computing and Communication FoundationsDivision of Computing and Communication + // Foundationsnsf_________::NSF::CISE/OADDirectorate for + // Computer & Information Science & EngineeringDirectorate for Computer & + // Information Science & + // Engineeringnsf:fundingStream"] + Funder f = new Funder(); + final Document doc; + try { + doc = new SAXReader().read(new StringReader(fundingtree)); + f.setShortName(((Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); + f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); + f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); + for (Object o : doc.selectNodes("//funding_level_0")) { + List node = ((Node) o).selectNodes("./name"); + f.setFundingStream(((Node) node.get(0)).getText()); + + } + + return f; + } catch (DocumentException e) { + e.printStackTrace(); + } + return f; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java new file mode 100644 index 0000000000..b62bf18e78 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkSplitForCommunity.java @@ -0,0 +1,50 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +/** + * Spark job to trigger the split of results associated to research community - reseach initiative/infrasctructure. The + * actual split is performed by the class CommunitySplit + */ +public class SparkSplitForCommunity implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkSplitForCommunity.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkSplitForCommunity.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String communityMapPath = parser.get("communityMapPath"); + + CommunitySplit split = new CommunitySplit(); + split.run(isSparkSessionManaged, inputPath, outputPath, communityMapPath); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java new file mode 100644 index 0000000000..1276d8495e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkUpdateProjectInfo.java @@ -0,0 +1,90 @@ + +package eu.dnetlib.dhp.oa.graph.dump.community; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + +public class SparkUpdateProjectInfo implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkUpdateProjectInfo.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkUpdateProjectInfo.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String preparedInfoPath = parser.get("preparedInfoPath"); + log.info("preparedInfoPath: {}", preparedInfoPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + extend(spark, inputPath, outputPath, preparedInfoPath);// , inputClazz); + }); + } + + private static void extend( + SparkSession spark, + String inputPath, + String outputPath, + String preparedInfoPath) { + Dataset result = Utils.readPath(spark, inputPath, CommunityResult.class); + Dataset resultProject = Utils.readPath(spark, preparedInfoPath, ResultProject.class); + result + .joinWith( + resultProject, result.col("id").equalTo(resultProject.col("resultId")), + "left") + .map(value -> { + CommunityResult r = value._1(); + Optional.ofNullable(value._2()).ifPresent(rp -> { + r.setProjects(rp.getProjectsList()); + }); + return r; + }, Encoders.bean(CommunityResult.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Append) + .json(outputPath); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Constants.java new file mode 100644 index 0000000000..4c1e1c08cf --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Constants.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.Serializable; + +public class Constants implements Serializable { + + public static final String IS_HOSTED_BY = "isHostedBy"; + public static final String HOSTS = "hosts"; + + public static final String IS_FUNDED_BY = "isFundedBy"; + public static final String FUNDS = "funds"; + + public static final String FUNDINGS = "fundings"; + + public static final String RESULT_ENTITY = "result"; + public static final String DATASOURCE_ENTITY = "datasource"; + public static final String CONTEXT_ENTITY = "context"; + public static final String ORGANIZATION_ENTITY = "organization"; + public static final String PROJECT_ENTITY = "project"; + + public static final String CONTEXT_ID = "00"; + public static final String CONTEXT_NS_PREFIX = "context_____"; + + // public static final String FUNDER_DS = "entityregistry::projects"; +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/ContextInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/ContextInfo.java new file mode 100644 index 0000000000..7befaaf6f3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/ContextInfo.java @@ -0,0 +1,84 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.Serializable; +import java.util.List; + +/** + * Deserialization of the information in the context needed to create Context Entities, and relations between context + * entities and datasources and projects + */ +public class ContextInfo implements Serializable { + private String id; + private String description; + private String type; + private String zenodocommunity; + private String name; + private List projectList; + private List datasourceList; + private List subject; + + public List getSubject() { + return subject; + } + + public void setSubject(List subject) { + this.subject = subject; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getDescription() { + return description; + } + + public void setDescription(String description) { + this.description = description; + } + + public String getType() { + return type; + } + + public void setType(String type) { + this.type = type; + } + + public String getZenodocommunity() { + return zenodocommunity; + } + + public void setZenodocommunity(String zenodocommunity) { + this.zenodocommunity = zenodocommunity; + } + + public List getProjectList() { + return projectList; + } + + public void setProjectList(List projectList) { + this.projectList = projectList; + } + + public List getDatasourceList() { + return datasourceList; + } + + public void setDatasourceList(List datasourceList) { + this.datasourceList = datasourceList; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextEntities.java new file mode 100644 index 0000000000..0f28438afb --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextEntities.java @@ -0,0 +1,105 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.io.Serializable; +import java.nio.charset.StandardCharsets; +import java.util.function.Consumer; +import java.util.function.Function; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; + +/** + * Writes on HDFS Context entities. It queries the Information System at the lookup url provided as parameter and + * collects the general information for contexes of type community or ri. The general information is the id of the + * context, its label, the subjects associated to the context, its zenodo community, description and type. This + * information is used to create a new Context Entity + */ +public class CreateContextEntities implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class); + private final Configuration conf; + private final BufferedWriter writer; + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + CreateContextEntities.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); + + final String hdfsNameNode = parser.get("nameNode"); + log.info("nameNode: {}", hdfsNameNode); + + final String isLookUpUrl = parser.get("isLookUpUrl"); + log.info("isLookUpUrl: {}", isLookUpUrl); + + final CreateContextEntities cce = new CreateContextEntities(hdfsPath, hdfsNameNode); + + log.info("Processing contexts..."); + cce.execute(Process::getEntity, isLookUpUrl); + + cce.close(); + + } + + private void close() throws IOException { + writer.close(); + } + + public CreateContextEntities(String hdfsPath, String hdfsNameNode) throws IOException { + this.conf = new Configuration(); + this.conf.set("fs.defaultFS", hdfsNameNode); + FileSystem fileSystem = FileSystem.get(this.conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + + } + + public void execute(final Function producer, String isLookUpUrl) + throws Exception { + + QueryInformationSystem queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); + + final Consumer consumer = ci -> writeEntity(producer.apply(ci)); + + queryInformationSystem.getContextInformation(consumer); + } + + protected void writeEntity(final R r) { + try { + writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); + // log.info("writing context : {}", new Gson().toJson(r)); + writer.newLine(); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextRelation.java new file mode 100644 index 0000000000..1290779321 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextRelation.java @@ -0,0 +1,124 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.BufferedWriter; +import java.io.IOException; +import java.io.OutputStreamWriter; +import java.io.Serializable; +import java.nio.charset.StandardCharsets; +import java.util.List; +import java.util.Optional; +import java.util.function.Consumer; +import java.util.function.Function; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.graph.*; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; + +/** + * Writes the set of new Relation between the context and datasources. At the moment the relation between the context + * and the project is not created because of a low coverage in the profiles of openaire ids related to projects + */ +public class CreateContextRelation implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CreateContextEntities.class); + private final Configuration conf; + private final BufferedWriter writer; + private final QueryInformationSystem queryInformationSystem; + + private static final String CONTEX_RELATION_DATASOURCE = "contentproviders"; + private static final String CONTEX_RELATION_PROJECT = "projects"; + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + CreateContextRelation.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); + + final String hdfsNameNode = parser.get("nameNode"); + log.info("nameNode: {}", hdfsNameNode); + + final String isLookUpUrl = parser.get("isLookUpUrl"); + log.info("isLookUpUrl: {}", isLookUpUrl); + + final CreateContextRelation cce = new CreateContextRelation(hdfsPath, hdfsNameNode, isLookUpUrl); + + log.info("Creating relation for datasource..."); + cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class)); + + log.info("Creating relations for projects... "); +// cce +// .execute( +// Process::getRelation, CONTEX_RELATION_PROJECT, +// ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); + + cce.close(); + + } + + private void close() throws IOException { + writer.close(); + } + + public CreateContextRelation(String hdfsPath, String hdfsNameNode, String isLookUpUrl) + throws IOException, ISLookUpException { + this.conf = new Configuration(); + this.conf.set("fs.defaultFS", hdfsNameNode); + + queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setIsLookUp(Utils.getIsLookUpService(isLookUpUrl)); + queryInformationSystem.execContextRelationQuery(); + + FileSystem fileSystem = FileSystem.get(this.conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fsDataOutputStream = fileSystem.append(hdfsWritePath); + } else { + fsDataOutputStream = fileSystem.create(hdfsWritePath); + } + + this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + + } + + public void execute(final Function> producer, String category, String prefix) { + + final Consumer consumer = ci -> producer.apply(ci).forEach(c -> writeEntity(c)); + + queryInformationSystem.getContextRelation(consumer, category, prefix); + } + + protected void writeEntity(final Relation r) { + try { + writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); + writer.newLine(); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java new file mode 100644 index 0000000000..86421cff51 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java @@ -0,0 +1,498 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.io.StringReader; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Node; +import org.dom4j.io.SAXReader; + +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.*; +import eu.dnetlib.dhp.schema.dump.oaf.graph.*; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Project; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Journal; +import eu.dnetlib.dhp.schema.oaf.OafEntity; + +/** + * Dumps of entities in the model defined in eu.dnetlib.dhp.schema.dump.oaf.graph. Results are dumped using the same + * Mapper as for eu.dnetlib.dhp.schema.dump.oaf.community, while for the other entities the mapping is defined below + */ +public class DumpGraphEntities implements Serializable { + + public void run(Boolean isSparkSessionManaged, + String inputPath, + String outputPath, + Class inputClazz, + String communityMapPath) { + + SparkConf conf = new SparkConf(); + + switch (ModelSupport.idPrefixMap.get(inputClazz)) { + case "50": + DumpProducts d = new DumpProducts(); + d + .run( + isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, Result.class, + true); + break; + case "40": + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + projectMap(spark, inputPath, outputPath, inputClazz); + + }); + break; + case "20": + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + organizationMap(spark, inputPath, outputPath, inputClazz); + + }); + break; + case "10": + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + datasourceMap(spark, inputPath, outputPath, inputClazz); + + }); + break; + } + + } + + private static void datasourceMap(SparkSession spark, String inputPath, String outputPath, + Class inputClazz) { + Utils + .readPath(spark, inputPath, inputClazz) + .map(d -> mapDatasource((eu.dnetlib.dhp.schema.oaf.Datasource) d), Encoders.bean(Datasource.class)) + .filter(Objects::nonNull) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static void projectMap(SparkSession spark, String inputPath, String outputPath, + Class inputClazz) { + Utils + .readPath(spark, inputPath, inputClazz) + .map(p -> mapProject((eu.dnetlib.dhp.schema.oaf.Project) p), Encoders.bean(Project.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Datasource mapDatasource(eu.dnetlib.dhp.schema.oaf.Datasource d) { + Datasource datasource = new Datasource(); + + datasource.setId(d.getId()); + + Optional + .ofNullable(d.getOriginalId()) + .ifPresent( + oId -> datasource.setOriginalId(oId.stream().filter(Objects::nonNull).collect(Collectors.toList()))); + + Optional + .ofNullable(d.getPid()) + .ifPresent( + pids -> pids + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList())); + + Optional + .ofNullable(d.getDatasourcetype()) + .ifPresent( + dsType -> datasource + .setDatasourcetype(ControlledField.newInstance(dsType.getClassid(), dsType.getClassname()))); + + Optional + .ofNullable(d.getOpenairecompatibility()) + .ifPresent(v -> datasource.setOpenairecompatibility(v.getClassname())); + + Optional + .ofNullable(d.getOfficialname()) + .ifPresent(oname -> datasource.setOfficialname(oname.getValue())); + + Optional + .ofNullable(d.getEnglishname()) + .ifPresent(ename -> datasource.setEnglishname(ename.getValue())); + + Optional + .ofNullable(d.getWebsiteurl()) + .ifPresent(wsite -> datasource.setWebsiteurl(wsite.getValue())); + + Optional + .ofNullable(d.getLogourl()) + .ifPresent(lurl -> datasource.setLogourl(lurl.getValue())); + + Optional + .ofNullable(d.getDateofvalidation()) + .ifPresent(dval -> datasource.setDateofvalidation(dval.getValue())); + + Optional + .ofNullable(d.getDescription()) + .ifPresent(dex -> datasource.setDescription(dex.getValue())); + + Optional + .ofNullable(d.getSubjects()) + .ifPresent( + sbjs -> datasource.setSubjects(sbjs.stream().map(sbj -> sbj.getValue()).collect(Collectors.toList()))); + + Optional + .ofNullable(d.getOdpolicies()) + .ifPresent(odp -> datasource.setPolicies(Arrays.asList(odp.getValue()))); + + Optional + .ofNullable(d.getOdlanguages()) + .ifPresent( + langs -> datasource + .setLanguages(langs.stream().map(lang -> lang.getValue()).collect(Collectors.toList()))); + + Optional + .ofNullable(d.getOdcontenttypes()) + .ifPresent( + ctypes -> datasource + .setContenttypes(ctypes.stream().map(ctype -> ctype.getValue()).collect(Collectors.toList()))); + + Optional + .ofNullable(d.getReleasestartdate()) + .ifPresent(rd -> datasource.setReleasestartdate(rd.getValue())); + + Optional + .ofNullable(d.getReleaseenddate()) + .ifPresent(ed -> datasource.setReleaseenddate(ed.getValue())); + + Optional + .ofNullable(d.getMissionstatementurl()) + .ifPresent(ms -> datasource.setMissionstatementurl(ms.getValue())); + + Optional + .ofNullable(d.getDatabaseaccesstype()) + .ifPresent(ar -> datasource.setAccessrights(ar.getValue())); + + Optional + .ofNullable(d.getDatauploadtype()) + .ifPresent(dut -> datasource.setUploadrights(dut.getValue())); + + Optional + .ofNullable(d.getDatabaseaccessrestriction()) + .ifPresent(dar -> datasource.setDatabaseaccessrestriction(dar.getValue())); + + Optional + .ofNullable(d.getDatauploadrestriction()) + .ifPresent(dur -> datasource.setDatauploadrestriction(dur.getValue())); + + Optional + .ofNullable(d.getVersioning()) + .ifPresent(v -> datasource.setVersioning(v.getValue())); + + Optional + .ofNullable(d.getCitationguidelineurl()) + .ifPresent(cu -> datasource.setCitationguidelineurl(cu.getValue())); + + Optional + .ofNullable(d.getPidsystems()) + .ifPresent(ps -> datasource.setPidsystems(ps.getValue())); + + Optional + .ofNullable(d.getCertificates()) + .ifPresent(c -> datasource.setCertificates(c.getValue())); + + Optional + .ofNullable(d.getPolicies()) + .ifPresent(ps -> datasource.setPolicies(ps.stream().map(p -> p.getValue()).collect(Collectors.toList()))); + + Optional + .ofNullable(d.getJournal()) + .ifPresent(j -> datasource.setJournal(getContainer(j))); + + return datasource; + + } + + private static Container getContainer(Journal j) { + Container c = new Container(); + + Optional + .ofNullable(j.getName()) + .ifPresent(n -> c.setName(n)); + + Optional + .ofNullable(j.getIssnPrinted()) + .ifPresent(issnp -> c.setIssnPrinted(issnp)); + + Optional + .ofNullable(j.getIssnOnline()) + .ifPresent(issno -> c.setIssnOnline(issno)); + + Optional + .ofNullable(j.getIssnLinking()) + .ifPresent(isnl -> c.setIssnLinking(isnl)); + + Optional + .ofNullable(j.getEp()) + .ifPresent(ep -> c.setEp(ep)); + + Optional + .ofNullable(j.getIss()) + .ifPresent(iss -> c.setIss(iss)); + + Optional + .ofNullable(j.getSp()) + .ifPresent(sp -> c.setSp(sp)); + + Optional + .ofNullable(j.getVol()) + .ifPresent(vol -> c.setVol(vol)); + + Optional + .ofNullable(j.getEdition()) + .ifPresent(edition -> c.setEdition(edition)); + + Optional + .ofNullable(j.getConferencedate()) + .ifPresent(cdate -> c.setConferencedate(cdate)); + + Optional + .ofNullable(j.getConferenceplace()) + .ifPresent(cplace -> c.setConferenceplace(cplace)); + + return c; + } + + private static Project mapProject(eu.dnetlib.dhp.schema.oaf.Project p) throws DocumentException { + Project project = new Project(); + + Optional + .ofNullable(p.getId()) + .ifPresent(id -> project.setId(id)); + + Optional + .ofNullable(p.getWebsiteurl()) + .ifPresent(w -> project.setWebsiteurl(w.getValue())); + + Optional + .ofNullable(p.getCode()) + .ifPresent(code -> project.setCode(code.getValue())); + + Optional + .ofNullable(p.getAcronym()) + .ifPresent(acronynim -> project.setAcronym(acronynim.getValue())); + + Optional + .ofNullable(p.getTitle()) + .ifPresent(title -> project.setTitle(title.getValue())); + + Optional + .ofNullable(p.getStartdate()) + .ifPresent(sdate -> project.setStartdate(sdate.getValue())); + + Optional + .ofNullable(p.getEnddate()) + .ifPresent(edate -> project.setEnddate(edate.getValue())); + + Optional + .ofNullable(p.getCallidentifier()) + .ifPresent(cide -> project.setCallidentifier(cide.getValue())); + + Optional + .ofNullable(p.getKeywords()) + .ifPresent(key -> project.setKeywords(key.getValue())); + + Optional> omandate = Optional.ofNullable(p.getOamandatepublications()); + Optional> oecsc39 = Optional.ofNullable(p.getEcsc39()); + boolean mandate = false; + if (omandate.isPresent()) { + if (omandate.get().getValue().equals("true")) { + mandate = true; + } + } + if (oecsc39.isPresent()) { + if (oecsc39.get().getValue().equals("true")) { + mandate = true; + } + } + + project.setOpenaccessmandateforpublications(mandate); + project.setOpenaccessmandatefordataset(false); + + Optional + .ofNullable(p.getEcarticle29_3()) + .ifPresent(oamandate -> project.setOpenaccessmandatefordataset(oamandate.getValue().equals("true"))); + + project + .setSubject( + Optional + .ofNullable(p.getSubjects()) + .map(subjs -> subjs.stream().map(s -> s.getValue()).collect(Collectors.toList())) + .orElse(new ArrayList<>())); + + Optional + .ofNullable(p.getSummary()) + .ifPresent(summary -> project.setSummary(summary.getValue())); + + Optional ofundedamount = Optional.ofNullable(p.getFundedamount()); + Optional> ocurrency = Optional.ofNullable(p.getCurrency()); + Optional ototalcost = Optional.ofNullable(p.getTotalcost()); + + if (ocurrency.isPresent()) { + if (ofundedamount.isPresent()) { + if (ototalcost.isPresent()) { + project + .setGranted( + Granted.newInstance(ocurrency.get().getValue(), ototalcost.get(), ofundedamount.get())); + } else { + project.setGranted(Granted.newInstance(ocurrency.get().getValue(), ofundedamount.get())); + } + } + } + + project + .setProgramme( + Optional + .ofNullable(p.getProgramme()) + .map( + programme -> programme + .stream() + .map(pg -> Programme.newInstance(pg.getCode(), pg.getDescription())) + .collect(Collectors.toList())) + .orElse(new ArrayList<>())); + + Optional>> ofundTree = Optional + .ofNullable(p.getFundingtree()); + List funList = new ArrayList<>(); + if (ofundTree.isPresent()) { + for (Field fundingtree : ofundTree.get()) { + funList.add(getFunder(fundingtree.getValue())); + } + } + project.setFunding(funList); + + return project; + } + + public static Funder getFunder(String fundingtree) throws DocumentException { + Funder f = new Funder(); + final Document doc; + + doc = new SAXReader().read(new StringReader(fundingtree)); + f.setShortName(((org.dom4j.Node) (doc.selectNodes("//funder/shortname").get(0))).getText()); + f.setName(((org.dom4j.Node) (doc.selectNodes("//funder/name").get(0))).getText()); + f.setJurisdiction(((org.dom4j.Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); + // f.setId(((org.dom4j.Node) (doc.selectNodes("//funder/id").get(0))).getText()); + + String id = ""; + String description = ""; + // List fundings = new ArrayList<>(); + int level = 0; + List nodes = doc.selectNodes("//funding_level_" + level); + while (nodes.size() > 0) { + for (org.dom4j.Node n : nodes) { + + List node = n.selectNodes("./id"); + id = ((org.dom4j.Node) node.get(0)).getText(); + id = id.substring(id.indexOf("::") + 2); + + node = n.selectNodes("./description"); + description += ((Node) node.get(0)).getText() + " - "; + + } + level += 1; + nodes = doc.selectNodes("//funding_level_" + level); + } + + if (!id.equals("")) { + Fundings fundings = new Fundings(); + fundings.setId(id); + fundings.setDescription(description.substring(0, description.length() - 3).trim()); + f.setFunding_stream(fundings); + } + + return f; + + } + + private static void organizationMap(SparkSession spark, String inputPath, String outputPath, + Class inputClazz) { + Utils + .readPath(spark, inputPath, inputClazz) + .map(o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { + Organization organization = new Organization(); + + Optional + .ofNullable(org.getLegalshortname()) + .ifPresent(value -> organization.setLegalshortname(value.getValue())); + + Optional + .ofNullable(org.getLegalname()) + .ifPresent(value -> organization.setLegalname(value.getValue())); + + Optional + .ofNullable(org.getWebsiteurl()) + .ifPresent(value -> organization.setWebsiteurl(value.getValue())); + + Optional + .ofNullable(org.getAlternativeNames()) + .ifPresent( + value -> organization + .setAlternativenames( + value + .stream() + .map(v -> v.getValue()) + .collect(Collectors.toList()))); + + Optional + .ofNullable(org.getCountry()) + .ifPresent( + value -> organization.setCountry(Qualifier.newInstance(value.getClassid(), value.getClassname()))); + + Optional + .ofNullable(org.getId()) + .ifPresent(value -> organization.setId(value)); + + Optional + .ofNullable(org.getPid()) + .ifPresent( + value -> organization + .setPid( + value + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + return organization; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Extractor.java new file mode 100644 index 0000000000..3daaed47f4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Extractor.java @@ -0,0 +1,197 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; + +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; + +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; +import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Result; + +/** + * Creates new Relations (as in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation) from the information in the Entity. + * The new Relations are created for the datasource in the collectedfrom and hostedby elements and for the context + * related to communities and research initiative/infrastructures. + * + * For collectedfrom elements it creates: datasource -> provides -> result and result -> isProvidedBy -> datasource + * For hostedby elements it creates: datasource -> hosts -> result and result -> isHostedBy -> datasource + * For context elements it creates: context <-> isRelatedTo <-> result + */ +public class Extractor implements Serializable { + + public void run(Boolean isSparkSessionManaged, + String inputPath, + String outputPath, + Class inputClazz, + String communityMapPath) { + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + extractRelationResult( + spark, inputPath, outputPath, inputClazz, Utils.getCommunityMap(spark, communityMapPath)); + }); + } + + private void extractRelationResult(SparkSession spark, + String inputPath, + String outputPath, + Class inputClazz, + CommunityMap communityMap) { + + Set hashCodes = new HashSet<>(); + + Utils + .readPath(spark, inputPath, inputClazz) + .flatMap((FlatMapFunction) value -> { + List relationList = new ArrayList<>(); + Optional + .ofNullable(value.getInstance()) + .ifPresent(inst -> inst.forEach(instance -> { + Optional + .ofNullable(instance.getCollectedfrom()) + .ifPresent( + cf -> getRelatioPair( + value, relationList, cf, + ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); + Optional + .ofNullable(instance.getHostedby()) + .ifPresent( + hb -> getRelatioPair( + value, relationList, hb, + Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); + })); + Set communities = communityMap.keySet(); + Optional + .ofNullable(value.getContext()) + .ifPresent(contexts -> contexts.forEach(context -> { + String id = context.getId(); + if (id.contains(":")) { + id = id.substring(0, id.indexOf(":")); + } + if (communities.contains(id)) { + String contextId = Utils.getContextId(id); + Provenance provenance = Optional + .ofNullable(context.getDataInfo()) + .map( + dinfo -> Optional + .ofNullable(dinfo.get(0).getProvenanceaction()) + .map( + paction -> Provenance + .newInstance( + paction.getClassid(), + dinfo.get(0).getTrust())) + .orElse(null)) + .orElse(null); + Relation r = getRelation( + value.getId(), contextId, + Constants.RESULT_ENTITY, + Constants.CONTEXT_ENTITY, + ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, provenance); + if (!hashCodes.contains(r.hashCode())) { + relationList + .add(r); + hashCodes.add(r.hashCode()); + } + r = getRelation( + contextId, value.getId(), + Constants.CONTEXT_ENTITY, + Constants.RESULT_ENTITY, + ModelConstants.RELATIONSHIP, + ModelConstants.IS_RELATED_TO, provenance); + if (!hashCodes.contains(r.hashCode())) { + relationList + .add( + r); + hashCodes.add(r.hashCode()); + } + + } + + })); + + return relationList.iterator(); + }, Encoders.bean(Relation.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + + } + + private static void getRelatioPair(R value, List relationList, KeyValue cf, + String result_dtasource, String datasource_result, + Set hashCodes) { + Provenance provenance = Optional + .ofNullable(cf.getDataInfo()) + .map( + dinfo -> Optional + .ofNullable(dinfo.getProvenanceaction()) + .map( + paction -> Provenance + .newInstance( + paction.getClassid(), + dinfo.getTrust())) + .orElse( + Provenance + .newInstance( + eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, + eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))) + .orElse( + Provenance + .newInstance( + eu.dnetlib.dhp.oa.graph.dump.Constants.HARVESTED, + eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST)); + Relation r = getRelation( + value.getId(), + cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, + result_dtasource, ModelConstants.PROVISION, + provenance); + if (!hashCodes.contains(r.hashCode())) { + relationList + .add(r); + hashCodes.add(r.hashCode()); + } + + r = getRelation( + cf.getKey(), value.getId(), + Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, + datasource_result, ModelConstants.PROVISION, + provenance); + + if (!hashCodes.contains(r.hashCode())) { + relationList + .add(r); + hashCodes.add(r.hashCode()); + } + + } + + private static Relation getRelation(String source, String target, String sourceType, String targetType, + String relName, String relType, Provenance provenance) { + Relation r = new Relation(); + r.setSource(Node.newInstance(source, sourceType)); + r.setTarget(Node.newInstance(target, targetType)); + r.setReltype(RelType.newInstance(relName, relType)); + r.setProvenance(provenance); + return r; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/MergedRels.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/MergedRels.java new file mode 100644 index 0000000000..5f59750eac --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/MergedRels.java @@ -0,0 +1,25 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.Serializable; + +public class MergedRels implements Serializable { + private String organizationId; + private String representativeId; + + public String getOrganizationId() { + return organizationId; + } + + public void setOrganizationId(String organizationId) { + this.organizationId = organizationId; + } + + public String getRepresentativeId() { + return representativeId; + } + + public void setRepresentativeId(String representativeId) { + this.representativeId = representativeId; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/OrganizationMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/OrganizationMap.java new file mode 100644 index 0000000000..11db7c25e4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/OrganizationMap.java @@ -0,0 +1,21 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; + +public class OrganizationMap extends HashMap> { + + public OrganizationMap() { + super(); + } + + public List get(String key) { + + if (super.get(key) == null) { + return new ArrayList<>(); + } + return super.get(key); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Process.java new file mode 100644 index 0000000000..7b7dafdf37 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Process.java @@ -0,0 +1,98 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; + +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; +import eu.dnetlib.dhp.schema.dump.oaf.graph.*; + +/** + * It process the ContextInfo information to produce a new Context Entity or a set of Relations between the + * generic context entity and datasource/projects related to the context. + * + */ +public class Process implements Serializable { + private static final Logger log = LoggerFactory.getLogger(Process.class); + + public static R getEntity(ContextInfo ci) { + try { + ResearchInitiative ri; + if (ci.getType().equals("community")) { + ri = new ResearchCommunity(); + ((ResearchCommunity) ri).setSubject(ci.getSubject()); + ri.setType(Constants.RESEARCH_COMMUNITY); + } else { + ri = new ResearchInitiative(); + ri.setType(Constants.RESEARCH_INFRASTRUCTURE); + } + ri.setId(Utils.getContextId(ci.getId())); + ri.setOriginalId(ci.getId()); + + ri.setDescription(ci.getDescription()); + ri.setName(ci.getName()); + ri.setZenodo_community(Constants.ZENODO_COMMUNITY_PREFIX + ci.getZenodocommunity()); + return (R) ri; + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + + public static List getRelation(ContextInfo ci) { + try { + + List relationList = new ArrayList<>(); + ci + .getDatasourceList() + .forEach(ds -> { + + String nodeType = ModelSupport.idPrefixEntity.get(ds.substring(0, 2)); + + String contextId = Utils.getContextId(ci.getId()); + relationList + .add( + Relation + .newInstance( + Node + .newInstance( + contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY), + Node.newInstance(ds, nodeType), + RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), + Provenance + .newInstance( + Constants.USER_CLAIM, + Constants.DEFAULT_TRUST))); + + relationList + .add( + Relation + .newInstance( + Node.newInstance(ds, nodeType), + Node + .newInstance( + contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY), + RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), + Provenance + .newInstance( + Constants.USER_CLAIM, + Constants.DEFAULT_TRUST))); + + }); + + return relationList; + + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystem.java new file mode 100644 index 0000000000..e74d8a44c7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystem.java @@ -0,0 +1,132 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.StringReader; +import java.sql.ResultSet; +import java.sql.SQLException; +import java.sql.Statement; +import java.util.*; +import java.util.function.Consumer; +import java.util.stream.Collectors; + +import org.dom4j.Document; +import org.dom4j.DocumentException; +import org.dom4j.Element; +import org.dom4j.Node; +import org.dom4j.io.SAXReader; +import org.jetbrains.annotations.NotNull; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class QueryInformationSystem { + + private ISLookUpService isLookUp; + private List contextRelationResult; + + private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and $x//context/param[./@name = 'status']/text() = 'all' " + + " return " + + "$x//context"; + + private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " + + + "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + + "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " + + + "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; + + public void getContextInformation(final Consumer consumer) throws ISLookUpException { + + isLookUp + .quickSearchProfile(XQUERY_ENTITY) + .forEach(c -> { + ContextInfo cinfo = new ContextInfo(); + String[] cSplit = c.split("@@"); + cinfo.setId(cSplit[0]); + cinfo.setName(cSplit[1]); + cinfo.setDescription(cSplit[2]); + if (!cSplit[3].trim().equals("")) { + cinfo.setSubject(Arrays.asList(cSplit[3].split(","))); + } + cinfo.setZenodocommunity(cSplit[4]); + cinfo.setType(cSplit[5]); + consumer.accept(cinfo); + }); + + } + + public List getContextRelationResult() { + return contextRelationResult; + } + + public void setContextRelationResult(List contextRelationResult) { + this.contextRelationResult = contextRelationResult; + } + + public ISLookUpService getIsLookUp() { + return isLookUp; + } + + public void setIsLookUp(ISLookUpService isLookUpService) { + this.isLookUp = isLookUpService; + } + + public void execContextRelationQuery() throws ISLookUpException { + contextRelationResult = isLookUp.quickSearchProfile(XQUERY); + + } + + public void getContextRelation(final Consumer consumer, String category, String prefix) { + + contextRelationResult.forEach(xml -> { + ContextInfo cinfo = new ContextInfo(); + final Document doc; + + try { + + doc = new SAXReader().read(new StringReader(xml)); + Element root = doc.getRootElement(); + cinfo.setId(root.attributeValue("id")); + + Iterator it = root.elementIterator(); + while (it.hasNext()) { + Element el = (Element) it.next(); + if (el.getName().equals("category")) { + String categoryId = el.attributeValue("id"); + categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); + if (categoryId.equals(category)) { + cinfo.setDatasourceList(getCategoryList(el, prefix)); + } + } + + } + consumer.accept(cinfo); + } catch (DocumentException e) { + e.printStackTrace(); + } + + }); + + } + + @NotNull + private List getCategoryList(Element el, String prefix) { + List datasourceList = new ArrayList<>(); + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + if (n.valueOf("./@name").equals("openaireId")) { + datasourceList.add(prefix + "|" + n.getText()); + } + } + + return datasourceList; + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkCollectAndSave.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkCollectAndSave.java new file mode 100644 index 0000000000..cb150210ab --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkCollectAndSave.java @@ -0,0 +1,89 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; + +/** + * Reads all the entities of the same type (Relation / Results) and saves them in the same folder + * + */ +public class SparkCollectAndSave implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkCollectAndSave.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkCollectAndSave.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath + "/result"); + run(spark, inputPath, outputPath); + + }); + + } + + private static void run(SparkSession spark, String inputPath, String outputPath) { + Utils + .readPath(spark, inputPath + "/result/publication", Result.class) + .union(Utils.readPath(spark, inputPath + "/result/dataset", Result.class)) + .union(Utils.readPath(spark, inputPath + "/result/otherresearchproduct", Result.class)) + .union(Utils.readPath(spark, inputPath + "/result/software", Result.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath + "/result"); + + Utils + .readPath(spark, inputPath + "/relation/publication", Relation.class) + .union(Utils.readPath(spark, inputPath + "/relation/dataset", Relation.class)) + .union(Utils.readPath(spark, inputPath + "/relation/orp", Relation.class)) + .union(Utils.readPath(spark, inputPath + "/relation/software", Relation.class)) + .union(Utils.readPath(spark, inputPath + "/relation/contextOrg", Relation.class)) + .union(Utils.readPath(spark, inputPath + "/relation/context", Relation.class)) + .union(Utils.readPath(spark, inputPath + "/relation/relation", Relation.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/relation"); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpEntitiesJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpEntitiesJob.java new file mode 100644 index 0000000000..441cfa32de --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpEntitiesJob.java @@ -0,0 +1,54 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.OafEntity; + +/** + * Spark Job that fires the dump for the entites + */ +public class SparkDumpEntitiesJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkDumpEntitiesJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkDumpEntitiesJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + final String communityMapPath = parser.get("communityMapPath"); + + Class inputClazz = (Class) Class.forName(resultClassName); + + DumpGraphEntities dg = new DumpGraphEntities(); + dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpRelationJob.java new file mode 100644 index 0000000000..59aad1f309 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpRelationJob.java @@ -0,0 +1,111 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; +import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; +import eu.dnetlib.dhp.schema.oaf.Relation; + +/** + * Dumps eu.dnetlib.dhp.schema.oaf.Relation in eu.dnetlib.dhp.schema.dump.oaf.graph.Relation + */ +public class SparkDumpRelationJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkDumpRelationJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkDumpRelationJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + dumpRelation(spark, inputPath, outputPath); + + }); + + } + + private static void dumpRelation(SparkSession spark, String inputPath, String outputPath) { + Utils + .readPath(spark, inputPath, Relation.class) + .map(relation -> { + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); + rel + .setSource( + Node + .newInstance( + relation.getSource(), + ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); + + rel + .setTarget( + Node + .newInstance( + relation.getTarget(), + ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); + + rel + .setReltype( + RelType + .newInstance( + relation.getRelClass(), + relation.getSubRelType())); + + Optional + .ofNullable(relation.getDataInfo()) + .ifPresent( + datainfo -> rel + .setProvenance( + Provenance + .newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust()))); + + return rel; + + }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkExtractRelationFromEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkExtractRelationFromEntities.java new file mode 100644 index 0000000000..f910dbee41 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkExtractRelationFromEntities.java @@ -0,0 +1,57 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.io.IOUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.QueryInformationSystem; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.oaf.Result; + +/** + * Spark job that fires the extraction of relations from entities + */ +public class SparkExtractRelationFromEntities implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkExtractRelationFromEntities.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkExtractRelationFromEntities.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final String resultClassName = parser.get("resultTableName"); + log.info("resultTableName: {}", resultClassName); + + final String communityMapPath = parser.get("communityMapPath"); + + Class inputClazz = (Class) Class.forName(resultClassName); + + Extractor extractor = new Extractor(); + extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkOrganizationRelation.java new file mode 100644 index 0000000000..f17e7c894c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkOrganizationRelation.java @@ -0,0 +1,160 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; +import java.util.function.Consumer; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.*; +import org.jetbrains.annotations.NotNull; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.google.gson.Gson; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.Provenance; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Node; +import eu.dnetlib.dhp.schema.dump.oaf.graph.RelType; +import eu.dnetlib.dhp.schema.oaf.Relation; + +/** + * Create new Relations between Context Entities and Organizations whose products are associated to the context. + * It produces relation such as: organization <-> isRelatedTo <-> context + */ +public class SparkOrganizationRelation implements Serializable { + private static final Logger log = LoggerFactory.getLogger(SparkOrganizationRelation.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkOrganizationRelation.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + final OrganizationMap organizationMap = new Gson() + .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); + log.info("organization map : {}", new Gson().toJson(organizationMap)); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + extractRelation(spark, inputPath, organizationMap, outputPath); + + }); + + } + + private static void extractRelation(SparkSession spark, String inputPath, OrganizationMap organizationMap, + String outputPath) { + Dataset relationDataset = Utils.readPath(spark, inputPath, Relation.class); + + relationDataset.createOrReplaceTempView("relation"); + + List relList = new ArrayList<>(); + + Dataset mergedRelsDataset = spark + .sql( + "SELECT target organizationId, source representativeId " + + "FROM relation " + + "WHERE datainfo.deletedbyinference = false " + + "AND relclass = 'merges' " + + "AND substr(source, 1, 2) = '20'") + .as(Encoders.bean(MergedRels.class)); + + mergedRelsDataset.map((MapFunction) mergedRels -> { + if (organizationMap.containsKey(mergedRels.getOrganizationId())) { + return mergedRels; + } + return null; + }, Encoders.bean(MergedRels.class)) + .filter(Objects::nonNull) + .collectAsList() + .forEach(getMergedRelsConsumer(organizationMap, relList)); + + organizationMap + .keySet() + .forEach( + oId -> organizationMap + .get(oId) + .forEach(community -> addRelations(relList, community, oId))); + + spark + .createDataset(relList, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + + } + + @NotNull + private static Consumer getMergedRelsConsumer(OrganizationMap organizationMap, + List relList) { + return mergedRels -> { + String oId = mergedRels.getOrganizationId(); + organizationMap + .get(oId) + .forEach(community -> addRelations(relList, community, mergedRels.getRepresentativeId())); + organizationMap.remove(oId); + }; + } + + private static void addRelations(List relList, String community, + String organization) { + + String id = Utils.getContextId(community); + log.info("create relation for organization: {}", organization); + relList + .add( + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation + .newInstance( + Node.newInstance(id, Constants.CONTEXT_ENTITY), + Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))), + RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), + Provenance + .newInstance( + eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, + eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); + + relList + .add( + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation + .newInstance( + Node.newInstance(organization, ModelSupport.idPrefixEntity.get(organization.substring(0, 2))), + Node.newInstance(id, Constants.CONTEXT_ENTITY), + RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP), + Provenance + .newInstance( + eu.dnetlib.dhp.oa.graph.dump.Constants.USER_CLAIM, + eu.dnetlib.dhp.oa.graph.dump.Constants.DEFAULT_TRUST))); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 5159fa9bb6..5b6ae72f18 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -24,7 +24,9 @@ public abstract class AbstractMdRecordToOafMapper { private final boolean invisible; protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4"; + protected static final String DATACITE_SCHEMA_KERNEL_4_SLASH = "http://datacite.org/schema/kernel-4/"; protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3"; + protected static final String DATACITE_SCHEMA_KERNEL_3_SLASH = "http://datacite.org/schema/kernel-3/"; protected static final Qualifier ORCID_PID_TYPE = qualifier( "ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES); protected static final Qualifier MAG_PID_TYPE = qualifier( @@ -55,7 +57,11 @@ public abstract class AbstractMdRecordToOafMapper { DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext); final Document doc = DocumentHelper - .parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3)); + .parseText( + xml + .replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_4_SLASH, DATACITE_SCHEMA_KERNEL_3) + .replaceAll(DATACITE_SCHEMA_KERNEL_3_SLASH, DATACITE_SCHEMA_KERNEL_3)); final KeyValue collectedFrom = getProvenanceDatasource( doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name"); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index da2ba47237..87c935d835 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -44,6 +44,7 @@ import java.util.Date; import java.util.List; import java.util.function.Consumer; import java.util.function.Function; +import java.util.function.Predicate; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -53,6 +54,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.DbClient; import eu.dnetlib.dhp.oa.graph.raw.common.AbstractMigrationApplication; +import eu.dnetlib.dhp.oa.graph.raw.common.VerifyNsPrefixPredicate; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Context; import eu.dnetlib.dhp.schema.oaf.DataInfo; @@ -113,6 +115,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final String hdfsPath = parser.get("hdfsPath"); log.info("hdfsPath: {}", hdfsPath); + final String nsPrefixBlacklist = parser.get("nsPrefixBlacklist"); + log.info("nsPrefixBlacklist: {}", nsPrefixBlacklist); + + final Predicate verifyNamespacePrefix = new VerifyNsPrefixPredicate(nsPrefixBlacklist); + final boolean processClaims = parser.get("action") != null && parser.get("action").equalsIgnoreCase("claims"); log.info("processClaims: {}", processClaims); @@ -123,23 +130,25 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i smdbe.execute("queryClaims.sql", smdbe::processClaims); } else { log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource); + smdbe.execute("queryDatasources.sql", smdbe::processDatasource, verifyNamespacePrefix); log.info("Processing projects..."); if (dbSchema.equalsIgnoreCase("beta")) { - smdbe.execute("queryProjects.sql", smdbe::processProject); + smdbe.execute("queryProjects.sql", smdbe::processProject, verifyNamespacePrefix); } else { - smdbe.execute("queryProjects_production.sql", smdbe::processProject); + smdbe.execute("queryProjects_production.sql", smdbe::processProject, verifyNamespacePrefix); } log.info("Processing orgs..."); - smdbe.execute("queryOrganizations.sql", smdbe::processOrganization); + smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix); log.info("Processing relationsNoRemoval ds <-> orgs ..."); - smdbe.execute("queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization); + smdbe + .execute( + "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization, verifyNamespacePrefix); log.info("Processing projects <-> orgs ..."); - smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization); + smdbe.execute("queryProjectOrganization.sql", smdbe::processProjectOrganization, verifyNamespacePrefix); } log.info("All done."); } @@ -163,10 +172,20 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } public void execute(final String sqlFile, final Function> producer) + throws Exception { + execute(sqlFile, producer, oaf -> true); + } + + public void execute(final String sqlFile, final Function> producer, + final Predicate predicate) throws Exception { final String sql = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/sql/" + sqlFile)); - final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> emitOaf(oaf)); + final Consumer consumer = rs -> producer.apply(rs).forEach(oaf -> { + if (predicate.test(oaf)) { + emitOaf(oaf); + } + }); dbClient.processResults(sql, consumer); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java index 62f8123bb3..6fe7bb9713 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java @@ -16,6 +16,8 @@ import org.apache.commons.lang3.StringUtils; import org.dom4j.Document; import org.dom4j.Node; +import com.google.common.collect.Lists; + import eu.dnetlib.dhp.common.PacePerson; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.oaf.Author; @@ -366,7 +368,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { @Override protected List prepareResultPids(final Document doc, final DataInfo info) { - final List res = new ArrayList<>(); + final Set res = new HashSet(); res .addAll( prepareListStructPropsWithValidQualifier( @@ -382,7 +384,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper { doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL' and @alternateIdentifierType != 'landingPage']", "@alternateIdentifierType", DNET_PID_TYPES, info)); - return res; + return Lists.newArrayList(res); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicate.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicate.java new file mode 100644 index 0000000000..1e99d298d7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicate.java @@ -0,0 +1,62 @@ + +package eu.dnetlib.dhp.oa.graph.raw.common; + +import java.util.HashSet; +import java.util.Set; +import java.util.function.Predicate; +import java.util.regex.Pattern; + +import org.apache.commons.lang3.StringUtils; + +import com.google.common.base.Splitter; + +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Relation; + +/** + * This predicate should be used to skip oaf objects using a blacklist of nsprefixes. + * + * @author michele + */ +public class VerifyNsPrefixPredicate implements Predicate { + + final Set invalids = new HashSet<>(); + + public VerifyNsPrefixPredicate(final String blacklist) { + if (StringUtils.isNotBlank(blacklist)) { + Splitter + .on(",") + .trimResults() + .omitEmptyStrings() + .split(blacklist) + .forEach(invalids::add); + } + } + + @Override + public boolean test(final Oaf oaf) { + if (oaf instanceof Datasource) { + return testValue(((Datasource) oaf).getNamespaceprefix().getValue()); + } else if (oaf instanceof OafEntity) { + return testValue(((OafEntity) oaf).getId()); + } else if (oaf instanceof Relation) { + return testValue(((Relation) oaf).getSource()) && testValue(((Relation) oaf).getTarget()); + } else { + return true; + } + } + + protected boolean testValue(final String s) { + if (StringUtils.isNotBlank(s)) { + for (final String invalid : invalids) { + if (Pattern.matches("^(\\d\\d\\|)?" + invalid + ".*$", s)) { + return false; + } + } + } + return true; + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/EBIAggregator.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/EBIAggregator.scala index 41fcd26362..d1bf39475a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/EBIAggregator.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/EBIAggregator.scala @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.sx.ebi import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown} import org.apache.spark.sql.{Encoder, Encoders} import org.apache.spark.sql.expressions.Aggregator @@ -35,6 +36,88 @@ object EBIAggregator { } + + def getDLIUnknownAggregator(): Aggregator[(String, DLIUnknown), DLIUnknown, DLIUnknown] = new Aggregator[(String, DLIUnknown), DLIUnknown, DLIUnknown]{ + + override def zero: DLIUnknown = new DLIUnknown() + + override def reduce(b: DLIUnknown, a: (String, DLIUnknown)): DLIUnknown = { + b.mergeFrom(a._2) + if (b.getId == null) + b.setId(a._2.getId) + b + } + + override def merge(wx: DLIUnknown, wy: DLIUnknown): DLIUnknown = { + wx.mergeFrom(wy) + if(wx.getId == null && wy.getId.nonEmpty) + wx.setId(wy.getId) + wx + } + override def finish(reduction: DLIUnknown): DLIUnknown = reduction + + override def bufferEncoder: Encoder[DLIUnknown] = + Encoders.kryo(classOf[DLIUnknown]) + + override def outputEncoder: Encoder[DLIUnknown] = + Encoders.kryo(classOf[DLIUnknown]) + } + + def getDLIDatasetAggregator(): Aggregator[(String, DLIDataset), DLIDataset, DLIDataset] = new Aggregator[(String, DLIDataset), DLIDataset, DLIDataset]{ + + override def zero: DLIDataset = new DLIDataset() + + override def reduce(b: DLIDataset, a: (String, DLIDataset)): DLIDataset = { + b.mergeFrom(a._2) + if (b.getId == null) + b.setId(a._2.getId) + b + } + + override def merge(wx: DLIDataset, wy: DLIDataset): DLIDataset = { + wx.mergeFrom(wy) + if(wx.getId == null && wy.getId.nonEmpty) + wx.setId(wy.getId) + wx + } + override def finish(reduction: DLIDataset): DLIDataset = reduction + + override def bufferEncoder: Encoder[DLIDataset] = + Encoders.kryo(classOf[DLIDataset]) + + override def outputEncoder: Encoder[DLIDataset] = + Encoders.kryo(classOf[DLIDataset]) + } + + + def getDLIPublicationAggregator(): Aggregator[(String, DLIPublication), DLIPublication, DLIPublication] = new Aggregator[(String, DLIPublication), DLIPublication, DLIPublication]{ + + override def zero: DLIPublication = new DLIPublication() + + override def reduce(b: DLIPublication, a: (String, DLIPublication)): DLIPublication = { + b.mergeFrom(a._2) + if (b.getId == null) + b.setId(a._2.getId) + b + } + + + override def merge(wx: DLIPublication, wy: DLIPublication): DLIPublication = { + wx.mergeFrom(wy) + if(wx.getId == null && wy.getId.nonEmpty) + wx.setId(wy.getId) + wx + } + override def finish(reduction: DLIPublication): DLIPublication = reduction + + override def bufferEncoder: Encoder[DLIPublication] = + Encoders.kryo(classOf[DLIPublication]) + + override def outputEncoder: Encoder[DLIPublication] = + Encoders.kryo(classOf[DLIPublication]) + } + + def getPublicationAggregator(): Aggregator[(String, Publication), Publication, Publication] = new Aggregator[(String, Publication), Publication, Publication]{ override def zero: Publication = new Publication() @@ -86,4 +169,7 @@ object EBIAggregator { + + + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala index 897bbd5407..d5cdb8a7cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkAddLinkUpdates.scala @@ -1,8 +1,9 @@ package eu.dnetlib.dhp.sx.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Instance, KeyValue, Oaf} +import eu.dnetlib.dhp.schema.oaf.{Author, Instance, Journal, KeyValue, Oaf, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.dhp.schema.scholexplorer.OafUtils.createQualifier -import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIRelation, OafUtils, ProvenaceInfo} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, OafUtils, ProvenaceInfo} +import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal} import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.scholexplorer.relation.RelationMapper import org.apache.commons.io.IOUtils @@ -12,6 +13,7 @@ import org.json4s import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse +import org.apache.spark.sql.functions._ import scala.collection.JavaConverters._ @@ -28,6 +30,64 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin } + + def journalToOAF(pj:PMJournal): Journal = { + val j = new Journal + j.setIssnPrinted(pj.getIssn) + j.setVol(pj.getVolume) + j.setName(pj.getTitle) + j.setIss(pj.getIssue) + j.setDataInfo(OafUtils.generateDataInfo()) + j + } + + + def pubmedTOPublication(input:PMArticle):DLIPublication = { + + + val dnetPublicationId = s"50|${DHPUtils.md5(s"${input.getPmid}::pmid")}" + + val p = new DLIPublication + p.setId(dnetPublicationId) + p.setDataInfo(OafUtils.generateDataInfo()) + p.setPid(List(OafUtils.createSP(input.getPmid.toLowerCase.trim, "pmid", "dnet:pid_types")).asJava) + p.setCompletionStatus("complete") + val pi = new ProvenaceInfo + pi.setId("dli_________::europe_pmc__") + pi.setName( "Europe PMC") + pi.setCompletionStatus("complete") + pi.setCollectionMode("collected") + p.setDlicollectedfrom(List(pi).asJava) + p.setCollectedfrom(List(generatePubmedDLICollectedFrom()).asJava) + + if (input.getAuthors != null && input.getAuthors.size() >0) { + var aths: List[Author] = List() + input.getAuthors.asScala.filter(a=> a!= null).foreach(a => { + val c = new Author + c.setFullname(a.getFullName) + c.setName(a.getForeName) + c.setSurname(a.getLastName) + aths = aths ::: List(c) + }) + if (aths.nonEmpty) + p.setAuthor(aths.asJava) + } + + + if (input.getJournal != null) + p.setJournal(journalToOAF(input.getJournal)) + p.setTitle(List(OafUtils.createSP(input.getTitle, "main title", "dnet:dataCite_title")).asJava) + p.setDateofacceptance(OafUtils.asField(input.getDate)) + val i = new Instance + i.setCollectedfrom(generatePubmedDLICollectedFrom()) + i.setDateofacceptance(p.getDateofacceptance) + i.setUrl(List(s"https://pubmed.ncbi.nlm.nih.gov/${input.getPmid}").asJava) + i.setInstancetype(createQualifier("0001", "Article", "dnet:publication_resource", "dnet:publication_resource")) + p.setInstance(List(i).asJava) + p + } + + def ebiLinksToOaf(input:(String, String)):List[Oaf] = { val pmid :String = input._1 val input_json :String = input._2 @@ -55,8 +115,8 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin val dnetPublicationId = s"50|${DHPUtils.md5(s"$pmid::pmid")}" targets.flatMap(l => { - val relation = new DLIRelation - val inverseRelation = new DLIRelation + val relation = new Relation + val inverseRelation = new Relation val targetDnetId = s"50|${DHPUtils.md5(s"${l.tpid.toLowerCase.trim}::${l.tpidType.toLowerCase.trim}")}" val relInfo = relationMapper.get(l.relation.toLowerCase) val relationSemantic = relInfo.getOriginal @@ -116,8 +176,16 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin val workingPath = parser.get("workingPath") implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - implicit val relEncoder: Encoder[DLIRelation] = Encoders.kryo(classOf[DLIRelation]) + implicit val oafpubEncoder: Encoder[Publication] = Encoders.kryo[Publication] + implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset]) + implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo(classOf[DLIPublication]) + implicit val atEncoder: Encoder[Author] = Encoders.kryo(classOf[Author]) + implicit val strEncoder:Encoder[String] = Encoders.STRING + implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) + implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) + implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) + val ds:Dataset[(String,String)] = spark.read.load(s"$workingPath/baseline_links_updates").as[(String,String)](Encoders.tuple(Encoders.STRING, Encoders.STRING)) @@ -129,10 +197,50 @@ case class EBILinks(relation:String, pubdate:String, tpid:String, tpidType:Strin val oDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/baseline_links_updates_oaf").as[Oaf] - oDataset.filter(p =>p.isInstanceOf[DLIRelation]).map(p => p.asInstanceOf[DLIRelation]).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_relation") + oDataset.filter(p =>p.isInstanceOf[Relation]).map(p => p.asInstanceOf[Relation]).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_relation") oDataset.filter(p =>p.isInstanceOf[DLIDataset]).map(p => p.asInstanceOf[DLIDataset]).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_dataset") + val idPublicationSolved:Dataset[String] = spark.read.load(s"$workingPath/baseline_links_updates").where(col("links").isNotNull).select("pmid").as[String] + val baseline:Dataset[(String, PMArticle)]= spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle].map(p=> (p.getPmid, p))(Encoders.tuple(strEncoder,PMEncoder)) + idPublicationSolved.joinWith(baseline, idPublicationSolved("pmid").equalTo(baseline("_1"))).map(k => pubmedTOPublication(k._2._2)).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_links_updates_publication") + + + val pmaDatasets = spark.read.load("/user/sandro.labruzzo/scholix/EBI/ebi_garr/baseline_dataset").as[PMArticle] + + pmaDatasets.map(p => pubmedTOPublication(p)).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_publication_all") + + val pubs: Dataset[(String,Publication)] = spark.read.load("/user/sandro.labruzzo/scholix/EBI/publication").as[Publication].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING,oafpubEncoder)) + val pubdate:Dataset[(String,DLIPublication)] = spark.read.load(s"$workingPath/baseline_publication_all").as[DLIPublication].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING,pubEncoder)) + + + + pubs.joinWith(pubdate, pubs("_1").equalTo(pubdate("_1"))).map(k => k._2._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_publication_ebi") + + + + val dt : Dataset[DLIDataset] = spark.read.load(s"$workingPath/dataset").as[DLIDataset] + val update : Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi_garr/baseline_links_updates_dataset").as[DLIDataset] + + + dt.union(update).map(d => (d.getId,d))(Encoders.tuple(Encoders.STRING, datEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getDLIDatasetAggregator().toColumn) + .map(p => p._2) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset_ebi") + + + val rel: Dataset[Relation] = spark.read.load(s"$workingPath/relation").as[Relation] + val relupdate : Dataset[Relation] = spark.read.load(s"$workingPath/ebi_garr/baseline_links_updates_relation").as[Relation] + + + rel.union(relupdate) + .map(d => (s"${d.getSource}::${d.getRelType}::${d.getTarget}", d))(Encoders.tuple(Encoders.STRING, relEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getRelationAggregator().toColumn) + .map(p => p._2) + .write.mode(SaveMode.Overwrite) + .save(s"$workingPath/baseline_relation_ebi") } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala index 60857f0fcf..9fc9704460 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/SparkCreateEBIDataFrame.scala @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.sx.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser} import eu.dnetlib.scholexplorer.relation.RelationMapper import org.apache.commons.io.IOUtils @@ -10,6 +11,7 @@ import org.apache.spark.rdd.RDD import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} import org.slf4j.{Logger, LoggerFactory} + import scala.collection.JavaConverters._ object SparkCreateEBIDataFrame { @@ -34,43 +36,43 @@ object SparkCreateEBIDataFrame { val relationMapper = RelationMapper.load implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset]) - implicit val pubEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication]) + implicit val datasetEncoder: Encoder[DLIDataset] = Encoders.kryo(classOf[DLIDataset]) + implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo(classOf[DLIPublication]) implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) - logger.info("Extract Publication and relation from publication_xml") - val oafPubsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/publication_xml").map(s => - { - new ObjectMapper().readValue(s, classOf[String]) - }).flatMap(s => { - val d = new PublicationScholexplorerParser - d.parseObject(s, relationMapper).asScala.iterator}) +// logger.info("Extract Publication and relation from publication_xml") +// val oafPubsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/publication_xml").map(s => +// { +// new ObjectMapper().readValue(s, classOf[String]) +// }).flatMap(s => { +// val d = new PublicationScholexplorerParser +// d.parseObject(s, relationMapper).asScala.iterator}) +// +// val mapper = new ObjectMapper() +// mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) +// spark.createDataset(oafPubsRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf") +// +// logger.info("Extract Publication and relation from dataset_xml") +// val oafDatsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/dataset_xml").map(s => +// { +// new ObjectMapper().readValue(s, classOf[String]) +// }).flatMap(s => { +// val d = new DatasetScholexplorerParser +// d.parseObject(s, relationMapper).asScala.iterator}) - val mapper = new ObjectMapper() - mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) - spark.createDataset(oafPubsRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/oaf") - - logger.info("Extract Publication and relation from dataset_xml") - val oafDatsRDD:RDD[Oaf] = sc.textFile(s"$workingPath/dataset_xml").map(s => - { - new ObjectMapper().readValue(s, classOf[String]) - }).flatMap(s => { - val d = new DatasetScholexplorerParser - d.parseObject(s, relationMapper).asScala.iterator}) - - spark.createDataset(oafDatsRDD).write.mode(SaveMode.Append).save(s"$workingPath/oaf") - val dataset: Dataset[OafDataset] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[OafDataset]).map(d => d.asInstanceOf[OafDataset]) - val publication: Dataset[Publication] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Publication]).map(d => d.asInstanceOf[Publication]) +// spark.createDataset(oafDatsRDD).write.mode(SaveMode.Append).save(s"$workingPath/oaf") + val dataset: Dataset[DLIDataset] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIDataset]).map(d => d.asInstanceOf[DLIDataset]) + val publication: Dataset[DLIPublication] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[DLIPublication]).map(d => d.asInstanceOf[DLIPublication]) val relations: Dataset[Relation] = spark.read.load(s"$workingPath/oaf").as[Oaf].filter(o => o.isInstanceOf[Relation]).map(d => d.asInstanceOf[Relation]) publication.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder)) .groupByKey(_._1)(Encoders.STRING) - .agg(EBIAggregator.getPublicationAggregator().toColumn) + .agg(EBIAggregator.getDLIPublicationAggregator().toColumn) .map(p => p._2) .write.mode(SaveMode.Overwrite).save(s"$workingPath/publication") dataset.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datasetEncoder)) .groupByKey(_._1)(Encoders.STRING) - .agg(EBIAggregator.getDatasetAggregator().toColumn) + .agg(EBIAggregator.getDLIDatasetAggregator().toColumn) .map(p => p._2) .write.mode(SaveMode.Overwrite).save(s"$workingPath/dataset") @@ -80,8 +82,5 @@ object SparkCreateEBIDataFrame { .map(p => p._2) .write.mode(SaveMode.Overwrite).save(s"$workingPath/relation") - - - relations.map(r => (r.getSource, r.getTarget))(Encoders.tuple(Encoders.STRING,Encoders.STRING)) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMAuthor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMAuthor.java index 4a21985424..e27c9adaad 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMAuthor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/ebi/model/PMAuthor.java @@ -25,7 +25,8 @@ public class PMAuthor implements Serializable { } public String getFullName() { - return String.format("%s, %s", this.foreName, this.lastName); + return String + .format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : ""); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java index f3d7fd40ff..7003b179dd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSXGeneratePidSimlarity.java @@ -10,7 +10,7 @@ import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; -import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; +import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.DHPUtils; import scala.Tuple2; @@ -55,18 +55,18 @@ public class SparkSXGeneratePidSimlarity { .equalsIgnoreCase(StringUtils.substringAfter(t._2(), "::"))) .distinct(); - JavaRDD simRel = datasetSimRel + JavaRDD simRel = datasetSimRel .union(publicationSimRel) .map( s -> { - final DLIRelation r = new DLIRelation(); + final Relation r = new Relation(); r.setSource(s._1()); r.setTarget(s._2()); r.setRelType("similar"); return r; }); spark - .createDataset(simRel.rdd(), Encoders.bean(DLIRelation.class)) + .createDataset(simRel.rdd(), Encoders.bean(Relation.class)) .distinct() .write() .mode(SaveMode.Overwrite) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java index 385ac4d1a2..05fb826db0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkScholexplorerCreateRawGraphJob.java @@ -31,7 +31,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; -import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.utils.DHPUtils; import net.minidev.json.JSONArray; @@ -156,9 +155,9 @@ public class SparkScholexplorerCreateRawGraphJob { SparkSXGeneratePidSimlarity .generateDataFrame( spark, sc, inputPath.replace("/relation", ""), targetPath.replace("/relation", "")); - RDD rdd = union + RDD rdd = union .mapToPair( - (PairFunction) f -> { + (PairFunction) f -> { final String source = getJPathString(SOURCEJSONPATH, f); final String target = getJPathString(TARGETJSONPATH, f); final String reltype = getJPathString(RELJSONPATH, f); @@ -175,7 +174,7 @@ public class SparkScholexplorerCreateRawGraphJob { source.toLowerCase(), reltype.toLowerCase(), target.toLowerCase())), - mapper.readValue(f, DLIRelation.class)); + mapper.readValue(f, Relation.class)); }) .reduceByKey( (a, b) -> { @@ -186,7 +185,7 @@ public class SparkScholexplorerCreateRawGraphJob { .rdd(); spark - .createDataset(rdd, Encoders.bean(DLIRelation.class)) + .createDataset(rdd, Encoders.bean(Relation.class)) .write() .mode(SaveMode.Overwrite) .save(targetPath); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala new file mode 100644 index 0000000000..d0df28b2df --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala @@ -0,0 +1,107 @@ +package eu.dnetlib.dhp.sx.graph + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown} +import eu.dnetlib.dhp.sx.ebi.EBIAggregator +import eu.dnetlib.dhp.sx.ebi.model.{PMArticle, PMAuthor, PMJournal} +import org.apache.commons.io.IOUtils +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.LoggerFactory + +object SparkSplitOafTODLIEntities { + + + def getKeyRelation(rel:Relation):String = { + s"${rel.getSource}::${rel.getRelType}::${rel.getTarget}" + + + } + + def main(args: Array[String]): Unit = { + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json"))) + val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass) + parser.parseArgument(args) + + val workingPath: String = parser.get("workingPath") + logger.info(s"Working dir path = $workingPath") + + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication] + implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset] + implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown] + implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation] + + + + val spark:SparkSession = SparkSession + .builder() + .appName(SparkSplitOafTODLIEntities.getClass.getSimpleName) + .config("spark.serializer", "org.apache.spark.serializer.KryoSerializer") + .master(parser.get("master")) + .getOrCreate() + + + + + val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf] + + val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset] + val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication] + val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation] + + + + OAFDataset + .filter(s => s != null && s.isInstanceOf[DLIPublication]) + .map(s =>s.asInstanceOf[DLIPublication]) + .union(ebi_publication) + .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getDLIPublicationAggregator().toColumn) + .map(p => p._2) + .repartition(1000) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/publication") + + OAFDataset + .filter(s => s != null && s.isInstanceOf[DLIDataset]) + .map(s =>s.asInstanceOf[DLIDataset]) + .union(ebi_dataset) + .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getDLIDatasetAggregator().toColumn) + .map(p => p._2) + .repartition(1000) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset") + + + OAFDataset + .filter(s => s != null && s.isInstanceOf[DLIUnknown]) + .map(s =>s.asInstanceOf[DLIUnknown]) + .map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, unkEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getDLIUnknownAggregator().toColumn) + .map(p => p._2) + .repartition(1000) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/unknown") + + + OAFDataset + .filter(s => s != null && s.isInstanceOf[Relation]) + .map(s =>s.asInstanceOf[Relation]) + .union(ebi_relation) + .map(d => (getKeyRelation(d), d))(Encoders.tuple(Encoders.STRING, relEncoder)) + .groupByKey(_._1)(Encoders.STRING) + .agg(EBIAggregator.getRelationAggregator().toColumn) + .map(p => p._2) + .repartition(1000) + .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation") + + + + + + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkXMLToOAFDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkXMLToOAFDataset.scala new file mode 100644 index 0000000000..c63ad43704 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkXMLToOAFDataset.scala @@ -0,0 +1,73 @@ +package eu.dnetlib.dhp.sx.graph + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} +import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser} +import eu.dnetlib.scholexplorer.relation.RelationMapper +import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.{IntWritable, Text} +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.LoggerFactory + +import scala.collection.JavaConverters._ + + +/** + * This new version of the Job read a sequential File containing XML stored in the aggregator and generates a Dataset OAF of heterogeneous + * entities like Dataset, Relation, Publication and Unknown + */ + +object SparkXMLToOAFDataset { + + + def main(args: Array[String]): Unit = { + val logger = LoggerFactory.getLogger(SparkXMLToOAFDataset.getClass) + val conf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkXMLToOAFDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_graph_scholix_parameters.json"))) + parser.parseArgument(args) + val spark = + SparkSession + .builder() + .config(conf) + .appName(SparkXMLToOAFDataset.getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + val sc = spark.sparkContext + + implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val datasetEncoder:Encoder[DLIDataset] = Encoders.kryo[DLIDataset] + implicit val publicationEncoder:Encoder[DLIPublication] = Encoders.kryo[DLIPublication] + implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation] + + val relationMapper = RelationMapper.load + + val inputPath: String = parser.get("sourcePath") + val entity: String = parser.get("entity") + val targetPath = parser.get("targetPath") + + logger.info(s"Input path is $inputPath") + logger.info(s"Entity path is $entity") + logger.info(s"Target Path is $targetPath") + + val scholixRdd:RDD[Oaf] = sc.sequenceFile(inputPath, classOf[IntWritable], classOf[Text]) + .map(s => s._2.toString) + .flatMap(s => { + entity match { + case "publication" => + val p = new PublicationScholexplorerParser + val l =p.parseObject(s, relationMapper) + if (l != null) l.asScala else List() + case "dataset" => + val d = new DatasetScholexplorerParser + val l =d.parseObject(s, relationMapper) + if (l != null) l.asScala else List() + } + }).filter(s => s!= null) + spark.createDataset(scholixRdd).write.mode(SaveMode.Append).save(targetPath) + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java index 75f28c1299..f56760c820 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java @@ -14,7 +14,6 @@ import org.apache.commons.logging.LogFactory; import eu.dnetlib.dhp.parser.utility.VtdUtilityParser; import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.scholexplorer.DLIRelation; import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown; import eu.dnetlib.dhp.schema.scholexplorer.ProvenaceInfo; import eu.dnetlib.dhp.utils.DHPUtils; @@ -175,8 +174,8 @@ public abstract class AbstractScholexplorerParser { .stream() .flatMap( n -> { - final List rels = new ArrayList<>(); - DLIRelation r = new DLIRelation(); + final List rels = new ArrayList<>(); + Relation r = new Relation(); r.setSource(parsedObject.getId()); final String relatedPid = n.getTextValue(); final String relatedPidType = n.getAttributes().get("relatedIdentifierType"); @@ -184,7 +183,6 @@ public abstract class AbstractScholexplorerParser { String relationSemantic = n.getAttributes().get("relationType"); String inverseRelation; final String targetId = generateId(relatedPid, relatedPidType, relatedType); - r.setDateOfCollection(dateOfCollection); if (relationMapper.containsKey(relationSemantic.toLowerCase())) { RelInfo relInfo = relationMapper.get(relationSemantic.toLowerCase()); relationSemantic = relInfo.getOriginal(); @@ -199,14 +197,13 @@ public abstract class AbstractScholexplorerParser { r.setCollectedfrom(parsedObject.getCollectedfrom()); r.setDataInfo(di); rels.add(r); - r = new DLIRelation(); + r = new Relation(); r.setDataInfo(di); r.setSource(targetId); r.setTarget(parsedObject.getId()); r.setRelType(inverseRelation); r.setRelClass("datacite"); r.setCollectedfrom(parsedObject.getCollectedfrom()); - r.setDateOfCollection(dateOfCollection); rels.add(r); if ("unknown".equalsIgnoreCase(relatedType)) result diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java index 60371fa536..11d9905ccd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/DatasetScholexplorerParser.java @@ -317,6 +317,15 @@ public class DatasetScholexplorerParser extends AbstractScholexplorerParser { .collect(Collectors.toList())); } + // TERRIBLE HACK TO AVOID EMPTY COLLECTED FROM + if (parsedObject.getDlicollectedfrom() == null) { + + final KeyValue cf = new KeyValue(); + cf.setKey("dli_________::europe_pmc__"); + cf.setValue("Europe PMC"); + parsedObject.setCollectedfrom(Collections.singletonList(cf)); + } + if (StringUtils.isNotBlank(resolvedURL)) { Instance i = new Instance(); i.setCollectedfrom(parsedObject.getCollectedfrom().get(0)); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json new file mode 100644 index 0000000000..6e42bfa643 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json @@ -0,0 +1,25 @@ + +[ + + { + "paramName":"is", + "paramLongName":"isLookUpUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": true + }, + { + "paramName":"nn", + "paramLongName":"nameNode", + "paramDescription": "the name node", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json new file mode 100644 index 0000000000..83967e2821 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json @@ -0,0 +1,24 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "hdp", + "paramLongName": "hdfsPath", + "paramDescription": "the path used to store the output archive", + "paramRequired": true + }, + { + "paramName":"nn", + "paramLongName":"nameNode", + "paramDescription": "the name node", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json new file mode 100644 index 0000000000..b1f4c026ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -0,0 +1,36 @@ +[ + + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the serialization of the community map", + "paramRequired": true + }, + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/workflow.xml new file mode 100644 index 0000000000..7321fd0764 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/oozie_app/workflow.xml @@ -0,0 +1,431 @@ + + + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + newDeposition + true if it is a brand new depositon. false for new version of an old deposition + + + conceptRecordId + for new version, the id of the record for the old deposition + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + + + + + + + + yarn + cluster + Dump table publication for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/publication + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table dataset for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dataset + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/otherresearchproduct + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/software + --communityMapPath${workingDir}/communityMap + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/publication + --outputPath${workingDir}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dataset + --outputPath${workingDir}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/otherresearchproduct + --outputPath${workingDir}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/software + --outputPath${workingDir}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + + + yarn + cluster + Split dumped result for community + eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${workingDir}/split + --communityMapPath${workingDir}/communityMap + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/split + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --communityMapPath${workingDir}/communityMap + --conceptRecordId${conceptRecordId} + --newDeposition${newDeposition} + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json new file mode 100644 index 0000000000..f2dc02ba90 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_input_parameters.json @@ -0,0 +1,29 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "pip", + "paramLongName": "preparedInfoPath", + "paramDescription": "the path of the association result projectlist", + "paramRequired": true + } +] + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json new file mode 100644 index 0000000000..82714d973d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/project_prep_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/result_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/result_schema.json new file mode 100644 index 0000000000..cb092110ec --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/result_schema.json @@ -0,0 +1,542 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "definitions": { + "AccessRight": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/" + }, + "label": { + "type": "string", + "description": "Label for the access mode" + }, + "scheme": { + "type": "string", + "description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/" + } + } + }, + "ControlledField": { + "type": "object", + "properties": { + "scheme": { + "type": "string", + "description": "The scheme for the resource" + }, + "value": { + "type": "string", + "description": "the value in the scheme" + } + } + }, + "KeyValue": { + "type": "object", + "properties": { + "key": { + "type": "string", + "description": "Description of key" + }, + "value": { + "type": "string", + "description": "Description of value" + } + } + }, + "Provenance": { + "type": "object", + "properties": { + "provenance": { + "type": "string", + "description": "The provenance of the information" + }, + "trust": { + "type": "string", + "description": "The trust associated to the information" + } + } + } + }, + "type": "object", + "properties": { + "author": { + "description": "List of authors of the research results", + "type": "array", + "items": { + "type": "object", + "properties": { + "affiliation": { + "description": "Affiliations of the author", + "type": "array", + "items": { + "type": "string", + "description": "One of the affiliation of the author" + } + }, + "fullname": { + "type": "string", + "description": "Fullname of the author" + }, + "name": { + "type": "string", + "description": "First name of the author" + }, + "pid": { + "type": "object", + "properties": { + "id": { + "allOf": [ + {"$ref": "#/definitions/ControlledField"}, + {"description": "The author's id and scheme. OpenAIRE currently supports 'ORCID'"} + ] + }, + "provenance": { + "allOf": [ + {"$ref": "#/definitions/Provenance"}, + {"description": "The provenance of the author's pid"} + ] + } + }, + "description": "Persistent identifier of the author (e.g. ORCID)" + }, + "rank": { + "type": "integer", + "description": "Order in which the author appears in the authors list" + }, + "surname": { + "type": "string", + "description": "Surname of the author" + } + }, + "description": "One of the author of the research result" + } + }, + "bestaccessright": { + "allOf": [ + {"$ref": "#/definitions/AccessRight"}, + {"description": "The openest access right associated to the manifestations of this research results"} + ] + }, + "codeRepositoryUrl": { + "type": "string", + "description": "Only for results with type 'software': the URL to the repository with the source code" + }, + "collectedfrom": { + "description": "Information about the sources from which the record has been collected", + "type": "array", + "items": { + "allOf": [ + {"$ref": "#/definitions/KeyValue"}, + {"description": "Key is the OpenAIRE identifier of the data source, value is its name"} + ] + } + }, + "contactgroup": { + "description": "Only for results with type 'software': Information on the group responsible for providing further information regarding the resource", + "type": "array", + "items": { + "type": "string" + } + }, + "contactperson": { + "description": "Only for results with type 'software': Information on the person responsible for providing further information regarding the resource", + "type": "array", + "items": { + "type": "string" + } + }, + "container": { + "type": "object", + "properties": { + "conferencedate": { + "type": "string", + "description": "Date of the conference" + }, + "conferenceplace": { + "type": "string", + "description": "Place of the conference" + }, + "edition": { + "type": "string", + "description": "Edition of the journal or conference proceeding" + }, + "ep": { + "type": "string", + "description": "End page" + }, + "iss": { + "type": "string", + "description": "Journal issue" + }, + "issnLinking": { + "type": "string", + "description": "Journal linking iisn" + }, + "issnOnline": { + "type": "string", + "description": "Journal online issn" + }, + "issnPrinted": { + "type": "string", + "description": "Journal printed issn" + }, + "name": { + "type": "string", + "description": "Name of the journal or conference" + }, + "sp": { + "type": "string", + "description": "Start page" + }, + "vol": { + "type": "string", + "description": "Volume" + } + }, + "description": "Container has information about the conference or journal where the result has been presented or published" + }, + "context": { + "description": "Reference to a relevant research infrastructure, initiative or community (RI/RC) among those collaborating with OpenAIRE. Please see https://connect.openaire.eu", + "type": "array", + "items": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "Code identifying the RI/RC" + }, + "label": { + "type": "string", + "description": "Label of the RI/RC" + }, + "provenance": { + "description": "Why this result is associated to the RI/RC.", + "type": "array", + "items": { + "allOf": [ + {"$ref": "#/definitions/Provenance"} + + ] + } + } + } + } + }, + "contributor": { + "description": "Contributors of this result", + "type": "array", + "items": { + "type": "string" + } + }, + "country": { + "description": "Country associated to this result", + "type": "array", + "items": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "ISO 3166-1 alpha-2 country code" + }, + "label": { + "type": "string", + "description": "English label of the country" + }, + "provenance": { + "allOf": [ + {"$ref": "#/definitions/Provenance"}, + {"description": "Why this result is associated to the country."} + ] + } + } + } + }, + "coverage": { + "type": "array", + "items": { + "type": "string" + } + }, + "dateofcollection": { + "type": "string", + "description": "When OpenAIRE collected the record the last time" + }, + "description": { + "type": "array", + "items": { + "type": "string" + } + }, + "documentationUrl": { + "description": "Only for results with type 'software': URL to the software documentation", + "type": "array", + "items": { + "type": "string" + + } + }, + "embargoenddate": { + "type": "string", + "description": "Date when the embargo ends and this result turns Open Access" + }, + "externalReference": { + "description": "Links to external resources like entries from thematic databases (e.g. Protein Data Bank)", + "type": "array", + "items": { + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "provenance": { + "allOf": [ + {"$ref": "#/definitions/Provenance"}, + {"description": "Why this result is linked to the external resource"} + ] + }, + "typology": { + "type": "string" + }, + "value": { + "type": "string" + } + } + } + }, + "format": { + + "type": "array", + "items": { + "type": "string" + } + }, + "geolocation": { + "description": "Geolocation information", + "type": "array", + "items": { + "type": "object", + "properties": { + "box": { + "type": "string" + }, + "place": { + "type": "string" + }, + "point": { + "type": "string" + } + } + } + }, + "id": { + "type": "string", + "description": "OpenAIRE identifier" + }, + "instance": { + "description": "Manifestations (i.e. different versions) of the result. For example: the pre-print and the published versions are two manifestations of the same research result", + "type": "array", + "items": { + "type": "object", + "properties": { + "accessright": { + "allOf": [ + {"$ref": "#/definitions/AccessRight"}, + {"description": "Access right of this instance"} + ] + }, + "collectedfrom": { + "allOf": [ + {"$ref": "#/definitions/KeyValue"}, + {"description": "Information about the source from which the instance has been collected. Key is the OpenAIRE identifier of the data source, value is its name"} + ] + }, + "hostedby": { + "allOf": [ + {"$ref": "#/definitions/KeyValue"}, + {"description": "Information about the source from which the instance can be viewed or downloaded. Key is the OpenAIRE identifier of the data source, value is its name"} + ] + }, + "license": { + "type": "string", + "description": "License applied to the instance" + }, + "publicationdate": { + "type": "string", + "description": "Publication date of the instance" + }, + "refereed": { + "type": "string", + "description": "Was the instance subject to peer-review? Possible values are 'Unknown', 'nonPeerReviewed', 'peerReviewed' (see also https://api.openaire.eu/vocabularies/dnet:review_levels)" + }, + "type": { + "type": "string", + "description": "Type of the instance. Possible values are listed at https://api.openaire.eu/vocabularies/dnet:publication_resource" + }, + "url": { + "description":"Location where the instance is accessible", + "type": "array", + "items": { + "type": "string" + } + } + } + } + }, + "language": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "alpha-3/ISO 639-2 code of the language" + }, + "label": { + "type": "string", + "description": "English label" + } + } + }, + "lastupdatetimestamp": { + "type": "integer", + "description": "Timestamp of last update of the record in OpenAIRE" + }, + "maintitle": { + "type": "string", + "description": "Title" + }, + "originalId": { + "description": "Identifiers of the record at the original sources", + "type": "array", + "items": { + "type": "string" + } + }, + "pid": { + "description": "Persistent identifiers of the result", + "type": "array", + "items": { + "allOf": [ + {"$ref": "#/definitions/ControlledField"}, + {"description": "scheme: list of available schemes are at https://api.openaire.eu/vocabularies/dnet:pid_types, value: the PID of the result "} + ] + } + }, + "programmingLanguage": { + "type": "string", + "description": "Only for results with type 'software': the programming language" + }, + "projects": { + "description": "List of projects (i.e. grants) that (co-)funded the production ofn the research results", + "type": "array", + "items": { + "type": "object", + "properties": { + "acronym": { + "type": "string", + "description": "Project acronym" + }, + "code": { + "type": "string", + "description": "Grant code" + }, + "funder": { + "type": "object", + "properties": { + "fundingStream": { + "type": "string", + "description": "Stream of funding (e.g. for European Commission can be H2020 or FP7)" + }, + "jurisdiction": { + "type": "string", + "description": "Geographical jurisdiction (e.g. for European Commission is EU, for Croatian Science Foundation is HR)" + }, + "name": { + "type": "string", + "description": "Name of the funder" + }, + "shortName": { + "type": "string", + "description": "Short name or acronym of the funder" + } + }, + "description": "Information about the funder funding the project" + }, + "id": { + "type": "string", + "description": "OpenAIRE identifier of the project" + }, + "provenance": { + "allOf": [ + {"$ref": "#/definitions/Provenance"}, + {"description": "Why this project is associated to the result"} + ] + }, + "title": { + "type": "string", + "description": "Title of the project" + } + } + } + }, + "publicationdate": { + "type": "string", + "description": "Date of publication" + }, + "publisher": { + "type": "string", + "description": "Publisher" + }, + "size": { + "type": "string", + "description": "Only for results with type 'dataset': the declared size of the dataset" + }, + "source": { + "description": "See definition of Dublin Core field dc:source", + "type": "array", + "items": { + "type": "string" + } + }, + "subjects": { + "description": "Keywords associated to the result", + "type": "array", + "items": { + "type": "object", + "properties": { + "provenance": { + "allOf": [ + {"$ref": "#/definitions/Provenance"}, + {"description": "Why this subject is associated to the result"} + ] + }, + "subject": { + "allOf": [ + {"$ref": "#/definitions/ControlledField"}, + {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary). "} + ] + } + } + } + }, + "subtitle": { + "type": "string", + "description": "Sub-title of the result" + }, + "tool": { + "description": "Only for results with type 'other': tool useful for the interpretation and/or re-used of the research product", + "type": "array", + "items": { + "type": "string" + } + }, + "type": { + "type": "string", + "description": "Type of the result: one of 'publication', 'dataset', 'software', 'other' (see also https://api.openaire.eu/vocabularies/dnet:result_typologies)" + }, + "version": { + "type": "string", + "description": "Version of the result" + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json new file mode 100644 index 0000000000..29812188a5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json @@ -0,0 +1,32 @@ + +[ + + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the serialization of the community map", + "paramRequired": false + }, + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json new file mode 100644 index 0000000000..4c3ec06e1b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json @@ -0,0 +1,51 @@ + +[ + { + "paramName":"nd", + "paramLongName":"newDeposition", + "paramDescription": "if it is a new deposition (true) or a new versione (false)", + "paramRequired": true + }, + { + "paramName":"cri", + "paramLongName":"conceptRecordId", + "paramDescription": "The id of the concept record for a new version", + "paramRequired": false + }, + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the serialization of the community map", + "paramRequired": false + }, +{ +"paramName":"hdfsp", +"paramLongName":"hdfsPath", +"paramDescription": "the path of the folder tofind files to send to Zenodo", +"paramRequired": true +}, +{ +"paramName": "nn", +"paramLongName": "nameNode", +"paramDescription": "the name node", +"paramRequired": true +}, +{ +"paramName": "at", +"paramLongName": "accessToken", +"paramDescription": "the access token for the deposition", +"paramRequired": false +}, +{ +"paramName":"cu", +"paramLongName":"connectionUrl", +"paramDescription": "the url to connect to deposit", +"paramRequired": false +}, +{ +"paramName":"m", +"paramLongName":"metadata", +"paramDescription": "metadata associated to the deposition", +"paramRequired": false +} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json new file mode 100644 index 0000000000..e1130c4f60 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_collect_and_save.json @@ -0,0 +1,24 @@ +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json new file mode 100644 index 0000000000..87de13d63b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_entity_parameter.json @@ -0,0 +1,24 @@ +[ + + { + "paramName":"is", + "paramLongName":"isLookUpUrl", + "paramDescription": "URL of the isLookUp Service", + "paramRequired": false + }, + { + "paramName": "hdfs", + "paramLongName": "hdfsPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "nn", + "paramLongName": "nameNode", + "paramDescription": "the name node", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json new file mode 100644 index 0000000000..3a4632af94 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_organization_parameters.json @@ -0,0 +1,30 @@ +[ + + { + "paramName":"ocm", + "paramLongName":"organizationCommunityMap", + "paramDescription": "the organization community map association", + "paramRequired": false + }, + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json new file mode 100644 index 0000000000..bc3e0cd517 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_parameters.json @@ -0,0 +1,35 @@ +[ + { + "paramName":"cmp", + "paramLongName":"communityMapPath", + "paramDescription": "the path to the serialization of the community map", + "paramRequired": true + }, + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName":"tn", + "paramLongName":"resultTableName", + "paramDescription": "the name of the result table we are currently working on", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json new file mode 100644 index 0000000000..2bfcac3bce --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/input_relationdump_parameters.json @@ -0,0 +1,26 @@ + + +[ + + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/workflow.xml new file mode 100644 index 0000000000..a1b984f9c7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/oozie_app/workflow.xml @@ -0,0 +1,588 @@ + + + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + newDeposition + true if it is a brand new depositon. false for new version of an old deposition + + + conceptRecordId + for new version, the id of the record for the old deposition + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + + + + + + + + + + + + yarn + cluster + Dump table publication + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Dump table organization + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/organization + --resultTableNameeu.dnetlib.dhp.schema.oaf.Organization + --outputPath${workingDir}/collect/organization + --communityMapPath${workingDir}/communityMap + + + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${workingDir}/collect/project + --communityMapPath${workingDir}/communityMap + + + + + + + + + yarn + cluster + Dump table datasource + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/datasource + --resultTableNameeu.dnetlib.dhp.schema.oaf.Datasource + --outputPath${workingDir}/collect/datasource + --communityMapPath${workingDir}/communityMap + + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.graph.SparkDumpRelationJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/relation + --outputPath${workingDir}/relation/relation + + + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextEntities + --hdfsPath${workingDir}/collect/context + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.graph.CreateContextRelation + --hdfsPath${workingDir}/relation/context + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.graph.SparkOrganizationRelation + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/relation + --outputPath${workingDir}/relation/contextOrg + --organizationCommunityMap${organizationCommunityMap} + + + + + + + + + + + + + + + + + + yarn + cluster + Extract Relations from publication + eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/relation/publication + --communityMapPath${workingDir}/communityMap + + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/relation/dataset + --communityMapPath${workingDir}/communityMap + + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/relation/orp + --communityMapPath${workingDir}/communityMap + + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.graph.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/relation/software + --communityMapPath${workingDir}/communityMap + + + + + + + + + + + + yarn + cluster + Collect Results and Relations and put them in the right path + eu.dnetlib.dhp.oa.graph.dump.graph.SparkCollectAndSave + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir} + --outputPath${workingDir}/collect + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/collect + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --communityMapPath${workingDir}/communityMap + --conceptRecordId${conceptRecordId} + --newDeposition${newDeposition} + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/context_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/context_schema.json new file mode 100644 index 0000000000..ba6609a50e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/context_schema.json @@ -0,0 +1,38 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "description": { + "type": "string", + "description": "Description of description" + }, + "id": { + "type": "string", + "description": "Description of id" + }, + "name": { + "type": "string", + "description": "Description of name" + }, + "originalId": { + "type": "string", + "description": "Description of originalId" + }, + "subject": { + "description": "Description of subject", + "type": "array", + "items": { + "type": "string", + "description": "Description of subject" + } + }, + "type": { + "type": "string", + "description": "Description of type" + }, + "zenodo_community": { + "type": "string", + "description": "Description of zenodo_community" + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/datasource_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/datasource_schema.json new file mode 100644 index 0000000000..f492620ee2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/datasource_schema.json @@ -0,0 +1,210 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "definitions": { + "ControlledField": { + "type": "object", + "properties": { + "scheme": { + "type": "string", + "description": "Description of scheme" + }, + "value": { + "type": "string", + "description": "Description of value" + } + } + } + }, + "type": "object", + "properties": { + "accessrights": { + "type": "string", + "description": "Description of accessrights" + }, + "certificates": { + "type": "string", + "description": "Description of certificates" + }, + "citationguidelineurl": { + "type": "string", + "description": "Description of citationguidelineurl" + }, + "contenttypes": { + "description": "Description of contenttypes", + "type": "array", + "items": { + "type": "string", + "description": "Description of contenttypes" + } + }, + "databaseaccessrestriction": { + "type": "string", + "description": "Description of databaseaccessrestriction" + }, + "datasourcetype": { + "allOf": [ + { + "$ref": "#/definitions/ControlledField" + }, + { + "description": "Description of datasourcetype" + } + ] + }, + "datauploadrestriction": { + "type": "string", + "description": "Description of datauploadrestriction" + }, + "dateofvalidation": { + "type": "string", + "description": "Description of dateofvalidation" + }, + "description": { + "type": "string", + "description": "Description of description" + }, + "englishname": { + "type": "string", + "description": "Description of englishname" + }, + "id": { + "type": "string", + "description": "Description of id" + }, + "journal": { + "type": "object", + "properties": { + "conferencedate": { + "type": "string", + "description": "Description of conferencedate" + }, + "conferenceplace": { + "type": "string", + "description": "Description of conferenceplace" + }, + "edition": { + "type": "string", + "description": "Description of edition" + }, + "ep": { + "type": "string", + "description": "Description of ep" + }, + "iss": { + "type": "string", + "description": "Description of iss" + }, + "issnLinking": { + "type": "string", + "description": "Description of issnLinking" + }, + "issnOnline": { + "type": "string", + "description": "Description of issnOnline" + }, + "issnPrinted": { + "type": "string", + "description": "Description of issnPrinted" + }, + "name": { + "type": "string", + "description": "Description of name" + }, + "sp": { + "type": "string", + "description": "Description of sp" + }, + "vol": { + "type": "string", + "description": "Description of vol" + } + }, + "description": "Description of journal" + }, + "languages": { + "description": "Description of languages", + "type": "array", + "items": { + "type": "string", + "description": "Description of languages" + } + }, + "logourl": { + "type": "string", + "description": "Description of logourl" + }, + "missionstatementurl": { + "type": "string", + "description": "Description of missionstatementurl" + }, + "officialname": { + "type": "string", + "description": "Description of officialname" + }, + "openairecompatibility": { + "type": "string", + "description": "Description of openairecompatibility" + }, + "originalId": { + "description": "Description of originalId", + "type": "array", + "items": { + "type": "string", + "description": "Description of originalId" + } + }, + "pid": { + "description": "Description of pid", + "type": "array", + "items": { + "allOf": [ + { + "$ref": "#/definitions/ControlledField" + }, + { + "description": "Description of pid" + } + ] + } + }, + "pidsystems": { + "type": "string", + "description": "Description of pidsystems" + }, + "policies": { + "description": "Description of policies", + "type": "array", + "items": { + "description": "Description of policies" + } + }, + "releaseenddate": { + "type": "string", + "description": "Description of releaseenddate" + }, + "releasestartdate": { + "type": "string", + "description": "Description of releasestartdate" + }, + "subjects": { + "description": "Description of subjects", + "type": "array", + "items": { + "type": "string", + "description": "Description of subjects" + } + }, + "uploadrights": { + "type": "string", + "description": "Description of uploadrights" + }, + "versioning": { + "type": "boolean", + "description": "Description of versioning" + }, + "websiteurl": { + "type": "string", + "description": "Description of websiteurl" + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/organization_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/organization_schema.json new file mode 100644 index 0000000000..3477c8370b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/organization_schema.json @@ -0,0 +1,62 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "alternativenames": { + "description": "Description of alternativenames", + "type": "array", + "items": { + "type": "string", + "description": "Description of alternativenames" + } + }, + "country": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "Description of code" + }, + "label": { + "type": "string", + "description": "Description of label" + } + }, + "description": "Description of country" + }, + "id": { + "type": "string", + "description": "Description of id" + }, + "legalname": { + "type": "string", + "description": "Description of legalname" + }, + "legalshortname": { + "type": "string", + "description": "Description of legalshortname" + }, + "pid": { + "description": "Description of pid", + "type": "array", + "items": { + "type": "object", + "properties": { + "scheme": { + "type": "string", + "description": "Description of scheme" + }, + "value": { + "type": "string", + "description": "Description of value" + } + }, + "description": "Description of pid" + } + }, + "websiteurl": { + "type": "string", + "description": "Description of websiteurl" + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/project_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/project_schema.json new file mode 100644 index 0000000000..9aba19f172 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/project_schema.json @@ -0,0 +1,134 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "type": "object", + "properties": { + "acronym": { + "type": "string", + "description": "Description of acronym" + }, + "callidentifier": { + "type": "string", + "description": "Description of callidentifier" + }, + "code": { + "type": "string", + "description": "Description of code" + }, + "enddate": { + "type": "string", + "description": "Description of enddate" + }, + "funding": { + "description": "Description of funding", + "type": "array", + "items": { + "type": "object", + "properties": { + "funding_stream": { + "type": "object", + "properties": { + "description": { + "type": "string", + "description": "Description of description" + }, + "id": { + "type": "string", + "description": "Description of id" + } + }, + "description": "Description of funding_stream" + }, + "jurisdiction": { + "type": "string", + "description": "Description of jurisdiction" + }, + "name": { + "type": "string", + "description": "Description of name" + }, + "shortName": { + "type": "string", + "description": "Description of shortName" + } + }, + "description": "Description of funding" + } + }, + "granted": { + "type": "object", + "properties": { + "currency": { + "type": "string", + "description": "Description of currency" + }, + "fundedamount": { + "type": "number", + "description": "Description of fundedamount" + }, + "totalcost": { + "type": "number", + "description": "Description of totalcost" + } + }, + "description": "Description of granted" + }, + "id": { + "type": "string", + "description": "Description of id" + }, + "keywords": { + "type": "string", + "description": "Description of keywords" + }, + "openaccessmandatefordataset": { + "type": "boolean", + "description": "Description of openaccessmandatefordataset" + }, + "openaccessmandateforpublications": { + "type": "boolean", + "description": "Description of openaccessmandateforpublications" + }, + "programme": { + "description": "Description of programme", + "type": "array", + "items": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "Description of code" + }, + "description": { + "type": "string", + "description": "Description of description" + } + }, + "description": "Description of programme" + } + }, + "startdate": { + "type": "string", + "description": "Description of startdate" + }, + "subject": { + "description": "Description of subject", + "type": "array", + "items": { + "type": "string", + "description": "Description of subject" + } + }, + "summary": { + "type": "string", + "description": "Description of summary" + }, + "title": { + "type": "string", + "description": "Description of title" + }, + "websiteurl": { + "type": "string", + "description": "Description of websiteurl" + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/relation_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/relation_schema.json new file mode 100644 index 0000000000..95a80d5cfe --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/relation_schema.json @@ -0,0 +1,69 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "definitions": { + "Node": { + "type": "object", + "properties": { + "id": { + "type": "string", + "description": "Description of id" + }, + "type": { + "type": "string", + "description": "Description of type" + } + } + } + }, + "type": "object", + "properties": { + "provenance": { + "type": "object", + "properties": { + "provenance": { + "type": "string", + "description": "Description of provenance" + }, + "trust": { + "type": "string", + "description": "Description of trust" + } + }, + "description": "Description of provenance" + }, + "reltype": { + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "Description of name" + }, + "type": { + "type": "string", + "description": "Description of type" + } + }, + "description": "Description of reltype" + }, + "source": { + "allOf": [ + { + "$ref": "#/definitions/Node" + }, + { + "description": "Description of source" + } + ] + }, + "target": { + "allOf": [ + { + "$ref": "#/definitions/Node" + }, + { + "description": "Description of target" + } + ] + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/result_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/result_schema.json new file mode 100644 index 0000000000..59708639bd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump_whole/schema/result_schema.json @@ -0,0 +1,520 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "definitions": { + "AccessRight": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "Description of code" + }, + "label": { + "type": "string", + "description": "Description of label" + }, + "scheme": { + "type": "string", + "description": "Description of scheme" + } + } + }, + "ControlledField": { + "type": "object", + "properties": { + "scheme": { + "type": "string", + "description": "Description of scheme" + }, + "value": { + "type": "string", + "description": "Description of value" + } + } + }, + "KeyValue": { + "type": "object", + "properties": { + "key": { + "type": "string", + "description": "Description of key" + }, + "value": { + "type": "string", + "description": "Description of value" + } + } + }, + "Provenance": { + "type": "object", + "properties": { + "provenance": { + "type": "string", + "description": "Description of provenance" + }, + "trust": { + "type": "string", + "description": "Description of trust" + } + } + } + }, + "type": "object", + "properties": { + "author": { + "description": "Description of author", + "type": "array", + "items": { + "type": "object", + "properties": { + "affiliation": { + "description": "Description of affiliation", + "type": "array", + "items": { + "type": "string", + "description": "Description of affiliation" + } + }, + "fullname": { + "type": "string", + "description": "Description of fullname" + }, + "name": { + "type": "string", + "description": "Description of name" + }, + "pid": { + "type": "object", + "properties": { + "id": { + "allOf": [ + { + "$ref": "#/definitions/ControlledField" + }, + { + "description": "Description of id" + } + ] + }, + "provenance": { + "allOf": [ + { + "$ref": "#/definitions/Provenance" + }, + { + "description": "Description of provenance" + } + ] + } + }, + "description": "Description of pid" + }, + "rank": { + "type": "integer", + "description": "Description of rank" + }, + "surname": { + "type": "string", + "description": "Description of surname" + } + }, + "description": "Description of author" + } + }, + "bestaccessright": { + "allOf": [ + { + "$ref": "#/definitions/AccessRight" + }, + { + "description": "Description of bestaccessright" + } + ] + }, + "codeRepositoryUrl": { + "type": "string", + "description": "Description of codeRepositoryUrl" + }, + "contactgroup": { + "description": "Description of contactgroup", + "type": "array", + "items": { + "type": "string", + "description": "Description of contactgroup" + } + }, + "contactperson": { + "description": "Description of contactperson", + "type": "array", + "items": { + "type": "string", + "description": "Description of contactperson" + } + }, + "container": { + "type": "object", + "properties": { + "conferencedate": { + "type": "string", + "description": "Description of conferencedate" + }, + "conferenceplace": { + "type": "string", + "description": "Description of conferenceplace" + }, + "edition": { + "type": "string", + "description": "Description of edition" + }, + "ep": { + "type": "string", + "description": "Description of ep" + }, + "iss": { + "type": "string", + "description": "Description of iss" + }, + "issnLinking": { + "type": "string", + "description": "Description of issnLinking" + }, + "issnOnline": { + "type": "string", + "description": "Description of issnOnline" + }, + "issnPrinted": { + "type": "string", + "description": "Description of issnPrinted" + }, + "name": { + "type": "string", + "description": "Description of name" + }, + "sp": { + "type": "string", + "description": "Description of sp" + }, + "vol": { + "type": "string", + "description": "Description of vol" + } + }, + "description": "Description of container" + }, + "contributor": { + "description": "Description of contributor", + "type": "array", + "items": { + "type": "string", + "description": "Description of contributor" + } + }, + "country": { + "description": "Description of country", + "type": "array", + "items": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "Description of code" + }, + "label": { + "type": "string", + "description": "Description of label" + }, + "provenance": { + "allOf": [ + { + "$ref": "#/definitions/Provenance" + }, + { + "description": "Description of provenance" + } + ] + } + }, + "description": "Description of country" + } + }, + "coverage": { + "description": "Description of coverage", + "type": "array", + "items": { + "type": "string", + "description": "Description of coverage" + } + }, + "dateofcollection": { + "type": "string", + "description": "Description of dateofcollection" + }, + "description": { + "description": "Description of description", + "type": "array", + "items": { + "type": "string", + "description": "Description of description" + } + }, + "documentationUrl": { + "description": "Description of documentationUrl", + "type": "array", + "items": { + "type": "string", + "description": "Description of documentationUrl" + } + }, + "embargoenddate": { + "type": "string", + "description": "Description of embargoenddate" + }, + "externalReference": { + "description": "Description of externalReference", + "type": "array", + "items": { + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "Description of name" + }, + "provenance": { + "allOf": [ + { + "$ref": "#/definitions/Provenance" + }, + { + "description": "Description of provenance" + } + ] + }, + "typology": { + "type": "string", + "description": "Description of typology" + }, + "value": { + "type": "string", + "description": "Description of value" + } + }, + "description": "Description of externalReference" + } + }, + "format": { + "description": "Description of format", + "type": "array", + "items": { + "type": "string", + "description": "Description of format" + } + }, + "geolocation": { + "description": "Description of geolocation", + "type": "array", + "items": { + "type": "object", + "properties": { + "box": { + "type": "string", + "description": "Description of box" + }, + "place": { + "type": "string", + "description": "Description of place" + }, + "point": { + "type": "string", + "description": "Description of point" + } + }, + "description": "Description of geolocation" + } + }, + "id": { + "type": "string", + "description": "Description of id" + }, + "instance": { + "description": "Description of instance", + "type": "array", + "items": { + "type": "object", + "properties": { + "accessright": { + "allOf": [ + { + "$ref": "#/definitions/AccessRight" + }, + { + "description": "Description of accessright" + } + ] + }, + "collectedfrom": { + "allOf": [ + { + "$ref": "#/definitions/KeyValue" + }, + { + "description": "Description of collectedfrom" + } + ] + }, + "hostedby": { + "allOf": [ + { + "$ref": "#/definitions/KeyValue" + }, + { + "description": "Description of hostedby" + } + ] + }, + "license": { + "type": "string", + "description": "Description of license" + }, + "publicationdate": { + "type": "string", + "description": "Description of publicationdate" + }, + "refereed": { + "type": "string", + "description": "Description of refereed" + }, + "type": { + "type": "string", + "description": "Description of type" + }, + "url": { + "description": "Description of url", + "type": "array", + "items": { + "type": "string", + "description": "Description of url" + } + } + }, + "description": "Description of instance" + } + }, + "language": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "Description of code" + }, + "label": { + "type": "string", + "description": "Description of label" + } + }, + "description": "Description of language" + }, + "lastupdatetimestamp": { + "type": "integer", + "description": "Description of lastupdatetimestamp" + }, + "maintitle": { + "type": "string", + "description": "Description of maintitle" + }, + "originalId": { + "description": "Description of originalId", + "type": "array", + "items": { + "type": "string", + "description": "Description of originalId" + } + }, + "pid": { + "description": "Description of pid", + "type": "array", + "items": { + "allOf": [ + { + "$ref": "#/definitions/ControlledField" + }, + { + "description": "Description of pid" + } + ] + } + }, + "programmingLanguage": { + "type": "string", + "description": "Description of programmingLanguage" + }, + "publicationdate": { + "type": "string", + "description": "Description of publicationdate" + }, + "publisher": { + "type": "string", + "description": "Description of publisher" + }, + "size": { + "type": "string", + "description": "Description of size" + }, + "source": { + "description": "Description of source", + "type": "array", + "items": { + "type": "string", + "description": "Description of source" + } + }, + "subjects": { + "description": "Description of subjects", + "type": "array", + "items": { + "type": "object", + "properties": { + "provenance": { + "allOf": [ + { + "$ref": "#/definitions/Provenance" + }, + { + "description": "Description of provenance" + } + ] + }, + "subject": { + "allOf": [ + { + "$ref": "#/definitions/ControlledField" + }, + { + "description": "Description of subject" + } + ] + } + }, + "description": "Description of subjects" + } + }, + "subtitle": { + "type": "string", + "description": "Description of subtitle" + }, + "tool": { + "description": "Description of tool", + "type": "array", + "items": { + "type": "string", + "description": "Description of tool" + } + }, + "type": { + "type": "string", + "description": "Description of type" + }, + "version": { + "type": "string", + "description": "Description of version" + } + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json index 6dfef32db0..b23ac65464 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/migrate_db_entities_parameters.json @@ -40,5 +40,11 @@ "paramLongName": "dbschema", "paramDescription": "the database schema according to the D-Net infrastructure (beta or production)", "paramRequired": true + }, + { + "paramName": "nsbl", + "paramLongName": "nsPrefixBlacklist", + "paramDescription": "a blacklist of nsprefixes (comma separeted)", + "paramRequired": false } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index d8b61b5ead..d8146d9a22 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -43,7 +43,11 @@ isLookupUrl the address of the lookUp service - + + nsPrefixBlacklist + + a blacklist of nsprefixes (comma separeted) + sparkDriverMemory memory for driver process @@ -131,6 +135,7 @@ --isLookupUrl${isLookupUrl} --actionclaims --dbschema${dbSchema} + --nsPrefixBlacklist${nsPrefixBlacklist} @@ -182,6 +187,7 @@ --postgresPassword${postgresPassword} --isLookupUrl${isLookupUrl} --dbschema${dbSchema} + --nsPrefixBlacklist${nsPrefixBlacklist} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml index 66eaeeb263..4c319d0378 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_claims/oozie_app/workflow.xml @@ -38,7 +38,11 @@ isLookupUrl the address of the lookUp service - + + nsPrefixBlacklist + + a blacklist of nsprefixes (comma separeted) + sparkDriverMemory memory for driver process @@ -113,6 +117,7 @@ --isLookupUrl${isLookupUrl} --actionclaims --dbschema${dbSchema} + --nsPrefixBlacklist${nsPrefixBlacklist} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index eea8d0a5ab..29d4269ef8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -25,7 +25,11 @@ isLookupUrl the address of the lookUp service - + + nsPrefixBlacklist + + a blacklist of nsprefixes (comma separeted) + sparkDriverMemory memory for driver process @@ -99,6 +103,7 @@ --postgresPassword${postgresPassword} --isLookupUrl${isLookupUrl} --dbschema${dbSchema} + --nsPrefixBlacklist${nsPrefixBlacklist} @@ -117,6 +122,7 @@ --isLookupUrl${isLookupUrl} --dbschema${dbSchema} --actionclaims + --nsPrefixBlacklist${nsPrefixBlacklist} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml index 8684181526..9b68cfb053 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_step1/oozie_app/workflow.xml @@ -28,6 +28,11 @@ isLookupUrl the address of the lookUp service + + nsPrefixBlacklist + + a blacklist of nsprefixes (comma separeted) + sparkDriverMemory memory for driver process @@ -67,6 +72,7 @@ -pguser${postgresUser} -pgpasswd${postgresPassword} -islookup${isLookupUrl} + --nsPrefixBlacklist${nsPrefixBlacklist} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/config-default.xml index cac3cc2bb0..17cd6c9a33 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/config-default.xml @@ -1,7 +1,7 @@ - + - - jobTracker - yarn - - - nameNode - hdfs://hadoop-rm1.garr-pa1.d4science.org:8020 - - - hive_metastore_uris - thrift://hadoop-edge3.garr-pa1.d4science.org:9083 - - - spark2YarnHistoryServerAddress - http://hadoop-rm2.garr-pa1.d4science.org:19888 - + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml index a5035c56c6..7e63362428 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/ebi/oozie_app/workflow.xml @@ -18,7 +18,7 @@ - + @@ -48,6 +48,28 @@ + + + yarn-cluster + cluster + Create EBI DataSet + + eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=1000 + ${sparkExtraOPT} + + --workingPath${workingPath} + --masteryarn + + + + + yarn-cluster @@ -71,27 +93,7 @@ - - - yarn-cluster - cluster - Create EBI DataSet - eu.dnetlib.dhp.sx.ebi.SparkCreateEBIDataFrame - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=1000 - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json index 1c02109d01..febcfc8981 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json @@ -1,7 +1,4 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the result data", "paramRequired": true}, - {"paramName":"td", "paramLongName":"targetDir", "paramDescription": "the name of the result data", "paramRequired": true}, - {"paramName":"e", "paramLongName":"entities", "paramDescription": "the entity type to be filtered", "paramRequired": true} + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the work dir path", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml index d74d68663f..c94394b1ee 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step1/oozie_app/workflow.xml @@ -101,12 +101,17 @@ yarn-cluster cluster Import ${entity} and related entities - eu.dnetlib.dhp.sx.graph.SparkScholexplorerGraphImporter + eu.dnetlib.dhp.sx.graph.SparkXMLToOAFDataset dhp-graph-mapper-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} - -mt yarn-cluster + + --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + ${sparkExtraOPT} + + -mt yarn --sourcePath${targetXMLPath} - --targetPath${targetEntityPath} + --targetPath${workingPath}/input/OAFDataset --entity${entity} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml index 46e2dc3f98..fabe7510bb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/step2/oozie_app/workflow.xml @@ -1,16 +1,8 @@ - sourcePath - the source path - - - targetPath - the source path - - - targetDir - the name of the path + workingPath + the working path sparkDriverMemory @@ -20,32 +12,13 @@ sparkExecutorMemory memory for individual executor - - entities - the entities to be extracted - - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - @@ -53,19 +26,18 @@ ${nameNode} yarn-cluster cluster - Extract ${entities} - eu.dnetlib.dhp.sx.graph.SparkExtractEntitiesJob + Extract DLI Entities + eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities dhp-graph-mapper-${projectVersion}.jar --executor-memory ${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 ${sparkExtraOPT} -mt yarn-cluster - --sourcePath${sourcePath} - --targetPath${targetPath} - --targetDir${targetDir} - --entities${entities} + --workingPath${workingPath} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java index 559a30b1ea..e1ef847c38 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctionTest.java @@ -7,6 +7,8 @@ import static org.mockito.Mockito.lenient; import java.io.IOException; import java.util.List; import java.util.Set; +import java.util.function.Predicate; +import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.IOUtils; @@ -19,9 +21,7 @@ import org.mockito.junit.jupiter.MockitoExtension; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Publication; -import eu.dnetlib.dhp.schema.oaf.Qualifier; -import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -62,10 +62,12 @@ public class CleaningFunctionTest { assertTrue(p_in instanceof Result); assertTrue(p_in instanceof Publication); - Publication p_out = OafCleaner.apply(p_in, mapping); + Publication p_out = OafCleaner.apply(CleanGraphSparkJob.fixVocabularyNames(p_in), mapping); assertNotNull(p_out); + assertNotNull(p_out.getPublisher()); + assertNull(p_out.getPublisher().getValue()); assertEquals("und", p_out.getLanguage().getClassid()); assertEquals("Undetermined", p_out.getLanguage().getClassname()); @@ -88,6 +90,16 @@ public class CleaningFunctionTest { Publication p_defaults = CleanGraphSparkJob.fixDefaults(p_out); assertEquals("CLOSED", p_defaults.getBestaccessright().getClassid()); + assertNull(p_out.getPublisher()); + + getAuthorPids(p_defaults).forEach(pid -> { + System.out + .println( + String + .format( + "%s [%s - %s]", pid.getValue(), pid.getQualifier().getClassid(), + pid.getQualifier().getClassname())); + }); // TODO add more assertions to verity the cleaned values System.out.println(MAPPER.writeValueAsString(p_out)); @@ -97,7 +109,7 @@ public class CleaningFunctionTest { */ } - private Stream getAuthorPidTypes(Publication pub) { + private Stream getAuthorPidTypes(Result pub) { return pub .getAuthor() .stream() @@ -106,6 +118,14 @@ public class CleaningFunctionTest { .map(s -> s.getQualifier()); } + private Stream getAuthorPids(Result pub) { + return pub + .getAuthor() + .stream() + .map(a -> a.getPid()) + .flatMap(p -> p.stream()); + } + private List vocs() throws IOException { return IOUtils .readLines(CleaningFunctionTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/terms.txt")); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java new file mode 100644 index 0000000000..d261320d4c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -0,0 +1,405 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.Arrays; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.google.gson.Gson; + +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.oaf.Dataset; +import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; + +@Disabled +public class DumpJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); + + private static CommunityMap map = new CommunityMap(); + + static { + map.put("egi", "EGI Federation"); + map.put("fet-fp7", "FET FP7"); + map.put("fet-h2020", "FET H2020"); + map.put("clarin", "CLARIN"); + map.put("fam", "Fisheries and Aquaculture Management"); + map.put("ni", "Neuroinformatics"); + map.put("mes", "European Marine Scinece"); + map.put("instruct", "Instruct-Eric"); + map.put("rda", "Research Data Alliance"); + map.put("elixir-gr", "ELIXIR GR"); + map.put("aginfra", "Agricultural and Food Sciences"); + map.put("dariah", "DARIAH EU"); + map.put("risis", "RISI"); + map.put("ee", "SDSN - Greece"); + map.put("oa-pg", "EC Post-Grant Open Access Pilot"); + map.put("beopen", "Transport Research"); + map.put("euromarine", "Euromarine"); + map.put("ifremer", "Ifremer"); + map.put("dh-ch", "Digital Humanities and Cultural Heritage"); + map.put("science-innovation-policy", "Science and Innovation Policy Studies"); + map.put("covid-19", "COVID-19"); + map.put("enrmaps", "Energy Research"); + map.put("epos", "EPOS"); + + } + + List communityMap = Arrays + .asList( + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + ""); + + private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testMap() { + System.out.println(new Gson().toJson(map)); + } + + @Test + public void testDataset() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + CommunityResult.class, false); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(90, verificationDataset.count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset + .filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'") + .count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset + .filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'") + .count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset + .filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'") + .count()); + + Assertions + .assertTrue( + verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset + .filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'") + .count()); + + Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90); + + Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); + +//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + + } + + @Test + public void testDataset2All() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + Result.class, true); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.Result.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.Result.class)); + + Assertions.assertEquals(5, verificationDataset.count()); + + verificationDataset.show(false); + } + + @Test + public void testDataset2Communities() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, + CommunityResult.class, false); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(0, verificationDataset.count()); + + verificationDataset.show(false); + } + + @Test + public void testPublication() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, false); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(74, verificationDataset.count()); + verificationDataset.show(false); + + Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); + +//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + + } + + @Test + public void testSoftware() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class, + CommunityResult.class, false); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(6, verificationDataset.count()); + + Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); + verificationDataset.show(false); + +//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + + } + + @Test + public void testORP() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class, + CommunityResult.class, false); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(3, verificationDataset.count()); + + Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); + verificationDataset.show(false); + +//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) + + } + + @Test + public void testRecord() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, false); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(2, verificationDataset.count()); + verificationDataset.show(false); + + Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count()); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java new file mode 100644 index 0000000000..803ae0416a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/GenerateJsonSchema.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.databind.JsonNode; +import com.github.victools.jsonschema.generator.*; + +import eu.dnetlib.dhp.schema.dump.oaf.graph.*; + +@Disabled +public class GenerateJsonSchema { + + @Test + public void generateSchema() { + SchemaGeneratorConfigBuilder configBuilder = new SchemaGeneratorConfigBuilder(SchemaVersion.DRAFT_7, + OptionPreset.PLAIN_JSON) + .with(Option.SCHEMA_VERSION_INDICATOR) + .without(Option.NONPUBLIC_NONSTATIC_FIELDS_WITHOUT_GETTERS); + configBuilder.forFields().withDescriptionResolver(field -> "Description of " + field.getDeclaredName()); + SchemaGeneratorConfig config = configBuilder.build(); + SchemaGenerator generator = new SchemaGenerator(config); + JsonNode jsonSchema = generator.generateSchema(Relation.class); + + System.out.println(jsonSchema.toString()); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java new file mode 100644 index 0000000000..0de4c8338a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/MakeTarTest.java @@ -0,0 +1,60 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.IOException; +import java.nio.file.Files; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +@Disabled +public class MakeTarTest { + private static String workingDir; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(MakeTarTest.class.getSimpleName()) + .toString(); + } + + @Test + public void testTar() throws IOException { + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") + .getPath()), + new Path(workingDir + "/zenodo/ni/part-00000")); + + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/egi") + .getPath()), + new Path(workingDir + "/zenodo/ni/part-00001")); + + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") + .getPath()), + new Path(workingDir + "/zenodo/dh-ch/part-00000")); + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/science-innovation-policy") + .getPath()), + new Path(workingDir + "/zenodo/ni/part-00002")); + + String inputPath = workingDir + "/zenodo/"; + + MakeTar.makeTArArchive(fs, inputPath, "/tmp/out"); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java new file mode 100644 index 0000000000..0e89084189 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -0,0 +1,239 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.community.ResultProject; +import eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject; + +public class PrepareResultProjectJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.PrepareResultProjectJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testNoMatch() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/no_match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + + Assertions.assertEquals(0, verificationDataset.count()); + + } + + @Test + public void testMatchOne() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_one") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + + Assertions.assertTrue(verificationDataset.count() == 1); + + Assertions + .assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + + verificationDataset.createOrReplaceTempView("table"); + + Dataset check = spark + .sql( + "Select projList.provenance.provenance " + + "from table " + + "lateral view explode (projectsList) pl as projList"); + + Assertions.assertEquals(1, check.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + + verificationDataset.show(false); + + } + + @Test + public void testMatch() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + + Assertions.assertTrue(verificationDataset.count() == 2); + + Assertions + .assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + Assertions + .assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + Assertions.assertEquals(3, resultExplodedProvenance.count()); + Assertions + .assertEquals( + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); + + Assertions + .assertEquals( + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); + + Assertions + .assertEquals( + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java new file mode 100644 index 0000000000..c6666342a0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java @@ -0,0 +1,116 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import static org.mockito.Mockito.lenient; + +import java.util.Arrays; +import java.util.List; +import java.util.Map; + +import org.dom4j.DocumentException; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class QueryInformationSystemTest { + + private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + List communityMap = Arrays + .asList( + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + "", + ""); + + @Mock + private ISLookUpService isLookUpService; + + private QueryInformationSystem queryInformationSystem; + + private Map map; + + @BeforeEach + public void setUp() throws ISLookUpException, DocumentException { + lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap); + queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setIsLookUp(isLookUpService); + map = queryInformationSystem.getCommunityMap(); + } + + @Test + public void testSize() throws ISLookUpException { + + Assertions.assertEquals(23, map.size()); + } + + @Test + public void testContent() { + Assertions.assertTrue(map.containsKey("egi") && map.get("egi").equals("EGI Federation")); + + Assertions.assertTrue(map.containsKey("fet-fp7") && map.get("fet-fp7").equals("FET FP7")); + Assertions.assertTrue(map.containsKey("fet-h2020") && map.get("fet-h2020").equals("FET H2020")); + Assertions.assertTrue(map.containsKey("clarin") && map.get("clarin").equals("CLARIN")); + Assertions.assertTrue(map.containsKey("rda") && map.get("rda").equals("Research Data Alliance")); + Assertions.assertTrue(map.containsKey("ee") && map.get("ee").equals("SDSN - Greece")); + Assertions + .assertTrue( + map.containsKey("dh-ch") && map.get("dh-ch").equals("Digital Humanities and Cultural Heritage")); + Assertions.assertTrue(map.containsKey("fam") && map.get("fam").equals("Fisheries and Aquaculture Management")); + Assertions.assertTrue(map.containsKey("ni") && map.get("ni").equals("Neuroinformatics")); + Assertions.assertTrue(map.containsKey("mes") && map.get("mes").equals("European Marine Science")); + Assertions.assertTrue(map.containsKey("instruct") && map.get("instruct").equals("Instruct-ERIC")); + Assertions.assertTrue(map.containsKey("elixir-gr") && map.get("elixir-gr").equals("ELIXIR GR")); + Assertions + .assertTrue(map.containsKey("aginfra") && map.get("aginfra").equals("Agricultural and Food Sciences")); + Assertions.assertTrue(map.containsKey("dariah") && map.get("dariah").equals("DARIAH EU")); + Assertions.assertTrue(map.containsKey("risis") && map.get("risis").equals("RISIS")); + Assertions.assertTrue(map.containsKey("epos") && map.get("epos").equals("EPOS")); + Assertions.assertTrue(map.containsKey("beopen") && map.get("beopen").equals("Transport Research")); + Assertions.assertTrue(map.containsKey("euromarine") && map.get("euromarine").equals("EuroMarine")); + Assertions.assertTrue(map.containsKey("ifremer") && map.get("ifremer").equals("Ifremer")); + Assertions.assertTrue(map.containsKey("oa-pg") && map.get("oa-pg").equals("EC Post-Grant Open Access Pilot")); + Assertions + .assertTrue( + map.containsKey("science-innovation-policy") + && map.get("science-innovation-policy").equals("Science and Innovation Policy Studies")); + Assertions.assertTrue(map.containsKey("covid-19") && map.get("covid-19").equals("COVID-19")); + Assertions.assertTrue(map.containsKey("enermaps") && map.get("enermaps").equals("Energy Research")); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java new file mode 100644 index 0000000000..42ad5634a7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java @@ -0,0 +1,143 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + +public class SplitForCommunityTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(SplitForCommunityTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SplitForCommunityTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SplitForCommunityTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/splitForCommunity") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + CommunitySplit split = new CommunitySplit(); + + split.run(false, sourcePath, workingDir.toString() + "/split", communityMapPath); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/split/dh-ch") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(19, verificationDataset.count()); + + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + + tmp = sc + .textFile(workingDir.toString() + "/split/egi") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + + tmp = sc + .textFile(workingDir.toString() + "/split/ni") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(5, verificationDataset.count()); + + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); + + tmp = sc + .textFile(workingDir.toString() + "/split/science-innovation-policy") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(4, verificationDataset.count()); + + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::0347b1cd516fc59e41ba92e0d74e4e9f'").count()); + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::1432beb6171baa5da8a85a7f99545d69'").count()); + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::1c8bd19e633976e314b88ce5c3f92d69'").count()); + Assertions + .assertEquals( + 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java new file mode 100644 index 0000000000..bd191c847e --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java @@ -0,0 +1,138 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; +import eu.dnetlib.dhp.schema.dump.oaf.Result; +import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; + +public class UpdateProjectInfoTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") + .getPath(); + + SparkUpdateProjectInfo.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-preparedInfoPath", sourcePath + "/preparedInfo", + "-outputPath", workingDir.toString() + "/result", + "-sourcePath", sourcePath + "/software.json" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + verificationDataset.show(false); + + Assertions.assertEquals(6, verificationDataset.count()); + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " + + + "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream " + + "from dataset " + + "lateral view explode(projects) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + + Assertions.assertEquals(3, resultExplodedProvenance.count()); + resultExplodedProvenance.show(false); + + Assertions + .assertEquals( + 2, + resultExplodedProvenance.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '123455'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' and code = '119027'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' and code = '123455'") + .count()); + + resultExplodedProvenance.show(false); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java new file mode 100644 index 0000000000..05dc423cbe --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/ZenodoUploadTest.java @@ -0,0 +1,153 @@ + +package eu.dnetlib.dhp.oa.graph.dump; + +import java.io.*; +import java.nio.file.Files; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.*; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Disabled; +import org.junit.jupiter.api.Test; + +import com.google.gson.Gson; + +import eu.dnetlib.dhp.common.api.MissingConceptDoiException; +import eu.dnetlib.dhp.common.api.ZenodoAPIClient; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; + +@Disabled +public class ZenodoUploadTest { + + private static String workingDir; + + private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions"; + private final String ACCESS_TOKEN = ""; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(eu.dnetlib.dhp.oa.graph.dump.UpdateProjectInfoTest.class.getSimpleName()) + .toString(); + } + + @Test + public void testNewDeposition() throws IOException { + CommunityMap communityMap = new CommunityMap(); + communityMap.put("ni", "Neuroinformatics"); + communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") + .getPath()), + new Path(workingDir + "/zenodo/ni/ni")); + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") + .getPath()), + new Path(workingDir + "/zenodo/dh-ch/dh-ch")); + + ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, + ACCESS_TOKEN); + client.newDeposition(); + + // the second boolean parameter here sets the recursion to true + RemoteIterator fileStatusListIterator = fs + .listFiles( + new Path(workingDir + "/zenodo"), true); + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + + String p_string = fileStatus.getPath().toString(); + + int index = p_string.lastIndexOf("/"); + String community = p_string.substring(0, index); + community = community.substring(community.lastIndexOf("/") + 1); + String community_name = communityMap.get(community).replace(" ", "_"); + // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); + System.out.println(community); + + // File f = new File("/tmp/" + community_name); + FSDataInputStream inputStream = fs.open(fileStatus.getPath()); + System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen())); + + } + + String metadata = "{\"metadata\":{\"access_right\":\"open\",\"communities\":[{\"identifier\":\"openaire-research-graph\"}],\"creators\":[{\"affiliation\":\"CNR - ISTI\",\"name\":\"Manghi, Paolo\",\"orcid\":\"0000-0001-7291-3210\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Atzori, Claudio\",\"orcid\":\"0000-0001-9613-6639\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Bardi, Alessia\",\"orcid\":\"0000-0002-1112-1292\"},{\"affiliation\":\"ISTI - CNR\",\"name\":\"Baglioni, Miriam\",\"orcid\":\"0000-0002-2273-9004\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Shirrwagen, Jochen\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Dimitropoulos, Harry\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"La Bruzzo, Sandro\",\"orcid\":\"0000-0003-2855-1245\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Foufoulas, Ioannis\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Löhden, Aenne\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Bäcker, Amelie\",\"orcid\":\"0000-0001-6015-2063\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Mannocci, Andrea\",\"orcid\":\"0000-0002-5193-7851\"},{\"affiliation\":\"University of Warsaw\",\"name\":\"Horst, Marek\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Czerniak, Andreas\",\"orcid\":\"0000-0003-3883-4169\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kiatropoulou, Katerina\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Kokogiannaki, Argiro\",\"orcid\":\"0000-0002-3880-0244\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"De Bonis, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Artini, Michele\"},{\"affiliation\":\"CNR - ISTI\",\"name\":\"Ottonello, Enrico\"},{\"affiliation\":\"Athena Research and Innovation Centre\",\"name\":\"Lempesis, Antonis\"},{\"affiliation\":\"CERN\",\"name\":\"Ioannidis, Alexandros\"},{\"affiliation\":\"University of Bielefeld\",\"name\":\"Summan, Friedrich\"}],\"description\":\"\\u003cp\\u003eThis dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE\\u003c/p\\u003e. \\u003cp\\u003eEach dataset is a zip containing a file with one json per line. Each json is compliant to the schema available at XXXX\\u003c/p\\u003e Note that the file that is offered is not a typical json file: each line contains a separate, self-contained json object. For more information please see http://jsonlines.org\",\"grants\":[{\"id\":\"777541\"},{\"id\":\"824091\"},{\"id\":\"824323\"}],\"keywords\":[\"Open Science\",\"Scholarly Communication\",\"Information Science\"],\"language\":\"eng\",\"license\":\"CC-BY-4.0\",\"title\":\"OpenAIRE Research Graph: Dumps for research communities and initiatives.\",\"upload_type\":\"dataset\",\"version\":\"1.0\"}}"; + + System.out.println(client.sendMretadata(metadata)); + + System.out.println(client.publish()); + + } + + @Test + public void testNewVersion() throws IOException, MissingConceptDoiException { + + ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, + ACCESS_TOKEN); + + client.newVersion("656628"); + + CommunityMap communityMap = new CommunityMap(); + communityMap.put("ni", "Neuroinformatics"); + communityMap.put("dh-ch", "Digital Humanities and Cultural Heritage"); + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/ni") + .getPath()), + new Path(workingDir + "/zenodo/ni/ni")); + fs + .copyFromLocalFile( + false, new Path(getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/zenodo/dh-ch") + .getPath()), + new Path(workingDir + "/zenodo/dh-ch/dh-ch")); + + RemoteIterator fileStatusListIterator = fs + .listFiles( + new Path(workingDir + "/zenodo"), true); + while (fileStatusListIterator.hasNext()) { + LocatedFileStatus fileStatus = fileStatusListIterator.next(); + + String p_string = fileStatus.getPath().toString(); + + int index = p_string.lastIndexOf("/"); + String community = p_string.substring(0, index); + community = community.substring(community.lastIndexOf("/") + 1); + String community_name = communityMap.get(community).replace(" ", "_"); + // fs.copyToLocalFile(fileStatus.getPath(), new Path("/tmp/" + community_name)); + System.out.println(community); + + // File f = new File("/tmp/" + community_name); + FSDataInputStream inputStream = fs.open(fileStatus.getPath()); + System.out.println(client.uploadIS(inputStream, community_name, fileStatus.getLen())); + + } + + System.out.println(client.publish()); + + } + + @Test + public void readCommunityMap() throws IOException { + LocalFileSystem fs = FileSystem.getLocal(new Configuration()); + System.out + .println( + new Gson() + .toJson( + Utils + .readCommunityMap( + fs, getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath()))); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateEntityTest.java new file mode 100644 index 0000000000..181dc8f1e0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateEntityTest.java @@ -0,0 +1,127 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static org.mockito.Mockito.lenient; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.Map; +import java.util.function.Consumer; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import com.google.gson.Gson; + +import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchCommunity; +import eu.dnetlib.dhp.schema.dump.oaf.graph.ResearchInitiative; +import eu.dnetlib.dhp.utils.DHPUtils; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class CreateEntityTest { + + private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " + + + "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + + "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " + + + "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; + + List communityMap = Arrays + .asList( + "clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin@@ri", + "ee@@Sustainable Development Solutions Network - Greece@@The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. " + + + "SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.@@SDG13 - Climate action,SDG8 - Decent work and economic growth,SDG15 - " + + + "Life on land,SDG2 - Zero hunger,SDG17 - Partnerships for the ´goals,SDG10 - Reduced inequalities,SDG5 - Gender equality,SDG12 - Responsible consumption and production,SDG14 - Life below water,SDG6 - Clean water and sanitation,SDG11 - Sustainable cities and communities,SDG1 - No poverty,SDG3 - Good health and well being,SDG7 - Affordable and clean energy,SDG4 - Quality education,SDG9 - Industry innovation and infrastructure,SDG16 - Peace justice and strong institutions@@oac_sdsn-greece@@community", + "dh-ch@@Digital Humanities and Cultural Heritage@@This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.@@modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels@@oac_dh-ch@@community", + "fam@@Fisheries and Aquaculture Management@@Conservation of marine resources for sustainable development. The Fisheries and Aquaculture community focus on resources (document, data, codes..) which have been produced in the framework of projects (H2020, FP7, ..) related to the domain of fisheries and aquaculture.@@Stock Assessment,pelagic,Acoustic,Fish farming,Fisheries,Fishermen,maximum sustainable yield,trawler,Fishing vessel,Fisherman,Fishing gear,mackerel,RFMO,Fish Aggregating Device,Bycatch,Fishery,common fisheries policy,Fishing fleet,Aquaculture@@fisheries@@community", + "ni@@Neuroinformatics@@The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.@@brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities@@oac_ni@@community", + "mes@@European Marine Science@@This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).@@marine,ocean,fish,aqua,sea@@oac_mes@@community", + "instruct@@Instruct-ERIC@@Instruct-ERIC is the European Research Infrastructure for Structural Biology@@@@oac_instruct@@community", + "elixir-gr@@The Greek National Node of the ESFRI European RI ELIXIR@@ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.@@@@oaa_elixir-gr@@ri", + "aginfra@@Agricultural and Food Sciences@@The scope of this community is to provide access to publications, research data, projects and software that are related to agricultural and food sciences@@animal production and health,fisheries and aquaculture,food safety and human nutrition,information management,food technology,agri-food education and extension,natural resources and environment,food system,engineering technology and Research,agriculture,food safety risk assessment,food security,farming practices and systems,plant production and protection,agri-food economics and policy,Agri-food,food distribution,forestry@@oac_aginfra@@community", + "dariah@@DARIAH EU@@The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents. @@@@dariah@@ri", + "epos@@European Plate Observing System@@EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of data, data products, and facilities from distributed research infrastructures for solid Earth science in Europe.@@@@@@ri", + "covid-19@@Corona Virus Disease@@This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.@@COVID19,SARS-CoV,HCoV-19,mesh:C000657245,MERS-CoV,Síndrome Respiratorio Agudo Severo,mesh:COVID-19,COVID2019,COVID-19,SARS-CoV-2,2019 novel coronavirus,severe acute respiratory syndrome coronavirus 2,Orthocoronavirinae,Coronaviridae,mesh:D045169,coronavirus,SARS,coronaviruses,coronavirus disease-19,sars cov 2,Middle East Respiratory Syndrome,Severe acute respiratory syndrome coronavirus 2,Severe Acute Respiratory Syndrome,coronavirus disease 2019,2019-nCoV@@covid-19@@community"); + + @Mock + private ISLookUpService isLookUpService; + + private QueryInformationSystem queryInformationSystem; + + @BeforeEach + public void setUp() throws ISLookUpException { + lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); + queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setIsLookUp(isLookUpService); + } + + @Test + public void test1() throws ISLookUpException, IOException { + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.getContextInformation(consumer); + + List riList = new ArrayList<>(); + cInfoList.forEach(cInfo -> riList.add(Process.getEntity(cInfo))); + + Assertions.assertEquals(12, riList.size()); + + riList.stream().forEach(c -> { + switch (c.getOriginalId()) { + case "mes": + Assertions + .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_COMMUNITY)); + Assertions.assertTrue(((ResearchCommunity) c).getSubject().size() == 5); + Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("marine")); + Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("ocean")); + Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("fish")); + Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("aqua")); + Assertions.assertTrue(((ResearchCommunity) c).getSubject().contains("sea")); + Assertions + .assertTrue( + c + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5(c.getOriginalId())))); + Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_mes")); + Assertions.assertTrue("mes".equals(c.getOriginalId())); + break; + case "clarin": + Assertions + .assertTrue(c.getType().equals(eu.dnetlib.dhp.oa.graph.dump.Constants.RESEARCH_INFRASTRUCTURE)); + Assertions + .assertTrue( + c + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5(c.getOriginalId())))); + Assertions.assertTrue(c.getZenodo_community().equals("https://zenodo.org/communities/oac_clarin")); + Assertions.assertTrue("clarin".equals(c.getOriginalId())); + break; + } + // TODO add check for all the others Entities + + }); + + riList.forEach(c -> System.out.println(new Gson().toJson(c))); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateRelationTest.java new file mode 100644 index 0000000000..bb2e402b20 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateRelationTest.java @@ -0,0 +1,569 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.util.*; +import java.util.function.Consumer; +import java.util.stream.Collectors; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import com.google.gson.Gson; + +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.utils.DHPUtils; + +public class CreateRelationTest { + + List communityContext = Arrays + .asList( + "\n" + + " all\n" + + " CLARIN\n" + + " https://www.clarin.eu/sites/default/files/clarin-frontpage-logo.jpg\n" + + + " Common Language Resources and Technology Infrastructure\n" + + " maria@clarin.eu,dieter@clarin.eu,f.m.g.dejong@uu.nl,paolo.manghi@isti.cnr.it\n" + + + " \n" + + " (Part of) the work reported here was made possible by using the CLARIN infrastructure.\n" + + + " The work reported here has received funding through <CLARIN national consortium member, e.g. CLARIN.SI>, <XYZ> project, grant no. <XYZ>.\n" + + + " The work reported here has received funding (through CLARIN ERIC) from the European Union’s Horizon 2020 research and innovation programme under grant agreement No <0-9> for project <XYZ>.\n" + + + " (E.g. No 676529 for project CLARIN-PLUS.)\n" + + " oac_clarin\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + " CLARIN-PLUS\n" + + " \n" + + " \n" + + " 676529\n" + + " http://www.clarin.eu\n" + + " EC\n" + + " H2020-INFRADEV-1-2015-1\n" + + " CLARIN+\n" + + " \n" + + " \n" + + " Common Language Resources and Technology Infrastructure\n" + + + " CLARIN\n" + + " 212230\n" + + " EC\n" + + " corda_______::ef782b2d85676aa3e5a907427feb18c4\n" + + " \n" + + " \n" + + " " + + "\n" + + " \n" + + " LINDAT/CLARIN repository\n" + + " LINDAT/CLARIN repository\n" + + " true\n" + + " \n" + + " \n" + + " \n" + + " \n" + + " CLARIN-D\n" + + " https://www.clarin-d.de/en/\n" + + " \n" + + " http://www.lrec-conf.org/proceedings/lrec2018/pdf/504.pdf\n" + + + " Germany\n" + + " \n" + + " \n" + + " \n" + + + " \n" + + "", + "\n" + + " all\n" + + " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\n" + + + " http://sanmamante.org/DH_CH_logo.png\n" + + " Digital Humanities and Cultural Heritage\n" + + " ileniagalluccio87@gmail.com,achille.felicetti@gmail.com,paolo.manghi@isti.cnr.it,tim.evans@york.ac.uk\n" + + + " modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels\n" + + + " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" + + + " oac_dh-ch\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + + " Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies\n" + + + " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" + + + " \n" + + " 654119\n" + + " http://www.parthenos-project.eu\n" + + " EC\n" + + " PARTHENOS\n" + + " \n" + + " \n" + + " \n" + + " \n" + + + " re3data_____::9ebe127e5f3a0bf401875690f3bb6b81\n" + + " The UK's largest collection of digital research data in the social sciences and humanities\n" + + + " UK Data Archive\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::c6cd4b532e12868c1d760a8d7cda6815\n" + + " Journal of Data Mining and Digital Humanities\n" + + " Journal of Data Mining and Digital Humanities\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b\n" + + " Frontiers in Digital Humanities\n" + + " Frontiers in Digital Humanities\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::6eb31d13b12bc06bbac06aef63cf33c9\n" + + " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" + + + " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" + + + " true\n" + + " \n" + + " \n" + + + " doajarticles::0da84e9dfdc8419576169e027baa8028\n" + + " Conservation Science in Cultural Heritage\n" + + " Conservation Science in Cultural Heritage\n" + + " true\n" + + " \n" + + " \n" + + + " re3data_____::84e123776089ce3c7a33db98d9cd15a8\n" + + " Electronic Archiving System\n" + + " EASY\n" + + " true\n" + + " \n" + + " \n" + + " openaire____::c5502a43e76feab55dd00cf50f519125\n" + + " DANS-KB Harvester\n" + + " Gemeenschappelijke Harvester DANS-KB\n" + + " true\n" + + " \n" + + " \n" + + " re3data_____::a48f09c562b247a9919acfe195549b47\n" + + " ads\n" + + " Archaeology Data Service\n" + + " true\n" + + " \n" + + " \n" + + " opendoar____::97275a23ca44226c9964043c8462be96\n" + + " KNAW Repository\n" + + " KNAW Repository\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::2899208a99aa7d142646e0a80bfeef05\n" + + " Internet Archaeology\n" + + " Internet Archaeology\n" + + " true\n" + + " \n" + + " \n" + + " \n" + + "\n", + "\n" + + " all\n" + + " The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\n" + + + " https://docs.google.com/drawings/u/0/d/10e191xGoGf4uaRluMqbt_7cCj6LSCs2a29im4CmWjqU/export/png\n" + + + " Neuroinformatics\n" + + " sorina.pop@creatis.insa-lyon.fr,camille.maumet@inria.fr,christian.barillot@irisa.fr,xavier.rolland@irisa.fr,axel.bonnet@creatis.insa-lyon.fr,paolo.manghi@isti.cnr.it\n" + + + " brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities\n" + + + " \n" + + " oac_ni\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + + " Formerly:OpenFMRI\n" + + " OpenNeuro\n" + + " true\n" + + " \n" + + " \n" + + " doajarticles::c7d3de67dc77af72f6747157441252ec\n" + + " Research Ideas and Outcomes\n" + + " Research Ideas and Outcomes\n" + + " true\n" + + " \n" + + " \n" + + " re3data_____::8515794670370f49c1d176c399c714f5\n" + + " Neuroimaging Informatics Tools and Resources Clearinghouse\n" + + + " NITRC\n" + + " true\n" + + " \n" + + " \n" + + " doajarticles::d640648c84b10d425f96f11c3de468f3\n" + + " Frontiers in Neuroinformatics\n" + + " Frontiers in Neuroinformatics\n" + + " true\n" + + " \n" + + " \n" + + " doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\n" + + " NeuroImage: Clinical\n" + + " NeuroImage: Clinical\n" + + " true\n" + + " \n" + + " \n" + + " rest________::fb1a3d4523c95e63496e3bc7ba36244b\n" + + " NeuroVault\n" + + " NeuroVault\n" + + " true\n" + + " \n" + + " \n" + + "\n", + "\n" + + " all\n" + + " Instruct-ERIC is the European Research Infrastructure for Structural Biology\n" + + + " https://instruct-eric.eu/templates/instructeric/images/logos/instruct-eric-logo-noline.png\n" + + + " Instruct-ERIC\n" + + " claudia@instruct-eric.eu,carazo@cnb.csic.es,echrysina@eie.gr,susan@instruct-eric.eu,naomi@instruct-eric.eu,natalie@instruct-eric.eu,pmarie@igbmc.fr,darren.hart@ibs.fr,claudia@strubi.ox.ac.uk,paolo.manghi@isti.cnr.it\n" + + + " \n" + + " The authors acknowledge the support and the use of resources of Instruct-ERIC.\n" + + + " The authors acknowledge the support and the use of resources of Instruct (PID # or APPID #), a Landmark ESFRI project\n" + + + " oac_instruct\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + + " Authentication and Authorisation For Research and Collaboration\n" + + + " \n" + + " 730941\n" + + " \n" + + " H2020-EINFRA-2016-1\n" + + " AARC2\n" + + " EC\n" + + " \n" + + " \n" + + + " Building data bridges between biological and medical infrastructures in Europe\n" + + + " \n" + + " 284209\n" + + " \n" + + " FP7-INFRASTRUCTURES-2011-1\n" + + " EC\n" + + " BioMedBridges\n" + + " \n" + + " \n" + + + " Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities\n" + + + " \n" + + " 283570\n" + + " \n" + + " FP7-INFRASTRUCTURES-2011-1\n" + + " EC\n" + + " BioStruct-X\n" + + " \n" + + " \n" + + + " Coordinated Research Infrastructures Building Enduring Life-science services\n" + + + " \n" + + " 654248\n" + + " \n" + + " H2020-INFRADEV-1-2014-1\n" + + " EC\n" + + " CORBEL\n" + + " \n" + + " \n" + + + " Infrastructure for NMR, EM and X-rays for translational research\n" + + + " \n" + + " 653706\n" + + " \n" + + " H2020-INFRAIA-2014-2015\n" + + " EC\n" + + " iNEXT\n" + + " \n" + + " \n" + + + " Integrated Structural Biology Infrastructure\n" + + " \n" + + " 211252\n" + + " \n" + + " FP7-INFRASTRUCTURES-2007-1\n" + + " EC\n" + + " INSTRUCT\n" + + " \n" + + " \n" + + + " Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research\n" + + + " \n" + + " 731005\n" + + " \n" + + " H2020-INFRADEV-2016-1\n" + + " EC\n" + + " INSTRUCT-ULTRA\n" + + " \n" + + " \n" + + + " Opening Synchrotron Light for Experimental Science and Applications in the Middle East\n" + + + " \n" + + " 730943\n" + + " \n" + + " H2020-INFRASUPP-2016-1\n" + + " EC\n" + + " OPEN SESAME\n" + + " \n" + + " \n" + + + " Infrastructure for Protein Production Platforms\n" + + + " \n" + + " 227764\n" + + " \n" + + " FP7-INFRASTRUCTURES-2008-1\n" + + " EC\n" + + " PCUBE\n" + + " \n" + + " \n" + + + " European Vaccine Research and Development Infrastructure\n" + + + " \n" + + " 730964\n" + + " \n" + + " H2020-INFRAIA-2016-1\n" + + " EC\n" + + " TRAMSVAC2\n" + + " \n" + + " \n" + + + " World-wide E-infrastructure for structural biology\n" + + + " \n" + + " 675858\n" + + " \n" + + " H2020-EINFRA-2015-1\n" + + " EC\n" + + " West-Life\n" + + " \n" + + " \n" + + " Expanding research infrastructure visibility to strengthen strategic partnerships\n" + + + " RI-VIS\n" + + " 824063\n" + + " EC\n" + + " corda__h2020::af93b591b76991d8437993a8f6fc6538\n" + + " \n" + + " \n" + + " \n" + + + " \n" + + + " \n" + + " instruct\n" + + " \n" + + " \n" + + " \n" + + + " west-life\n" + + " \n" + + " \n" + + " \n" + + " \n" + + + " \n" + + " FRISBI\n" + + " aHR0cDovL2ZyaXNiaS5ldS9zdGF0aWMvaW1hZ2VzL2xvZ29zL2xvZ28tZnJpc2JpLnBuZw==\n" + + + " aHR0cDovL2ZyaXNiaS5ldS8=\n" + + " \n" + + " \n" + + " RI-VIS\n" + + " aHR0cHM6Ly9yaS12aXMuZXUvbmV0d29yay9yaXZpcy90ZW1wbGF0ZXMvcml2aXMvaW1hZ2VzL1JJLVZJU0xvZ29GaW5hbC0wNi5wbmc=\n" + + + " aHR0cHM6Ly9yaS12aXMuZXU=\n" + + " \n" + + " \n" + + " CIISB\n" + + " aHR0cDovL2JpYy5jZWl0ZWMuY3ovZmlsZXMvMjkyLzEyNS5KUEc=\n" + + " aHR0cHM6Ly93d3cuY2lpc2Iub3Jn\n" + + " \n" + + " \n" + + "\n", + "\n" + + " all\n" + + " ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\n" + + + " https://elixir-greece.org/sites/default/files/ELIXIR_GREECE_white_background.png\n" + + + " The Greek National Node of the ESFRI European RI ELIXIR\n" + + " vergoulis@imis.athena-innovation.gr,schatz@imis.athena-innovation.gr,paolo.manghi@isti.cnr.it\n" + + + " \n" + + " \n" + + " oaa_elixir-gr\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + + " \n" + + " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + + " bio.tools\n" + + " bio.tools\n" + + " false\n" + + " \n" + + " \n" + + " \n" + + " \n" + + + " \n" + + " \n" + + " ATHENA RC\n" + + " aHR0cHM6Ly9lbGl4aXItZ3JlZWNlLm9yZy9zaXRlcy9kZWZhdWx0L2ZpbGVzL3N0eWxlcy90aHVtYm5haWwvcHVibGljL3BhcnRuZXJfbG9nb3MvYXRoZW5hX2xvZ28uanBnP2l0b2s9VXdGWFNpZng=\n" + + + " aHR0cHM6Ly93d3cuYXRoZW5hLWlubm92YXRpb24uZ3IvZW4=\n" + + " \n" + + " \n" + + + ""); + + private QueryInformationSystem queryInformationSystem; + + private Map map; + + @BeforeEach + public void setUp() { + + queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setContextRelationResult(communityContext); + } + + @Test + public void test1() { + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.getIdPrefix(Datasource.class)); + + cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); + + List rList = new ArrayList<>(); + + cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); + + Assertions.assertEquals(34, rList.size()); + + Assertions + .assertTrue( + rList + .stream() + .map(r -> r.getSource().getId()) + .collect(Collectors.toSet()) + .contains( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))); + + Assertions + .assertEquals( + 10, + rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))) + .collect(Collectors.toList()) + .size()); + + Assertions + .assertEquals( + 10, + rList + .stream() + .filter( + r -> r + .getTarget() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))) + .collect(Collectors.toList()) + .size()); + + Set tmp = rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))) + .map(r -> r.getTarget().getId()) + .collect(Collectors.toSet()); + + Assertions + .assertTrue( + tmp.contains("10|re3data_____::9ebe127e5f3a0bf401875690f3bb6b81") && + tmp.contains("10|doajarticles::c6cd4b532e12868c1d760a8d7cda6815") && + tmp.contains("10|doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b") && + tmp.contains("10|doajarticles::6eb31d13b12bc06bbac06aef63cf33c9") && + tmp.contains("10|doajarticles::0da84e9dfdc8419576169e027baa8028") && + tmp.contains("10|re3data_____::84e123776089ce3c7a33db98d9cd15a8") && + tmp.contains("10|openaire____::c5502a43e76feab55dd00cf50f519125") && + tmp.contains("10|re3data_____::a48f09c562b247a9919acfe195549b47") && + tmp.contains("10|opendoar____::97275a23ca44226c9964043c8462be96") && + tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05")); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpOrganizationProjectDatasourceTest.java new file mode 100644 index 0000000000..d855f279d2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpOrganizationProjectDatasourceTest.java @@ -0,0 +1,146 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Organization; +import eu.dnetlib.dhp.schema.oaf.Project; + +public class DumpOrganizationProjectDatasourceTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(DumpOrganizationProjectDatasourceTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpOrganizationProjectDatasourceTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void dumpOrganizationTest() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/organization") + .getPath(); + + DumpGraphEntities dg = new DumpGraphEntities(); + + dg.run(false, sourcePath, workingDir.toString() + "/dump", Organization.class, null); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dump") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); + + Assertions.assertEquals(34, verificationDataset.count()); + + verificationDataset.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + + } + + @Test + public void dumpProjectTest() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/project") + .getPath(); + + DumpGraphEntities dg = new DumpGraphEntities(); + + dg.run(false, sourcePath, workingDir.toString() + "/dump", Project.class, null); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dump") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Project.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Project.class)); + + Assertions.assertEquals(12, verificationDataset.count()); + + verificationDataset.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + + } + + @Test + public void dumpDatasourceTest() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/datasource") + .getPath(); + + DumpGraphEntities dg = new DumpGraphEntities(); + + dg.run(false, sourcePath, workingDir.toString() + "/dump", Datasource.class, null); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/dump") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.Datasource.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Datasource.class)); + + Assertions.assertEquals(5, verificationDataset.count()); + + verificationDataset.foreach(o -> System.out.println(OBJECT_MAPPER.writeValueAsString(o))); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpRelationTest.java new file mode 100644 index 0000000000..611b49fcb2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpRelationTest.java @@ -0,0 +1,130 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; + +public class DumpRelationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(DumpRelationTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(DumpRelationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpRelationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpRelationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") + .getPath(); + + SparkDumpRelationJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + + verificationDataset.createOrReplaceTempView("table"); + + Dataset check = spark + .sql( + "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " + + + "from table "); + + Assertions.assertEquals(22, check.filter("name = 'isProvidedBy'").count()); + Assertions + .assertEquals( + 22, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); + Assertions + .assertEquals( + 7, check + .filter( + "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + + "and provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); + Assertions + .assertEquals( + 1, check + .filter( + "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + + "and provenance = 'Inferred by OpenAIRE'") + .count()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/ExtractRelationFromEntityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/ExtractRelationFromEntityTest.java new file mode 100644 index 0000000000..820a899ce0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/ExtractRelationFromEntityTest.java @@ -0,0 +1,109 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class ExtractRelationFromEntityTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(ExtractRelationFromEntityTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(ExtractRelationFromEntityTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(ExtractRelationFromEntityTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(ExtractRelationFromEntityTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + Extractor ex = new Extractor(); + ex + .run( + false, sourcePath, workingDir.toString() + "/relation", + // eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); + eu.dnetlib.dhp.schema.oaf.Publication.class, communityMapPath); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + + Assertions + .assertEquals( + 9, + verificationDataset.filter("source.id = '50|dedup_wf_001::15270b996fa8fd2fb5723daeab3685c3'").count()); + + Assertions + .assertEquals( + 9, + verificationDataset.filter("source.id = '50|dedup_wf_001::15270b996fa8fd2fb5723daxab3685c3'").count()); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/FunderParsingTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/FunderParsingTest.java new file mode 100644 index 0000000000..0374a1568a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/FunderParsingTest.java @@ -0,0 +1,69 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import org.dom4j.DocumentException; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.schema.dump.oaf.graph.Funder; + +public class FunderParsingTest { + + @Test + public void testFunderTwoLevels() throws DocumentException { + + String funding_Stream = "nsf_________::NSFNSFNational Science " + + + "FoundationUSnsf_________::NSF::CISE/OAD::CISE/CCFDivision " + + + "of Computing and Communication FoundationsDivision of Computing and Communication " + + "Foundationsnsf_________::NSF::CISE/OADDirectorate for " + + + "Computer & Information Science & EngineeringDirectorate for Computer & " + + "Information Science & Engineeringnsf:fundingStream"; + + Funder f = DumpGraphEntities.getFunder(funding_Stream); + + Assertions.assertEquals("NSF", f.getShortName()); + Assertions.assertEquals("National Science Foundation", f.getName()); + Assertions.assertEquals("US", f.getJurisdiction()); + + Assertions.assertEquals("NSF::CISE/OAD::CISE/CCF", f.getFunding_stream().getId()); + Assertions + .assertEquals( + "Directorate for Computer & Information Science & Engineering - Division of Computing and Communication Foundations", + f.getFunding_stream().getDescription()); + + } + + @Test + public void testFunderThreeeLevels() throws DocumentException { + String funding_stream = "ec__________::EC" + + "EC" + + "European Commission" + + "EU" + + "" + + "ec__________::EC::H2020::ERC::ERC-COG" + + "Consolidator Grant" + + "ERC-COGec:h2020toas" + + "ec__________::EC::H2020::ERC" + + "European Research Council" + + "ERCec:h2020fundings" + + "ec__________::EC::H2020H2020" + + "Horizon 2020 Framework Programme" + + "ec:h2020fundings"; + + Funder f = DumpGraphEntities.getFunder(funding_stream); + + Assertions.assertEquals("EC", f.getShortName()); + Assertions.assertEquals("European Commission", f.getName()); + Assertions.assertEquals("EU", f.getJurisdiction()); + + Assertions.assertEquals("EC::H2020::ERC::ERC-COG", f.getFunding_stream().getId()); + Assertions + .assertEquals( + "Horizon 2020 Framework Programme - European Research Council - Consolidator Grant", + f.getFunding_stream().getDescription()); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystemTest.java new file mode 100644 index 0000000000..074bed1985 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/QueryInformationSystemTest.java @@ -0,0 +1,807 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import static org.mockito.Mockito.lenient; + +import java.util.*; +import java.util.function.Consumer; + +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class QueryInformationSystemTest { + + private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and $x//context/param[./@name = 'status']/text() = 'all' " + + " return " + + "$x//context"; + + private static final String XQUERY_ENTITY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + "where $x//context[./@type='community' or ./@type = 'ri'] and $x//context/param[./@name = 'status']/text() = 'all' return " + + + "concat(data($x//context/@id) , '@@', $x//context/param[./@name =\"name\"]/text(), '@@', " + + "$x//context/param[./@name=\"description\"]/text(), '@@', $x//context/param[./@name = \"subject\"]/text(), '@@', " + + + "$x//context/param[./@name = \"zenodoCommunity\"]/text(), '@@', $x//context/@type)"; + + List communityMap = Arrays + .asList( + "clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin@@ri", + "ee@@Sustainable Development Solutions Network - Greece@@The UN Sustainable Development Solutions Network (SDSN) has been operating since 2012 under the auspices of the UN Secretary-General. " + + + "SDSN mobilizes global scientific and technological expertise to promote practical solutions for sustainable development, including the implementation of the Sustainable Development Goals (SDGs) and the Paris Climate Agreement. The Greek hub of SDSN has been included in the SDSN network in 2017 and is co-hosted by ICRE8: International Center for Research on the Environment and the Economy and the Political Economy of Sustainable Development Lab.@@SDG13 - Climate action,SDG8 - Decent work and economic growth,SDG15 - " + + + "Life on land,SDG2 - Zero hunger,SDG17 - Partnerships for the ´goals,SDG10 - Reduced inequalities,SDG5 - Gender equality,SDG12 - Responsible consumption and production,SDG14 - Life below water,SDG6 - Clean water and sanitation,SDG11 - Sustainable cities and communities,SDG1 - No poverty,SDG3 - Good health and well being,SDG7 - Affordable and clean energy,SDG4 - Quality education,SDG9 - Industry innovation and infrastructure,SDG16 - Peace justice and strong institutions@@oac_sdsn-greece@@community", + "dh-ch@@Digital Humanities and Cultural Heritage@@This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.@@modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels@@oac_dh-ch@@community", + "fam@@Fisheries and Aquaculture Management@@Conservation of marine resources for sustainable development. The Fisheries and Aquaculture community focus on resources (document, data, codes..) which have been produced in the framework of projects (H2020, FP7, ..) related to the domain of fisheries and aquaculture.@@Stock Assessment,pelagic,Acoustic,Fish farming,Fisheries,Fishermen,maximum sustainable yield,trawler,Fishing vessel,Fisherman,Fishing gear,mackerel,RFMO,Fish Aggregating Device,Bycatch,Fishery,common fisheries policy,Fishing fleet,Aquaculture@@fisheries@@community", + "ni@@Neuroinformatics@@The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.@@brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities@@oac_ni@@community", + "mes@@European Marine Science@@This community was initially defined to include a very broad range of topics, with the intention to generate a number of more focused and sustainable dashboards for research communities and initiatives. As outlined in the logo of this community, we intend to setup a community dashboard for EuroMarine (a consortium of 56 research and academic organisations) and monitoring dashboards for marine research initiatives, including infrastructures (e.g. EMBRC & EMSO), advisory boards (e.g. Marine Boards & ICES), and transnational funding bodies (e.g. JPI-Oceans and Tara Foundation).@@marine,ocean,fish,aqua,sea@@oac_mes@@community", + "instruct@@Instruct-ERIC@@Instruct-ERIC is the European Research Infrastructure for Structural Biology@@@@oac_instruct@@community", + "elixir-gr@@The Greek National Node of the ESFRI European RI ELIXIR@@ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.@@@@oaa_elixir-gr@@ri", + "aginfra@@Agricultural and Food Sciences@@The scope of this community is to provide access to publications, research data, projects and software that are related to agricultural and food sciences@@animal production and health,fisheries and aquaculture,food safety and human nutrition,information management,food technology,agri-food education and extension,natural resources and environment,food system,engineering technology and Research,agriculture,food safety risk assessment,food security,farming practices and systems,plant production and protection,agri-food economics and policy,Agri-food,food distribution,forestry@@oac_aginfra@@community", + "dariah@@DARIAH EU@@The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support digitally-enabled research and teaching across the arts and humanities. It develops, maintains and operates an infrastructure in support of ICT-based research practices and sustains researchers in using them to build, analyse and interpret digital resources. DARIAH was established as a European Research Infrastructure Consortium (ERIC) in August 2014. Currently, DARIAH has 18 Members and several cooperating partners in eight non-member countries. Here you will find a growing collection of DARIAH-affiliated research outputs and other documents. @@@@dariah@@ri", + "epos@@European Plate Observing System@@EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of data, data products, and facilities from distributed research infrastructures for solid Earth science in Europe.@@@@@@ri", + "covid-19@@Corona Virus Disease@@This portal provides access to publications, research data, projects and software that may be relevant to the Corona Virus Disease (COVID-19). The OpenAIRE COVID-19 Gateway aggregates COVID-19 related records, links them and provides a single access point for discovery and navigation. We tag content from the OpenAIRE Research Graph (10,000+ data sources) and additional sources. All COVID-19 related research results are linked to people, organizations and projects, providing a contextualized navigation.@@COVID19,SARS-CoV,HCoV-19,mesh:C000657245,MERS-CoV,Síndrome Respiratorio Agudo Severo,mesh:COVID-19,COVID2019,COVID-19,SARS-CoV-2,2019 novel coronavirus,severe acute respiratory syndrome coronavirus 2,Orthocoronavirinae,Coronaviridae,mesh:D045169,coronavirus,SARS,coronaviruses,coronavirus disease-19,sars cov 2,Middle East Respiratory Syndrome,Severe acute respiratory syndrome coronavirus 2,Severe Acute Respiratory Syndrome,coronavirus disease 2019,2019-nCoV@@covid-19@@community"); + + List communityContext = Arrays + .asList( + "\n" + + " all\n" + + " CLARIN\n" + + " https://www.clarin.eu/sites/default/files/clarin-frontpage-logo.jpg\n" + + + " Common Language Resources and Technology Infrastructure\n" + + " maria@clarin.eu,dieter@clarin.eu,f.m.g.dejong@uu.nl,paolo.manghi@isti.cnr.it\n" + + + " \n" + + " (Part of) the work reported here was made possible by using the CLARIN infrastructure.\n" + + + " The work reported here has received funding through <CLARIN national consortium member, e.g. CLARIN.SI>, <XYZ> project, grant no. <XYZ>.\n" + + + " The work reported here has received funding (through CLARIN ERIC) from the European Union’s Horizon 2020 research and innovation programme under grant agreement No <0-9> for project <XYZ>.\n" + + + " (E.g. No 676529 for project CLARIN-PLUS.)\n" + + " oac_clarin\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + " CLARIN-PLUS\n" + + " \n" + + " \n" + + " 676529\n" + + " http://www.clarin.eu\n" + + " EC\n" + + " H2020-INFRADEV-1-2015-1\n" + + " CLARIN+\n" + + " \n" + + " \n" + + " Common Language Resources and Technology Infrastructure\n" + + + " CLARIN\n" + + " 212230\n" + + " EC\n" + + " corda_______::ef782b2d85676aa3e5a907427feb18c4\n" + + " \n" + + " \n" + + " " + + "\n" + + " \n" + + " LINDAT/CLARIN repository\n" + + " LINDAT/CLARIN repository\n" + + " true\n" + + " \n" + + " \n" + + " \n" + + " \n" + + " CLARIN-D\n" + + " https://www.clarin-d.de/en/\n" + + " \n" + + " http://www.lrec-conf.org/proceedings/lrec2018/pdf/504.pdf\n" + + + " Germany\n" + + " \n" + + " \n" + + " \n" + + + " \n" + + "", + "\n" + + " all\n" + + " This community gathers research results, data, scientific publications and projects related to the domain of Digital Humanities. This broad definition includes Humanities, Cultural Heritage, History, Archaeology and related fields.\n" + + + " http://sanmamante.org/DH_CH_logo.png\n" + + " Digital Humanities and Cultural Heritage\n" + + " ileniagalluccio87@gmail.com,achille.felicetti@gmail.com,paolo.manghi@isti.cnr.it,tim.evans@york.ac.uk\n" + + + " modern art,monuments,europeana data model,sites,field walking,frescoes,LIDO metadata schema,art history,excavation,Arts and Humanities General,cities,coins,temples,numismatics,lithics,roads,environmental archaeology,digital cultural heritage,archaeological reports,history,CRMba,churches,cultural heritage,archaeological stratigraphy,religious art,buidings,digital humanities,survey,archaeological sites,linguistic studies,bioarchaeology,architectural orders,palaeoanthropology,fine arts,europeana,CIDOC CRM,decorations,classic art,stratigraphy,digital archaeology,intangible cultural heritage,walls,humanities,chapels,CRMtex,Language and Literature,paintings,archaeology,fair data,mosaics,burials,architecture,medieval art,castles,CARARE metadata schema,statues,natural language processing,inscriptions,CRMsci,vaults,contemporary art,Arts and Humanities,CRMarchaeo,pottery,site,architectural,vessels\n" + + + " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" + + + " oac_dh-ch\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + + " Pooling Activities, Resources and Tools for Heritage E-research Networking, Optimization and Synergies\n" + + + " The present work has been partially supported by the PARTHENOS project, funded by the European Commission (Grant Agreement No. 654119) under the HORIZON 2020 - INFRADEV-4-2014/2015 call\n" + + + " \n" + + " 654119\n" + + " http://www.parthenos-project.eu\n" + + " EC\n" + + " PARTHENOS\n" + + " \n" + + " \n" + + " \n" + + " \n" + + + " re3data_____::9ebe127e5f3a0bf401875690f3bb6b81\n" + + " The UK's largest collection of digital research data in the social sciences and humanities\n" + + + " UK Data Archive\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::c6cd4b532e12868c1d760a8d7cda6815\n" + + " Journal of Data Mining and Digital Humanities\n" + + " Journal of Data Mining and Digital Humanities\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b\n" + + " Frontiers in Digital Humanities\n" + + " Frontiers in Digital Humanities\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::6eb31d13b12bc06bbac06aef63cf33c9\n" + + " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" + + + " Il Capitale Culturale: Studies on the Value of Cultural Heritage\n" + + + " true\n" + + " \n" + + " \n" + + + " doajarticles::0da84e9dfdc8419576169e027baa8028\n" + + " Conservation Science in Cultural Heritage\n" + + " Conservation Science in Cultural Heritage\n" + + " true\n" + + " \n" + + " \n" + + + " re3data_____::84e123776089ce3c7a33db98d9cd15a8\n" + + " Electronic Archiving System\n" + + " EASY\n" + + " true\n" + + " \n" + + " \n" + + " openaire____::c5502a43e76feab55dd00cf50f519125\n" + + " DANS-KB Harvester\n" + + " Gemeenschappelijke Harvester DANS-KB\n" + + " true\n" + + " \n" + + " \n" + + " re3data_____::a48f09c562b247a9919acfe195549b47\n" + + " ads\n" + + " Archaeology Data Service\n" + + " true\n" + + " \n" + + " \n" + + " opendoar____::97275a23ca44226c9964043c8462be96\n" + + " KNAW Repository\n" + + " KNAW Repository\n" + + " true\n" + + " \n" + + " \n" + + + " doajarticles::2899208a99aa7d142646e0a80bfeef05\n" + + " Internet Archaeology\n" + + " Internet Archaeology\n" + + " true\n" + + " \n" + + " \n" + + " \n" + + "\n", + "\n" + + " all\n" + + " The neuroinformatics dashboard gathers research outputs from the 'neuroinformatics' community at large including the fields of: neuroscience, neuroinformatics, brain imaging databases and standards, brain imaging techniques, neuroimaging methods including statistics and machine learning. The dashboard covers a wide range of imaging methods including (but not limited to): MRI, TEP, EEG, MEG, and studies involving human participants as well as animal studies.\n" + + + " https://docs.google.com/drawings/u/0/d/10e191xGoGf4uaRluMqbt_7cCj6LSCs2a29im4CmWjqU/export/png\n" + + + " Neuroinformatics\n" + + " sorina.pop@creatis.insa-lyon.fr,camille.maumet@inria.fr,christian.barillot@irisa.fr,xavier.rolland@irisa.fr,axel.bonnet@creatis.insa-lyon.fr,paolo.manghi@isti.cnr.it\n" + + + " brain mapping,brain imaging,electroencephalography,arterial spin labelling,brain fingerprinting,brain,neuroimaging,Multimodal Brain Image Analysis,fMRI,neuroinformatics,fetal brain,brain ultrasonic imaging,topographic brain mapping,diffusion tensor imaging,computerized knowledge assessment,connectome mapping,brain magnetic resonance imaging,brain abnormalities\n" + + + " \n" + + " oac_ni\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + + " Formerly:OpenFMRI\n" + + " OpenNeuro\n" + + " true\n" + + " \n" + + " \n" + + " doajarticles::c7d3de67dc77af72f6747157441252ec\n" + + " Research Ideas and Outcomes\n" + + " Research Ideas and Outcomes\n" + + " true\n" + + " \n" + + " \n" + + " re3data_____::8515794670370f49c1d176c399c714f5\n" + + " Neuroimaging Informatics Tools and Resources Clearinghouse\n" + + + " NITRC\n" + + " true\n" + + " \n" + + " \n" + + " doajarticles::d640648c84b10d425f96f11c3de468f3\n" + + " Frontiers in Neuroinformatics\n" + + " Frontiers in Neuroinformatics\n" + + " true\n" + + " \n" + + " \n" + + " doajarticles::0c0e74daa5d95504eade9c81ebbd5b8a\n" + + " NeuroImage: Clinical\n" + + " NeuroImage: Clinical\n" + + " true\n" + + " \n" + + " \n" + + " rest________::fb1a3d4523c95e63496e3bc7ba36244b\n" + + " NeuroVault\n" + + " NeuroVault\n" + + " true\n" + + " \n" + + " \n" + + "\n", + "\n" + + " all\n" + + " Instruct-ERIC is the European Research Infrastructure for Structural Biology\n" + + + " https://instruct-eric.eu/templates/instructeric/images/logos/instruct-eric-logo-noline.png\n" + + + " Instruct-ERIC\n" + + " claudia@instruct-eric.eu,carazo@cnb.csic.es,echrysina@eie.gr,susan@instruct-eric.eu,naomi@instruct-eric.eu,natalie@instruct-eric.eu,pmarie@igbmc.fr,darren.hart@ibs.fr,claudia@strubi.ox.ac.uk,paolo.manghi@isti.cnr.it\n" + + + " \n" + + " The authors acknowledge the support and the use of resources of Instruct-ERIC.\n" + + + " The authors acknowledge the support and the use of resources of Instruct (PID # or APPID #), a Landmark ESFRI project\n" + + + " oac_instruct\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + + " Authentication and Authorisation For Research and Collaboration\n" + + + " \n" + + " 730941\n" + + " \n" + + " H2020-EINFRA-2016-1\n" + + " AARC2\n" + + " EC\n" + + " \n" + + " \n" + + + " Building data bridges between biological and medical infrastructures in Europe\n" + + + " \n" + + " 284209\n" + + " \n" + + " FP7-INFRASTRUCTURES-2011-1\n" + + " EC\n" + + " BioMedBridges\n" + + " \n" + + " \n" + + + " Transnational access and enhancement of integrated Biological Structure determination at synchrotron X-ray radiation facilities\n" + + + " \n" + + " 283570\n" + + " \n" + + " FP7-INFRASTRUCTURES-2011-1\n" + + " EC\n" + + " BioStruct-X\n" + + " \n" + + " \n" + + + " Coordinated Research Infrastructures Building Enduring Life-science services\n" + + + " \n" + + " 654248\n" + + " \n" + + " H2020-INFRADEV-1-2014-1\n" + + " EC\n" + + " CORBEL\n" + + " \n" + + " \n" + + + " Infrastructure for NMR, EM and X-rays for translational research\n" + + + " \n" + + " 653706\n" + + " \n" + + " H2020-INFRAIA-2014-2015\n" + + " EC\n" + + " iNEXT\n" + + " \n" + + " \n" + + + " Integrated Structural Biology Infrastructure\n" + + " \n" + + " 211252\n" + + " \n" + + " FP7-INFRASTRUCTURES-2007-1\n" + + " EC\n" + + " INSTRUCT\n" + + " \n" + + " \n" + + + " Releasing the full potential of Instruct to expand and consolidate infrastructure services for integrated structural life science research\n" + + + " \n" + + " 731005\n" + + " \n" + + " H2020-INFRADEV-2016-1\n" + + " EC\n" + + " INSTRUCT-ULTRA\n" + + " \n" + + " \n" + + + " Opening Synchrotron Light for Experimental Science and Applications in the Middle East\n" + + + " \n" + + " 730943\n" + + " \n" + + " H2020-INFRASUPP-2016-1\n" + + " EC\n" + + " OPEN SESAME\n" + + " \n" + + " \n" + + + " Infrastructure for Protein Production Platforms\n" + + + " \n" + + " 227764\n" + + " \n" + + " FP7-INFRASTRUCTURES-2008-1\n" + + " EC\n" + + " PCUBE\n" + + " \n" + + " \n" + + + " European Vaccine Research and Development Infrastructure\n" + + + " \n" + + " 730964\n" + + " \n" + + " H2020-INFRAIA-2016-1\n" + + " EC\n" + + " TRAMSVAC2\n" + + " \n" + + " \n" + + + " World-wide E-infrastructure for structural biology\n" + + + " \n" + + " 675858\n" + + " \n" + + " H2020-EINFRA-2015-1\n" + + " EC\n" + + " West-Life\n" + + " \n" + + " \n" + + " Expanding research infrastructure visibility to strengthen strategic partnerships\n" + + + " RI-VIS\n" + + " 824063\n" + + " EC\n" + + " corda__h2020::af93b591b76991d8437993a8f6fc6538\n" + + " \n" + + " \n" + + " \n" + + + " \n" + + + " \n" + + " instruct\n" + + " \n" + + " \n" + + " \n" + + + " west-life\n" + + " \n" + + " \n" + + " \n" + + " \n" + + + " \n" + + " FRISBI\n" + + " aHR0cDovL2ZyaXNiaS5ldS9zdGF0aWMvaW1hZ2VzL2xvZ29zL2xvZ28tZnJpc2JpLnBuZw==\n" + + + " aHR0cDovL2ZyaXNiaS5ldS8=\n" + + " \n" + + " \n" + + " RI-VIS\n" + + " aHR0cHM6Ly9yaS12aXMuZXUvbmV0d29yay9yaXZpcy90ZW1wbGF0ZXMvcml2aXMvaW1hZ2VzL1JJLVZJU0xvZ29GaW5hbC0wNi5wbmc=\n" + + + " aHR0cHM6Ly9yaS12aXMuZXU=\n" + + " \n" + + " \n" + + " CIISB\n" + + " aHR0cDovL2JpYy5jZWl0ZWMuY3ovZmlsZXMvMjkyLzEyNS5KUEc=\n" + + " aHR0cHM6Ly93d3cuY2lpc2Iub3Jn\n" + + " \n" + + " \n" + + "\n", + "\n" + + " all\n" + + " ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open, easily accessible and state -of- the- art services to the Greek and the international academic community and other stakeholders, such as industry and the health sector. More importantly, by providing these services, the infrastructure facilitates discoveries in the field of the life-sciences, having strong spill over effects in promoting innovation in sectors such as discovery of new drug targets and development of novel therapeutic agents, development of innovative diagnostics, personalized medicine, and development of innovative biotechnological products and processes.\n" + + + " https://elixir-greece.org/sites/default/files/ELIXIR_GREECE_white_background.png\n" + + + " The Greek National Node of the ESFRI European RI ELIXIR\n" + + " vergoulis@imis.athena-innovation.gr,schatz@imis.athena-innovation.gr,paolo.manghi@isti.cnr.it\n" + + + " \n" + + " \n" + + " oaa_elixir-gr\n" + + " 2018-03-01T12:00:00\n" + + " \n" + + " \n" + + + " \n" + + " rest________::b8e502674c3c3499d5374e9b2ea6d8d5\n" + + " bio.tools\n" + + " bio.tools\n" + + " false\n" + + " \n" + + " \n" + + " \n" + + " \n" + + + " \n" + + " \n" + + " ATHENA RC\n" + + " aHR0cHM6Ly9lbGl4aXItZ3JlZWNlLm9yZy9zaXRlcy9kZWZhdWx0L2ZpbGVzL3N0eWxlcy90aHVtYm5haWwvcHVibGljL3BhcnRuZXJfbG9nb3MvYXRoZW5hX2xvZ28uanBnP2l0b2s9VXdGWFNpZng=\n" + + + " aHR0cHM6Ly93d3cuYXRoZW5hLWlubm92YXRpb24uZ3IvZW4=\n" + + " \n" + + " \n" + + + ""); + + @Mock + private ISLookUpService isLookUpService; + + private QueryInformationSystem queryInformationSystem; + + private Map map; + + @BeforeEach + public void setUp() throws ISLookUpException { + lenient().when(isLookUpService.quickSearchProfile(XQUERY_ENTITY)).thenReturn(communityMap); + lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityContext); + queryInformationSystem = new QueryInformationSystem(); + queryInformationSystem.setIsLookUp(isLookUpService); + } + + @Test + public void testSizeEntity() throws ISLookUpException { + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.getContextInformation(consumer); + + Assertions.assertEquals(12, cInfoList.size()); + } + + @Test + public void testSizeRelation() throws ISLookUpException { + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.execContextRelationQuery(); + queryInformationSystem.getContextRelation(consumer, "contentproviders", "10|"); + + Assertions.assertEquals(5, cInfoList.size()); + } + + @Test + public void testContentRelation() throws ISLookUpException { + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.execContextRelationQuery(); + queryInformationSystem.getContextRelation(consumer, "contentproviders", "10"); + + cInfoList.forEach(contextInfo -> { + switch (contextInfo.getId()) { + case "elixir-gr": + Assertions.assertEquals(1, contextInfo.getDatasourceList().size()); + Assertions + .assertEquals( + "10|rest________::b8e502674c3c3499d5374e9b2ea6d8d5", + contextInfo.getDatasourceList().get(0)); + break; + case "instruct": + Assertions.assertEquals(0, contextInfo.getDatasourceList().size()); + break; + case "ni": + Assertions.assertEquals(6, contextInfo.getDatasourceList().size()); + Assertions + .assertTrue( + contextInfo + .getDatasourceList() + .contains("10|rest________::fb1a3d4523c95e63496e3bc7ba36244b")); + break; + case "dh-ch": + Assertions.assertEquals(10, contextInfo.getDatasourceList().size()); + break; + case "clarin": + Assertions.assertEquals(0, contextInfo.getDatasourceList().size()); + break; + } + }); + } + + @Test + public void testContentEntity() throws ISLookUpException { + + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + queryInformationSystem.getContextInformation(consumer); + + cInfoList.forEach(context -> { + switch (context.getId()) { + case "clarin":// clarin@@Common Language Resources and Technology Infrastructure@@CLARIN@@@@oac_clarin", + Assertions + .assertEquals("Common Language Resources and Technology Infrastructure", context.getName()); + Assertions.assertEquals("CLARIN", context.getDescription()); + Assertions + .assertTrue( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals("oac_clarin", context.getZenodocommunity()); + Assertions.assertEquals("ri", context.getType()); + break; + case "ee": + Assertions.assertEquals("Sustainable Development Solutions Network - Greece", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(17, context.getSubject().size()); + Assertions.assertEquals("oac_sdsn-greece", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + break; + case "dh-ch": + Assertions.assertEquals("Digital Humanities and Cultural Heritage", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(67, context.getSubject().size()); + Assertions.assertEquals("oac_dh-ch", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + break; + case "fam": + Assertions.assertEquals("Fisheries and Aquaculture Management", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith("Conservation of marine resources for sustainable development")); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(19, context.getSubject().size()); + Assertions.assertEquals("fisheries", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + break; + case "ni": + Assertions.assertEquals("Neuroinformatics", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith("The neuroinformatics dashboard gathers research outputs from the")); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(18, context.getSubject().size()); + Assertions.assertEquals("oac_ni", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + Assertions.assertTrue(context.getSubject().contains("brain")); + break; + case "mes": + Assertions.assertEquals("European Marine Science", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith( + "This community was initially defined to include a very broad range of topics")); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(5, context.getSubject().size()); + Assertions.assertEquals("oac_mes", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + Assertions.assertTrue(context.getSubject().contains("sea")); + Assertions.assertTrue(context.getSubject().contains("fish")); + Assertions.assertTrue(context.getSubject().contains("ocean")); + Assertions.assertTrue(context.getSubject().contains("aqua")); + Assertions.assertTrue(context.getSubject().contains("marine")); + break; + case "instruct": + Assertions.assertEquals("Instruct-ERIC", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .equals( + "Instruct-ERIC is the European Research Infrastructure for Structural Biology")); + Assertions + .assertTrue( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals("oac_instruct", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + + break; + case "elixir-gr": + Assertions + .assertEquals("The Greek National Node of the ESFRI European RI ELIXIR", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith( + "ELIXIR-GR enhances the potential of the Greek bioinformatics community to offer open")); + Assertions + .assertTrue( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals("oaa_elixir-gr", context.getZenodocommunity()); + Assertions.assertEquals("ri", context.getType()); + + break; + case "aginfra": + Assertions.assertEquals("Agricultural and Food Sciences", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith( + "The scope of this community is to provide access to publications, research data, projects and software")); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(18, context.getSubject().size()); + Assertions.assertEquals("oac_aginfra", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + Assertions.assertTrue(context.getSubject().contains("food distribution")); + break; + case "dariah": + Assertions.assertEquals("DARIAH EU", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith( + "The Digital Research Infrastructure for the Arts and Humanities (DARIAH) aims to enhance and support ")); + Assertions + .assertTrue( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + + Assertions.assertEquals("dariah", context.getZenodocommunity()); + Assertions.assertEquals("ri", context.getType()); + + break; + case "epos": + Assertions.assertEquals("European Plate Observing System", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith( + "EPOS, the European Plate Observing System, is a long-term plan to facilitate integrated use of ")); + Assertions + .assertTrue( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + + Assertions.assertEquals("", context.getZenodocommunity()); + Assertions.assertEquals("ri", context.getType()); + + break; + case "covid-19": + Assertions.assertEquals("Corona Virus Disease", context.getName()); + Assertions.assertTrue(context.getDescription().length() > 0); + Assertions + .assertTrue( + context + .getDescription() + .startsWith( + "This portal provides access to publications, research data, projects and ")); + Assertions + .assertFalse( + Optional + .ofNullable(context.getSubject()) + .map(value -> false) + .orElse(true)); + Assertions.assertEquals(25, context.getSubject().size()); + Assertions.assertEquals("covid-19", context.getZenodocommunity()); + Assertions.assertEquals("community", context.getType()); + Assertions.assertTrue(context.getSubject().contains("coronavirus disease 2019")); + break; + + } + }); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/RelationFromOrganizationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/RelationFromOrganizationTest.java new file mode 100644 index 0000000000..f4816bb79d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/graph/RelationFromOrganizationTest.java @@ -0,0 +1,120 @@ + +package eu.dnetlib.dhp.oa.graph.dump.graph; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.neethi.Assertion; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; +import eu.dnetlib.dhp.utils.DHPUtils; + +public class RelationFromOrganizationTest { + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(RelationFromOrganizationTest.class); + + private static HashMap map = new HashMap<>(); + + String organizationCommunityMap = "{\"20|grid________::afaa39865943381c51f76c08725ffa75\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e8dbe14cca9bf6fce09d468872f813f8\":[\"mes\",\"euromarine\"], \"20|snsf________::9b253f265e3bef5cae6d881fdf61aceb\":[\"mes\",\"euromarine\"],\"20|rcuk________::e054eea0a47665af8c3656b5785ccf76\":[\"mes\",\"euromarine\"],\"20|corda__h2020::edc18d67c9b11fb616ca9f6e1db1b151\":[\"mes\",\"euromarine\"],\"20|rcuk________::d5736d9da90521ddcdc7828a05a85e9a\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f5d418d3aa1cf817ddefcc3fdc039f27\":[\"mes\",\"euromarine\"],\"20|snsf________::8fa091f8f25a846779acb4ea97b50aef\":[\"mes\",\"euromarine\"],\"20|corda__h2020::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|corda_______::81e020977211c2c40fae2e1a50bffd71\":[\"mes\",\"euromarine\"],\"20|snsf________::31d0a100e54e3cdb3c6f52d91e638c78\":[\"mes\",\"euromarine\"],\"20|corda__h2020::ea379ef91b8cc86f9ac5edc4169292db\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f75ee2ee48e5cb0ec8c8d30aaa8fef70\":[\"mes\",\"euromarine\"],\"20|rcuk________::e16010089551a1a9182a94604fc0ea59\":[\"mes\",\"euromarine\"],\"20|corda__h2020::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|corda_______::38531a2cce7c5c347ffc439b07c1f43b\":[\"mes\",\"euromarine\"],\"20|grid________::b2cbbf5eadbbf87d534b022bad3191d7\":[\"mes\",\"euromarine\"],\"20|snsf________::74730ef1439d7f7636a8be58a6b471b8\":[\"mes\",\"euromarine\"],\"20|nsf_________::ad72e19043a5a467e35f9b444d11563e\":[\"mes\",\"euromarine\"],\"20|rcuk________::0fc3e92500290902a2d38ec2445e74c3\":[\"mes\",\"euromarine\"],\"20|grid________::ad2c29905da0eb3c06b3fa80cacd89ea\":[\"mes\",\"euromarine\"],\"20|corda__h2020::30b53e4d63d3724f00acb9cbaca40860\":[\"mes\",\"euromarine\"],\"20|corda__h2020::f60f84bee14ad93f0db0e49af1d5c317\":[\"mes\",\"euromarine\"], \"20|corda__h2020::7bf251ac3765b5e89d82270a1763d09f\":[\"mes\",\"euromarine\"], \"20|corda__h2020::65531bd11be9935948c7f2f4db1c1832\":[\"mes\",\"euromarine\"], \"20|corda__h2020::e0e98f86bbc76638bbb72a8fe2302946\":[\"mes\",\"euromarine\"], \"20|snsf________::3eb43582ac27601459a8d8b3e195724b\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af2481dab65d06c8ea0ae02b5517b9b6\":[\"mes\",\"euromarine\"], \"20|corda__h2020::c19d05cfde69a50d3ebc89bd0ee49929\":[\"mes\",\"euromarine\"], \"20|corda__h2020::af0bfd9fc09f80d9488f56d71a9832f0\":[\"mes\",\"euromarine\"], \"20|rcuk________::f33c02afb0dc66c49d0ed97ca5dd5cb0\":[\"beopen\"], " + + + "\"20|grid________::a867f78acdc5041b34acfe4f9a349157\":[\"beopen\"], \"20|grid________::7bb116a1a9f95ab812bf9d2dea2be1ff\":[\"beopen\"], \"20|corda__h2020::6ab0e0739dbe625b99a2ae45842164ad\":[\"beopen\"], \"20|corda__h2020::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda_______::8ba50792bc5f4d51d79fca47d860c602\":[\"beopen\"], \"20|corda__h2020::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::e70e9114979e963eef24666657b807c3\":[\"beopen\"], \"20|corda_______::15911e01e9744d57205825d77c218737\":[\"beopen\"], \"20|opendoar____::056a41e24e2a9a67215e87bbee6a80ab\":[\"beopen\"], \"20|opendoar____::7f67f2e6c6fbb0628f8160fcd3d92ae3\":[\"beopen\"], \"20|grid________::a8ecfd7c084e561168bcbe6bf0daf3e3\":[\"beopen\"], \"20|corda_______::7bbe6cc5d8ec1864739a04b0d020c9e9\":[\"beopen\"], \"20|corda_______::3ff558e30c2e434d688539548300b050\":[\"beopen\"], \"20|corda__h2020::5ffee5b3b83b33a8cf0e046877bd3a39\":[\"beopen\"], \"20|corda__h2020::5187217e2e806a6df3579c46f82401bc\":[\"beopen\"], \"20|grid________::5fa7e2709bcd945e26bfa18689adeec1\":[\"beopen\"], \"20|corda_______::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|corda__h2020::d8696683c53027438031a96ad27c3c07\":[\"beopen\"], \"20|rcuk________::23a79ebdfa59790864e4a485881568c1\":[\"beopen\"], \"20|corda__h2020::b76cf8fe49590a966953c37e18608af9\":[\"beopen\"], \"20|grid________::d2f0204126ee709244a488a4cd3b91c2\":[\"beopen\"], \"20|corda__h2020::05aba9d2ed17533d15221e5655ac11e6\":[\"beopen\"], \"20|grid________::802401579481dc32062bdee69f5e6a34\":[\"beopen\"], \"20|corda__h2020::3f6d9d54cac975a517ba6b252c81582d\":[\"beopen\"]}"; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(RelationFromOrganizationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(RelationFromOrganizationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(RelationFromOrganizationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/graph/relation") + .getPath(); + + SparkOrganizationRelation.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath, + "-organizationCommunityMap", organizationCommunityMap + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + + verificationDataset.createOrReplaceTempView("table"); + + Assertions.assertEquals(170, verificationDataset.count()); + + Dataset checkDs = spark + .sql( + "Select source.id, source.type " + + "from table "); + + Assertions.assertEquals(2, checkDs.filter("substr(id, 4, 5) = 'dedup' ").count()); + + Assertions.assertEquals(0, checkDs.filter("id = '20|grid________::afaa39865943381c51f76c08725ffa75'").count()); + + Assertions.assertEquals(25, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("beopen") + "'").count()); + + Assertions + .assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("euromarine") + "'").count()); + + Assertions.assertEquals(30, checkDs.filter("id = '00|context_____::" + DHPUtils.md5("mes") + "'").count()); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index b157f7ec6d..2c10f8f580 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -5,9 +5,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertFalse; import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertTrue; -import static org.mockito.ArgumentMatchers.anyString; import static org.mockito.Mockito.lenient; -import static org.mockito.Mockito.when; import java.io.IOException; import java.util.List; @@ -21,8 +19,9 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctionTest; -import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils; import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.Author; @@ -266,6 +265,50 @@ public class MappersTest { assertTrue(s.getInstance().size() > 0); } + // @Test + void testDataset_2() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_dataset_2.xml")); + + final List list = new OdfToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + } + + @Test + void testClaimDedup() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_dedup.xml")); + final List list = new OafToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + } + + @Test + void testNakala() throws IOException { + final String xml = IOUtils.toString(getClass().getResourceAsStream("odf_nakala.xml")); + final List list = new OdfToOafMapper(vocs, false).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + assertEquals(1, list.size()); + assertTrue(list.get(0) instanceof Dataset); + + final Dataset d = (Dataset) list.get(0); + + assertValidId(d.getId()); + assertValidId(d.getCollectedfrom().get(0).getKey()); + assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue())); + assertEquals(1, d.getAuthor().size()); + assertEquals(0, d.getSubject().size()); + assertEquals(1, d.getInstance().size()); + assertEquals(1, d.getPid().size()); + } + private void assertValidId(final String id) { assertEquals(49, id.length()); assertEquals('|', id.charAt(2)); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicateTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicateTest.java new file mode 100644 index 0000000000..a14fb4ae33 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/common/VerifyNsPrefixPredicateTest.java @@ -0,0 +1,92 @@ + +package eu.dnetlib.dhp.oa.graph.raw.common; + +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertTrue; + +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Field; +import eu.dnetlib.dhp.schema.oaf.Project; +import eu.dnetlib.dhp.schema.oaf.Relation; + +class VerifyNsPrefixPredicateTest { + + private VerifyNsPrefixPredicate predicate; + + @BeforeEach + void setUp() throws Exception { + predicate = new VerifyNsPrefixPredicate("corda,nsf,wt"); + } + + @Test + void testTestValue() { + assertFalse(predicate.testValue("corda__2020")); + assertFalse(predicate.testValue("nsf________")); + assertFalse(predicate.testValue("nsf")); + assertFalse(predicate.testValue("corda")); + assertFalse(predicate.testValue("10|corda_______::fjkdsfjksdhfksj")); + assertFalse(predicate.testValue("20|corda_______::fjkdsfjksdhfksj")); + + assertTrue(predicate.testValue("xxxxxx_____")); + assertTrue(predicate.testValue("10|xxxxxx_____::sdasdasaddasad")); + + assertTrue(predicate.testValue(null)); + assertTrue(predicate.testValue("")); + } + + @Test + void testTest_ds_true() { + final Field prefix = new Field<>(); + prefix.setValue("xxxxxx______"); + + final Datasource ds = new Datasource(); + ds.setNamespaceprefix(prefix); + + assertTrue(predicate.test(ds)); + } + + @Test + void testTest_ds_false() { + final Field prefix = new Field<>(); + prefix.setValue("corda__2020"); + + final Datasource ds = new Datasource(); + ds.setNamespaceprefix(prefix); + + assertFalse(predicate.test(ds)); + } + + @Test + void testTest_rel_true() { + final Relation rel = new Relation(); + rel.setSource("10|yyyyyy______:sdfsfsffsdfs"); + rel.setTarget("10|xxxxxx______:sdfsfsffsdfs"); + assertTrue(predicate.test(rel)); + } + + @Test + void testTest_rel_false() { + final Relation rel = new Relation(); + rel.setSource("10|corda_______:sdfsfsffsdfs"); + rel.setTarget("10|xxxxxx______:sdfsfsffsdfs"); + assertFalse(predicate.test(rel)); + } + + @Test + void testTest_proj_true() { + final Project p = new Project(); + p.setId("10|xxxxxx______:sdfsfsffsdfs"); + assertTrue(predicate.test(p)); + } + + @Test + void testTest_proj_false() { + final Project p = new Project(); + p.setId("10|corda_____:sdfsfsffsdfs"); + assertFalse(predicate.test(p)); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json index 5d0c0d1ed8..f51eed067d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json @@ -59,6 +59,28 @@ "schemename": "dnet:pid_types" }, "value": "qwerty" + }, + { + "dataInfo": { + "deletedbyinference": false, + "inferenceprovenance": "", + "inferred": false, + "invisible": false, + "provenanceaction": { + "classid": "sysimport:crosswalk:datasetarchive", + "classname": "sysimport:crosswalk:datasetarchive", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + }, + "trust": "0.9" + }, + "qualifier": { + "classid": "ORCID", + "classname": "ORCID", + "schemeid": "", + "schemename": "" + }, + "value": "asdasd" } ], "rank": 2, @@ -186,6 +208,9 @@ } ], "bestaccessright": null, + "publisher": { + "value": null + }, "collectedfrom": [ { "key": "10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747", diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt index 05484c8e50..729296522b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt @@ -951,6 +951,7 @@ dnet:countries @=@ ZW @=@ ABW dnet:protocols @=@ oai @=@ OAI-PMH dnet:protocols @=@ oai @=@ OAI_PMH dnet:pid_types @=@ orcid @=@ ORCID12 +dnet:pid_types @=@ handle @=@ hdl dnet:review_levels @=@ 0000 @=@ UNKNOWN dnet:review_levels @=@ 0002 @=@ 80 大阪経大学会「Working Paper」 dnet:review_levels @=@ 0002 @=@ AO diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index 59bed7c3a0..93cc00eca4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1045,6 +1045,7 @@ dnet:pid_types @=@ dnet:pid_types @=@ pmid @=@ pmid dnet:pid_types @=@ dnet:pid_types @=@ urn @=@ urn dnet:pid_types @=@ dnet:pid_types @=@ who @=@ WHO Identifier dnet:pid_types @=@ dnet:pid_types @=@ drks @=@ DRKS Identifier +dnet:pid_types @=@ dnet:pid_types @=@ handle @=@ Handle dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ACM @=@ An ACM classification term that can be associated to your publications dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/ARXIV @=@ An ARXIV classification term that can be associated to your publications dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/SUBJECT/DDC @=@ A Dewey Decimal classification term (DDC) that can be associated to your publications diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo new file mode 100644 index 0000000000..7f35634f53 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/preparedInfo @@ -0,0 +1,2 @@ +{"projectsList":[{"code":"123455","funder":{"jurisdiction":"FI","name":"Academy of Finland","shortName":"AKA"},"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach"},{"code":"119027","funder":{"fundingStream":"H2020","jurisdiction":"EU","name":"European Commission","shortName":"EC"},"id":"40|aka_________::03376222b28a3aebf2730ac514818d04","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"EGFR Tyrosine Kinase Inhibitors and LKB1 Tumor Suppressor in Non-Small-Cell Lung Cancer"}],"resultId":"50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb"} +{"projectsList":[{"code":"123455","funder":{"jurisdiction":"FI","name":"Academy of Finland","shortName":"AKA"},"id":"40|aka_________::0f7d119de1f656b5763a16acf876fed6","provenance":{"provenance":"sysimport:crosswalk:entityregistry","trust":"0.900000000000000022"},"title":"Business services for rural bioenergy entrepreneurship in Finland: a network analysis approach"}],"resultId":"50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo/software.json 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Исследование кластеров, как инструмент управления АПК отдельного региона, в частности Кабардино-Балкарской Республики, позволяет выявить факторы, обуславливающие необходимость данного процесса с одной стороны, а также выявлять резервы и иные возможности для общего развития эффективности АПК России и активации внедрения инновационных механизмов в сельское хозяйство."},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"The Article is devoted to the study of the concept of cluster and their use as a management tool to improve the efficiency of the agro-industrial complex of the KabardinoBalkaria Republic. The prerequisites and features of agribusiness clustering both in a separate region and in Russia as a whole are considered. 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Whereas there are several different web-based predictors for \u03b1-helical membrane proteins, currently there is no freely available prediction method for \u03b2-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of \u03b2-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. 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TR3959 + Doğuş Üniversitesi, Fen Edebiyat Fakültesi, Fizik Bölümü + TR3959 + urn:issn:1748-0221 + VOLUME=7;ISSUE=1;ISSN=1748-0221;TITLE=Journal of Instrumentation + ATLAS Collaboration Mitsou, Vasiliki Fiorini, Luca Ros Martínez, Eduardo Castillo + Giménez, María Victoria Fuster Verdú, Juan A. García García, Carmen Cabrera Urbán, + Susana Martí García, Salvador Salt Cairols, José Lacasta Llácer, Carlos Valls Ferrer, + Juan Antonio Higón Rodríguez, Emilio Ferrer Soria, Antonio González de la Hoz, Santiago + Kaci, Mohammed Hernández Jiménez, Yesenia Villaplana Pérez, Miguel 2012 A study of the + material in the ATLAS inner detector using secondary hadronic interactions Journal Of + Instrumentation 7 P01013 1 41 + Journal of Instrumentation, 7(1) + Aad, G; Abbott, B; Abdallah, J; Abdelalim, AA; Abdesselam, A; Abdinov, O;  et + al.(2012). A study of the material in the ATLAS inner detector using secondary hadronic + interactions. Journal of Instrumentation, 7(1). doi: 10.1088/1748-0221/7/01/P01013. UC + Santa Cruz: Retrieved from: http://www.escholarship.org/uc/item/05j2j2br + Journal of Instrumentation, 7 + VOLUME=7;ISSN=1748-0221;TITLE=Journal of Instrumentation + 1748-0221 + Journal of Instrumentation 7, P01013 (2012). + doi:10.1088/1748-0221/7/01/P01013 + A measurement of the material in the ATLAS inner detector using secondary hadronic + interactions + und + Detector modelling and simulations I + (interaction of radiation with matter, interaction of photons with matter, interaction + of hadrons with matter, etc); Particle tracking detectors (Solid-state detectors); Si + microstrip and pad detectors; Large detector systems for particle and astroparticle + physics + of photons with matter, interaction of + hadrons with matter, etc) + Particle Physics - Experiment + Detector Modelling and + Simulations + Detector modelling and simulations I + (interaction of radiation with matter, interaction of photons with matter, interaction + of hadrons with matter, etc) + Large detector systems for particle and + astroparticle physics + Detector modelling and simulations I + (interaction of radiation with matter, interaction + Large Detector Systems + 530 + Science & Technology + :Ciências Físicas [Ciências + Naturais] + High Energy Physics - + Experiment + Detectors de radiació + Física nuclear + ddc:610 + Si microstrip and pad + detectors + Particle tracking detectors (Solid-state + detectors) + Col·lisions (Física nuclear) + Particle Tracking Detectors + IOP Publishing + application/pdf + application/pdf + application/pdf + application/pdf + application/pdf + application/pdf + 2016-05-02 + The ATLAS inner detector is used to reconstruct secondary vertices due to + hadronic interactions of primary collision products, so probing the location and amount + of material in the inner region of ATLAS. Data collected in 7 TeV pp collisions at the + LHC, with a minimum bias trigger, are used for comparisons with simulated events. The + reconstructed secondary vertices have spatial resolutions ranging from ~ 200μm to 1 mm. + The overall material description in the simulation is validated to within an + experimental uncertainty of about 7%. This will lead to a better understanding of the + reconstruction of various objects such as tracks, leptons, jets, and missing transverse + momentum. We acknowledge the support of ANPCyT, Argentina; YerPhI, Armenia; ARC, + Australia; BMWF, Austria; ANAS, Azerbaijan; SSTC, Belarus; CNPq and FAPESP, Brazil; + NSERC, NRC and CFI, Canada; CERN; CONICYT, Chile; CAS, MOST and NSFC, China; + COLCIENCIAS, Colombia; MSMT CR, MPO CR and VSC CR, Czech Republic; DNRF, DNSRC and + Lundbeck Foundation, Denmark; ARTEMIS, European Union; IN2P3-CNRS, CEA-DSM/IRFU, France; + GNAS, Georgia; BMBF, DFG, HGF, MPG and AvH Foundation, Germany; GSRT, Greece; ISF, + MINERVA, GIF, DIP and Benoziyo Center, Israel; INFN, Italy; MEXT and JSPS, Japan; CNRST, + Morocco; FOM and NWO, Netherlands; RCN, Norway; MNiSW, Poland; GRICES and FCT, Portugal; + MERYS (MECTS), Romania; MES of Russia and ROSATOM, Russian Federation; JINR; MSTD, + Serbia; MSSR, Slovakia; ARRS and MVZT, Slovenia; DST/NRF, South Africa; MICINN, Spain; + SRC and Wallenberg Foundation, Sweden; SER, SNSF and Cantons of Bern and Geneva, + Switzerland; NSC, Taiwan; TAEK, Turkey; STFC, the Royal Society and Leverhulme Trust, + United Kingdom; DOE and NSF, United States of America. + info:eu-repo/semantics/publishedVersion + NARCIS + DSpace@Dogus + Lancaster EPrints + CERN Document Server + DESY Publication Database + OpenAIRE + Publikationenserver der Georg-August-Universität Göttingen + arXiv.org e-Print Archive + CORE (RIOXX-UK Aggregator) + eScholarship - University of California + Universidade do Minho: RepositoriUM + Dokuz Eylul University Open Archive System + Repositori d'Objectes Digitals per a l'Ensenyament la Recerca i la + Cultura + info:eu-repo/semantics/altIdentifier/doi/10.1088/1748-0221/7/01/P01013 + info:eu-repo/semantics/altIdentifier/doi/10.1088/1748-0221/7/01/P01013. + Article + http://hdl.handle.net/11376/1605 + Article + http://www.escholarship.org/uc/item/05j2j2br + Unknown + http://cds.cern.ch/record/1394292 + Article + http://eprints.lancs.ac.uk/68235/ + Article + http://hdl.handle.net/10550/36188 + Article + http://eprints.gla.ac.uk/65933/1/65933.pdf + Preprint + http://arxiv.org/abs/1110.6191 + Article + http://dare.uva.nl/personal/pure/en/publications/a-study-of-the-material-in-the-atlas-inner-detector-using-secondary-hadronic-interactions(6b7667e2-04e2-4a66-92a8-ff4edbf61a17).html + Article + http://hdl.handle.net/1822/48768 + Article + http://resolver.sub.uni-goettingen.de/purl?gs-1/12231 + Article + http://bib-pubdb1.desy.de/search?p=id:%22PHPPUBDB-21212%22 + http://bib-pubdb1.desy.de/record/96807/files/CERN-PH-EP-2011-147_1110.6191v2.pdf + http://bib-pubdb1.desy.de//record/96807/files/CERN-PH-EP-2011-147_1110.6191v2.pdf + http://bib-pubdb1.desy.de/record/96807 + Article + http://arxiv.org/abs/1110.6191 + Article + http://hdl.handle.net/11376/1605 + http://dx.doi.org/10.1088/1748-0221/7/01/P01013 + Article + http://hdl.handle.net/2066/93736 + ATLAS Collaboration + 0001 + 0002 + 2016-05-02 + OPEN + und + + + + + + + + + file%3A%2F%2F%2Fsrv%2Fclaims%2Frecords%2Fpublication%2Fopenaire + + + + + + + false + false + 0.9 + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset_2.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset_2.xml new file mode 100644 index 0000000000..17a87bcb7a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset_2.xml @@ -0,0 +1,75 @@ + + + + opentrials__::0000bf8e63d3d7e6b88421eabafae3f6 + feabb67c-1fd1-423b-aec6-606d04ce53c6 + 2019-03-27T15:15:22.22Z + opentrials__ + 2019-04-17T16:04:20.586Z + + + + https://clinicaltrials.gov/ct2/show/NCT02321059 + + http://apps.who.int/trialsearch/Trial3.aspx?trialid=NCT02321059 + NCT02321059 + + + + Jensen, Kristian K + + + + Validation of the Goodstrength System for Assessment of Abdominal Wall Strength in Patients With Incisional Hernia + + nct + + Denmark + + 0037 + + Patients with an incisional hernia in the midline and controls with an intact abdominal wall are examined twice with one week apart, in order to establish the test-retest reliability and internal and external validity of the Goodstrength trunk dynamometer. + + + OPEN + 0037 + 2014-11-11 + + + + + false + false + 0.9 + + + + + + + + + file:///var/lib/dnet/data/opentrials/opentrials.csv + + + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_nakala.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_nakala.xml new file mode 100644 index 0000000000..105d0c413f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_nakala.xml @@ -0,0 +1,88 @@ + + + + r3f5b9831893::cca7367159bc3ff90cd2f75bf9dc21c4 + oai:nakala.fr:hdl_11280_847e01df + 2020-08-01T00:16:24.742Z + r3f5b9831893 + oai:nakala.fr:hdl_11280_847e01df + 2020-06-08T01:01:38Z + hdl_11280_2b09fc10 + hdl_11280_c1bc48d0 + hdl_11280_57c8db3a + 2020-08-01T00:31:35.625Z + + + + 277 + http://hdl.handle.net/11280/847e01df + + http://hdl.handle.net/http://hdl.handle.net/11280/847e01df + + http://nakala.fr/data/11280/847e01df + + + DHAAP + + + + CVP_Notice277-1 place du Docteur Antoine Béclère _PHO02.jpg + + + Hôpital Saint-Antoine. Fragment de dalle funéraire trouvée en décembre 1932. Paris (XIIème arr.). Photographie d'Albert Citerne (1876-1970). Plaque de verre, 1932. Département Histoire de l'Architecture et Archéologie de Paris. + Nfa_1146 + Hôpital Saint-Antoine. Fragment de dalle funéraire trouvée en décembre 1932. Paris (XIIème arr.). Photographie d'Albert Citerne (1876-1970). Plaque de verre, 1932. Département Histoire de l'Architecture et Archéologie de Paris. + + Nakala by Huma-Num + + + DHAAP, Pôle Archéologique + + + + 1932 + + StillImage + + + + + http://hdl.handle.net/11280/847e01df + 0025 + + OPEN + und + + + + + + + https%3A%2F%2Fwww.nakala.fr%2Foai_oa%2F11280%2F8892ab4b + oai:nakala.fr:hdl_11280_847e01df + 2020-06-08T01:01:38Z + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/dmf.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/dmf.xml index 58defb67bc..836e0b9a09 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/dmf.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/dmf.xml @@ -1,66 +1,53 @@ - - aaadf8b3-01a8-4cc2-9964-63cfb19df3b4_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU= - oai:pangaea.de:doi:10.1594/PANGAEA.821876 - r3d100010134 - r3d100010134::000083be706192d2d839915694ecfd47 -2020-01-08T04:12:12.287 - 2020-01-08T03:24:10.865Z - - oai:pangaea.de:doi:10.1594/PANGAEA.821876 - citable - - - - 10.1594/pangaea.821876 - Macke, AndreasKalisch, John - Total Sky Imager observations during POLARSTERN cruise ANT-XXVI/4 on 2010-05-14 with links to images - -PANGAEA - Data Publisher for Earth & Environmental Science - - 2010-05-14T00:13:47/2010-05-14T23:55:47 - - - - DATE/TIME - - LATITUDE - - LONGITUDE - - Uniform resource locator/link to image - - Total Sky Imager - - ANT-XXVI/4 - - Polarstern - - - dataset - - - dli_resolver::cf447a378b0b6603593f8b0e57242695 - - http://hs.pangaea.de/images/airphoto/ps/ps75/2010-05-14/ant-xxvi_4_2010-05-14_tsi-images-links.zip - - dli_resolver::f0f5975d20991cffd222c6002ddd5821 - - - - - - - complete - - - - - - - - + xmlns:oaf="http://namespace.openaire.eu/oaf" + xmlns:dri="http://www.driver-repository.eu/namespace/dri" + xmlns:dc="http://purl.org/dc/elements/1.1/"> + + aaadf8b3-01a8-4cc2-9964-63cfb19df3b4_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU= + oai:pangaea.de:doi:10.1594/PANGAEA.432865 + r3d100010134 + r3d100010134::00002f60593fd1f758fb838fafb46795 + 2020-02-18T03:05:02.534Z + + oai:pangaea.de:doi:10.1594/PANGAEA.432865 + citable topicOceans + + + + 10.1594/pangaea.432865 + + Daily sea level from coastal tide gauge station Woods_Hole in 1978 (Research quality database) + + PANGAEA - Data Publisher for Earth & Environmental Science + 2006 + + 1978-01-01T12:00:00/1978-12-31T12:00:00 + + + + WOCE Sea Level, WSL + + + + DATE/TIME + Sea level + Tide gauge station + SeaLevel + World Ocean Circulation Experiment (WOCE) + + + + http://store.pangaea.de/Projects/WOCE/SeaLevel_rqds/Woods_Hole.txt + + + + + + + complete + collected + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala index 86b68fbd2a..abac41b89a 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala @@ -6,7 +6,7 @@ import java.time.format.DateTimeFormatter import eu.dnetlib.dhp.common.PacePerson import eu.dnetlib.dhp.schema.action.AtomicAction import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty} -import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import eu.dnetlib.dhp.utils.DHPUtils import org.apache.commons.lang3.StringUtils import org.codehaus.jackson.map.ObjectMapper @@ -46,7 +46,7 @@ object DLIToOAF { "IsReferencedBy" -> ("isRelatedTo", "relationship"), "References" -> ("isRelatedTo", "relationship"), "IsRelatedTo" -> ("isRelatedTo", "relationship"), - "IsSupplementedBy" -> ("IsSupplementedBy", "supplement"), + "IsSupplementedBy" -> ("isSupplementedBy", "supplement"), "Cites" -> ("cites", "citation"), "Unknown" -> ("isRelatedTo", "relationship"), "IsSourceOf" -> ("isRelatedTo", "relationship"), @@ -273,29 +273,29 @@ object DLIToOAF { } - def convertDLIRelation(r: DLIRelation): Relation = { - - val result = new Relation - if (!relationTypeMapping.contains(r.getRelType)) - return null - - if (r.getCollectedFrom == null || r.getCollectedFrom.size() == 0 || (r.getCollectedFrom.size() == 1 && r.getCollectedFrom.get(0) == null)) - return null - val t = relationTypeMapping.get(r.getRelType) - - result.setRelType("resultResult") - result.setRelClass(t.get._1) - result.setSubRelType(t.get._2) - result.setCollectedfrom(r.getCollectedFrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava) - result.setSource(generateId(r.getSource)) - result.setTarget(generateId(r.getTarget)) - - if (result.getSource.equals(result.getTarget)) - return null - result.setDataInfo(generateDataInfo()) - - result - } +// def convertDLIRelation(r: DLIRelation): Relation = { +// +// val result = new Relation +// if (!relationTypeMapping.contains(r.getRelType)) +// return null +// +// if (r.getProperties == null || r.getProperties.size() == 0 || (r.getProperties.size() == 1 && r.getProperties.get(0) == null)) +// return null +// val t = relationTypeMapping.get(r.getRelType) +// +// result.setRelType("resultResult") +// result.setRelClass(t.get._1) +// result.setSubRelType(t.get._2) +// result.setCollectedfrom(r.getProperties.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava) +// result.setSource(generateId(r.getSource)) +// result.setTarget(generateId(r.getTarget)) +// +// if (result.getSource.equals(result.getTarget)) +// return null +// result.setDataInfo(generateDataInfo()) +// +// result +// } def convertDLIDatasetTOOAF(d: DLIDataset): Dataset = { diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala index fd8f2d136d..165c3340b3 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala @@ -2,7 +2,7 @@ package eu.dnetlib.dhp.`export` import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset} -import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import org.apache.commons.io.IOUtils import org.apache.hadoop.io.Text import org.apache.hadoop.io.compress.GzipCodec @@ -39,14 +39,13 @@ object SparkExportContentForOpenAire { implicit val pubEncoder: Encoder[Publication] = Encoders.bean(classOf[Publication]) implicit val datEncoder: Encoder[OafDataset] = Encoders.bean(classOf[OafDataset]) implicit val relEncoder: Encoder[Relation] = Encoders.bean(classOf[Relation]) - implicit val dliRelEncoder: Encoder[DLIRelation] = Encoders.bean(classOf[DLIRelation]) + import spark.implicits._ val relRDD:RDD[Relation] = sc.textFile(s"$workingPath/relation_j") - .map(s => new ObjectMapper().readValue(s, classOf[DLIRelation])) + .map(s => new ObjectMapper().readValue(s, classOf[Relation])) .filter(p => p.getDataInfo.getDeletedbyinference == false) - .map(DLIToOAF.convertDLIRelation).filter(p=>p!= null) spark.createDataset(relRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS") val datRDD:RDD[OafDataset] = sc.textFile(s"$workingPath/dataset") diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java new file mode 100644 index 0000000000..1b5849f356 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DropAndCreateESIndex.java @@ -0,0 +1,97 @@ + +package eu.dnetlib.dhp.provision; + +import java.util.Map; + +import org.apache.commons.io.IOUtils; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpDelete; +import org.apache.http.client.methods.HttpPut; +import org.apache.http.entity.StringEntity; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; +import org.codehaus.jackson.map.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class DropAndCreateESIndex { + + public static void main(String[] args) throws Exception { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + DropAndCreateESIndex.class + .getResourceAsStream( + "/eu/dnetlib/dhp/provision/dropAndCreateIndex.json"))); + parser.parseArgument(args); + + final String index = parser.get("index"); + + final String cluster = parser.get("cluster"); + final String clusterJson = IOUtils + .toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/cluster.json")); + + final Map clusterMap = new ObjectMapper().readValue(clusterJson, Map.class); + + final String ip = clusterMap.get(cluster).split(",")[0]; + + System.out.println(ip); + + final String url = "http://%s:9200/%s_%s"; + + CloseableHttpClient client = HttpClients.createDefault(); + + HttpDelete delete = new HttpDelete(String.format(url, ip, index, "object")); + + CloseableHttpResponse response = client.execute(delete); + + System.out.println("deleting Index SUMMARY"); + System.out.println(response.getStatusLine()); + client.close(); + client = HttpClients.createDefault(); + + delete = new HttpDelete(String.format(url, ip, index, "scholix")); + + response = client.execute(delete); + + System.out.println("deleting Index SCHOLIX"); + System.out.println(response.getStatusLine()); + client.close(); + client = HttpClients.createDefault(); + + final String summaryConf = IOUtils + .toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/summary_index.json")); + + final String scholixConf = IOUtils + .toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/scholix_index.json")); + + HttpPut put = new HttpPut(String.format(url, ip, index, "object")); + + StringEntity entity = new StringEntity(summaryConf); + put.setEntity(entity); + put.setHeader("Accept", "application/json"); + put.setHeader("Content-type", "application/json"); + + System.out.println("creating First Index SUMMARY"); + response = client.execute(put); + + client.close(); + client = HttpClients.createDefault(); + + System.out.println(response.getStatusLine()); + + System.out.println("creating Index SCHOLIX"); + put = new HttpPut(String.format(url, ip, index, "scholix")); + + entity = new StringEntity(scholixConf); + put.setEntity(entity); + put.setHeader("Accept", "application/json"); + put.setHeader("Content-type", "application/json"); + + response = client.execute(put); + System.out.println(response.getStatusLine()); + client.close(); + + } +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala new file mode 100644 index 0000000000..81bdb29418 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala @@ -0,0 +1,38 @@ +package eu.dnetlib.dhp.provision + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.provision.scholix.Scholix +import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary +import org.apache.commons.io.IOUtils +import org.apache.hadoop.io.compress.GzipCodec +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} +import org.codehaus.jackson.map.ObjectMapper + +object SparkConvertDatasetToJson { + + def main(args: Array[String]): Unit = { + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertDatasetToJson.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/dataset2Json.json"))) + parser.parseArgument(args) + val conf = new SparkConf + val spark = SparkSession.builder.config(conf).appName(SparkConvertDatasetToJson.getClass.getSimpleName).master(parser.get("master")).getOrCreate + + implicit val summaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] + implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix] + + + val workingPath = parser.get("workingPath") + + + + spark.read.load(s"$workingPath/summary").as[ScholixSummary] + .map(s => new ObjectMapper().writeValueAsString(s))(Encoders.STRING) + .rdd.repartition(500).saveAsTextFile(s"$workingPath/summary_json", classOf[GzipCodec]) + + spark.read.load(s"$workingPath/scholix").as[Scholix] + .map(s => new ObjectMapper().writeValueAsString(s))(Encoders.STRING) + .rdd.repartition(2000).saveAsTextFile(s"$workingPath/scholix_json", classOf[GzipCodec]) + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java deleted file mode 100644 index df167f104f..0000000000 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.java +++ /dev/null @@ -1,34 +0,0 @@ - -package eu.dnetlib.dhp.provision; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.sql.*; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -/** - * SparkExtractRelationCount is a spark job that takes in input relation RDD and retrieve for each item in relation - * which are the number of - Related Dataset - Related Publication - Related Unknown - */ -public class SparkExtractRelationCount { - - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkExtractRelationCount.class - .getResourceAsStream( - "/eu/dnetlib/dhp/provision/input_related_entities_parameters.json"))); - parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkExtractRelationCount.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - - final String workingDirPath = parser.get("workingDirPath"); - - final String relationPath = parser.get("relationPath"); - DatasetJoiner.startJoin(spark, relationPath, workingDirPath + "/relatedItemCount"); - } -} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DatasetJoiner.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.scala similarity index 53% rename from dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DatasetJoiner.scala rename to dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.scala index afc33c34a3..d6e36ac877 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/DatasetJoiner.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkExtractRelationCount.scala @@ -1,12 +1,32 @@ package eu.dnetlib.dhp.provision -import org.apache.spark.sql.SparkSession +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.schema.oaf.Relation +import org.apache.commons.io.IOUtils +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.apache.spark.sql.functions.{coalesce, col, count, lit} -object DatasetJoiner { - def startJoin(spark: SparkSession, relPath:String, targetPath:String) { - val relation = spark.read.load(relPath) +/** + * SparkExtractRelationCount is a spark job that takes in input relation RDD and retrieve for each item in relation + * which are the number of - Related Dataset - Related Publication - Related Unknown + */ +object SparkExtractRelationCount { + + + def main(args: Array[String]): Unit = { + + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExtractRelationCount.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/input_related_entities_parameters.json"))) + parser.parseArgument(args) + val spark = SparkSession.builder.appName(SparkExtractRelationCount.getClass.getSimpleName).master(parser.get("master")).getOrCreate + + val workingDirPath = parser.get("workingDirPath") + + val relationPath = parser.get("relationPath") + + implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation] + + val relation = spark.read.load(relationPath).as[Relation].map(r =>r)(Encoders.bean(classOf[Relation])) val relatedPublication = relation .where("target like '50%'") @@ -34,7 +54,7 @@ object DatasetJoiner { coalesce(col("dataset"),lit(0)).alias("relatedDataset"), coalesce(col("unknown"),lit(0)).alias("relatedUnknown") ) - firstJoin.write.mode("overwrite").save(targetPath) + firstJoin.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/relatedItemCount") } } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java deleted file mode 100644 index f9f3a58ce6..0000000000 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholix.java +++ /dev/null @@ -1,109 +0,0 @@ - -package eu.dnetlib.dhp.provision; - -import org.apache.commons.io.IOUtils; -import org.apache.hadoop.io.compress.GzipCodec; -import org.apache.spark.SparkConf; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SaveMode; -import org.apache.spark.sql.SparkSession; - -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.provision.scholix.*; -import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; -import eu.dnetlib.dhp.schema.oaf.Relation; -import scala.Tuple2; - -public class SparkGenerateScholix { - - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkGenerateScholix.class - .getResourceAsStream( - "/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))); - parser.parseArgument(args); - SparkConf conf = new SparkConf(); - conf.set("spark.sql.shuffle.partitions", "4000"); - conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); - final SparkSession spark = SparkSession - .builder() - .config(conf) - .appName(SparkExtractRelationCount.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - - conf - .registerKryoClasses( - new Class[] { - Scholix.class, ScholixCollectedFrom.class, ScholixEntityId.class, - ScholixIdentifier.class, ScholixRelationship.class, ScholixResource.class - }); - - final String graphPath = parser.get("graphPath"); - final String workingDirPath = parser.get("workingDirPath"); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - final Dataset scholixSummary = spark - .read() - .load(workingDirPath + "/summary") - .as(Encoders.bean(ScholixSummary.class)); - final Dataset rels = spark.read().load(graphPath + "/relation").as(Encoders.bean(Relation.class)); - - Dataset firstJoin = scholixSummary - .joinWith(rels, scholixSummary.col("id").equalTo(rels.col("source"))) - .map( - (MapFunction, Scholix>) f -> Scholix - .generateScholixWithSource(f._1(), f._2()), - Encoders.bean(Scholix.class)); - - firstJoin.write().mode(SaveMode.Overwrite).save(workingDirPath + "/scholix_1"); - - Dataset scholix_final = spark - .read() - .load(workingDirPath + "/scholix_1") - .as(Encoders.bean(Scholix.class)); - - scholixSummary - .map( - (MapFunction) ScholixResource::fromSummary, - Encoders.bean(ScholixResource.class)) - .repartition(1000) - .write() - .mode(SaveMode.Overwrite) - .save(workingDirPath + "/scholix_target"); - - Dataset target = spark - .read() - .load(workingDirPath + "/scholix_target") - .as(Encoders.bean(ScholixResource.class)); - - scholix_final - .joinWith( - target, scholix_final.col("identifier").equalTo(target.col("dnetIdentifier")), "inner") - .map( - (MapFunction, Scholix>) f -> { - final Scholix scholix = f._1(); - final ScholixResource scholixTarget = f._2(); - scholix.setTarget(scholixTarget); - scholix.generateIdentifier(); - scholix.generatelinkPublisher(); - return scholix; - }, - Encoders.kryo(Scholix.class)) - .javaRDD() - .map( - s -> { - ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(s); - }) - .saveAsTextFile(workingDirPath + "/scholix_json", GzipCodec.class); - } -} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholixIndex.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholixIndex.scala new file mode 100644 index 0000000000..dbf6de05f3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateScholixIndex.scala @@ -0,0 +1,62 @@ +package eu.dnetlib.dhp.provision + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.provision.scholix.{Scholix, ScholixResource} +import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary +import eu.dnetlib.dhp.schema.oaf.Relation +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} + +object SparkGenerateScholixIndex { + + + def main(args: Array[String]): Unit = { + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateScholixIndex.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))) + parser.parseArgument(args) + val conf = new SparkConf + conf.set("spark.sql.shuffle.partitions", "4000") + val spark = SparkSession.builder.config(conf).appName(SparkGenerateScholixIndex.getClass.getSimpleName).master(parser.get("master")).getOrCreate + + val graphPath = parser.get("graphPath") + val workingDirPath = parser.get("workingDirPath") + + + implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] + implicit val relEncoder:Encoder[Relation] = Encoders.kryo[Relation] + implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix] + implicit val tupleScholix:Encoder[(String,Scholix)]=Encoders.tuple(Encoders.STRING, scholixEncoder) + + + val scholixSummary:Dataset[(String,ScholixSummary)] = spark.read.load(s"$workingDirPath/summary").as[ScholixSummary] + .map(s => (s.getId, s))(Encoders.tuple(Encoders.STRING, summaryEncoder)) + val sourceRelations:Dataset[(String,Relation)]= spark.read.load(s"$graphPath/relation").as[Relation] + .map(r => (r.getSource,r))(Encoders.tuple(Encoders.STRING, relEncoder)) + + scholixSummary.joinWith(sourceRelations, scholixSummary("_1").equalTo(sourceRelations("_1")), "inner") + .map(r=> { + val summary = r._1._2 + val relation = r._2._2 + + (relation.getTarget, Scholix.generateScholixWithSource(summary,relation)) + + }).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/scholix_source") + + val sTarget:Dataset[(String,Scholix)] = spark.read.load(s"$workingDirPath/scholix_source").as[(String, Scholix)] + + sTarget.joinWith(scholixSummary, sTarget("_1").equalTo(scholixSummary("_1")), "inner").map(i => { + val summary = i._2._2 + val scholix = i._1._2 + + val scholixResource = ScholixResource.fromSummary(summary) + scholix.setTarget(scholixResource) + scholix.generateIdentifier() + scholix.generatelinkPublisher() + scholix + }).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/scholix") + + + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java deleted file mode 100644 index 04bde10996..0000000000 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummary.java +++ /dev/null @@ -1,106 +0,0 @@ - -package eu.dnetlib.dhp.provision; - -import org.apache.commons.io.IOUtils; -import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Dataset; -import org.apache.spark.sql.Encoders; -import org.apache.spark.sql.SparkSession; - -import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; -import eu.dnetlib.dhp.utils.DHPUtils; -import scala.Tuple2; - -public class SparkGenerateSummary { - - private static final String jsonIDPath = "$.id"; - - public static void main(String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - SparkGenerateSummary.class - .getResourceAsStream( - "/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))); - parser.parseArgument(args); - final SparkSession spark = SparkSession - .builder() - .appName(SparkExtractRelationCount.class.getSimpleName()) - .master(parser.get("master")) - .getOrCreate(); - - final String graphPath = parser.get("graphPath"); - final String workingDirPath = parser.get("workingDirPath"); - - final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - - Dataset rInfo = spark - .read() - .load(workingDirPath + "/relatedItemCount") - .as(Encoders.bean(RelatedItemInfo.class)); - - Dataset entity = spark - .createDataset( - sc - .textFile( - graphPath + "/publication," + graphPath + "/dataset," + graphPath + "/unknown") - .map( - s -> ScholixSummary - .fromJsonOAF( - ProvisionUtil.getItemTypeFromId(DHPUtils.getJPathString(jsonIDPath, s)), - s)) - .rdd(), - Encoders.bean(ScholixSummary.class)); - - Dataset summaryComplete = rInfo - .joinWith(entity, rInfo.col("source").equalTo(entity.col("id"))) - .map( - (MapFunction, ScholixSummary>) t -> { - ScholixSummary scholixSummary = t._2(); - RelatedItemInfo relatedItemInfo = t._1(); - scholixSummary.setRelatedDatasets(relatedItemInfo.getRelatedDataset()); - scholixSummary - .setRelatedPublications( - relatedItemInfo.getRelatedPublication()); - scholixSummary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown()); - return scholixSummary; - }, - Encoders.bean(ScholixSummary.class)); - - summaryComplete.write().save(workingDirPath + "/summary"); - - // JavaPairRDD relationCount = - // sc.textFile(workingDirPath+"/relatedItemCount").mapToPair((PairFunction) i -> new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)); - // - // JavaPairRDD entities = - // sc.textFile(graphPath + "/publication") - // .filter(ProvisionUtil::isNotDeleted) - // .mapToPair((PairFunction) i -> new - // Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) - // .union( - // sc.textFile(graphPath + "/dataset") - // .filter(ProvisionUtil::isNotDeleted) - // .mapToPair((PairFunction) - // i -> - // new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) - // ) - // .union( - // sc.textFile(graphPath + "/unknown") - // .filter(ProvisionUtil::isNotDeleted) - // .mapToPair((PairFunction) - // i -> - // new Tuple2<>(DHPUtils.getJPathString(jsonIDPath, i), i)) - // ); - // entities.join(relationCount).map((Function>, - // String>) k -> - // ScholixSummary.fromJsonOAF(ProvisionUtil.getItemTypeFromId(k._1()), - // k._2()._1(), k._2()._2())).saveAsTextFile(workingDirPath+"/summary", GzipCodec.class); - // - // - // ; - - } -} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummaryIndex.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummaryIndex.scala new file mode 100644 index 0000000000..bf3d0342b6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkGenerateSummaryIndex.scala @@ -0,0 +1,70 @@ +package eu.dnetlib.dhp.provision + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary +import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown} +import org.apache.commons.io.IOUtils +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} + +object SparkGenerateSummaryIndex { + + def main(args: Array[String]): Unit = { + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkGenerateSummaryIndex.getClass.getResourceAsStream("/eu/dnetlib/dhp/provision/input_generate_summary_parameters.json"))) + parser.parseArgument(args) + val spark = SparkSession.builder.appName(SparkGenerateSummaryIndex.getClass.getSimpleName).master(parser.get("master")).getOrCreate + + val graphPath = parser.get("graphPath") + val workingDirPath = parser.get("workingDirPath") + + implicit val relatedItemInfoEncoders: Encoder[RelatedItemInfo] = Encoders.bean(classOf[RelatedItemInfo]) + implicit val datasetEncoder:Encoder[DLIDataset] = Encoders.kryo[DLIDataset] + implicit val publicationEncoder:Encoder[DLIPublication] = Encoders.kryo[DLIPublication] + implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation] + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + implicit val oafWithIdEncoder: Encoder[(String, Oaf)] = Encoders.tuple(Encoders.STRING, oafEncoder) + implicit val scholixSummaryEncoder: Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary] + implicit val scholixSummaryEncoderTuple: Encoder[(String,ScholixSummary)] = Encoders.tuple(Encoders.STRING,scholixSummaryEncoder) + + + val pubs = spark.read.load(s"$graphPath/publication").as[Oaf].map(o => (o.asInstanceOf[DLIPublication].getId, o)) + val dats = spark.read.load(s"$graphPath/dataset").as[Oaf].map(o => (o.asInstanceOf[DLIDataset].getId, o)) + val ukn = spark.read.load(s"$graphPath/unknown").as[Oaf].map(o => (o.asInstanceOf[DLIUnknown].getId, o)) + + + val summary:Dataset[(String,ScholixSummary)] = pubs.union(dats).union(ukn).map(o =>{ + val s = ScholixSummary.fromOAF(o._2) + (s.getId,s) + }) + + + val relatedItemInfoDs:Dataset[RelatedItemInfo] = spark.read.load(s"$workingDirPath/relatedItemCount").as[RelatedItemInfo] + + + summary.joinWith(relatedItemInfoDs, summary("_1").equalTo(relatedItemInfoDs("source")), "inner") + .map(i => { + val summary = i._1._2 + val relatedItemInfo = i._2 + summary.setRelatedDatasets(relatedItemInfo.getRelatedDataset) + summary.setRelatedPublications(relatedItemInfo.getRelatedPublication) + summary.setRelatedUnknown(relatedItemInfo.getRelatedUnknown) + summary + }).filter(s => s.getLocalIdentifier != null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/summary") + + + + + + + + + + + + + + + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java index 78d8730806..1b435bea3f 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkIndexCollectionOnES.java @@ -8,15 +8,12 @@ import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SparkSession; import org.elasticsearch.spark.rdd.api.java.JavaEsSpark; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary; public class SparkIndexCollectionOnES { @@ -39,33 +36,20 @@ public class SparkIndexCollectionOnES { final String sourcePath = parser.get("sourcePath"); final String index = parser.get("index"); final String idPath = parser.get("idPath"); - final String type = parser.get("type"); - final String indexHost = parser.get("esHost"); + final String cluster = parser.get("cluster"); + final String clusterJson = IOUtils + .toString(DropAndCreateESIndex.class.getResourceAsStream("/eu/dnetlib/dhp/provision/cluster.json")); + + final Map clusterMap = new ObjectMapper().readValue(clusterJson, Map.class); final SparkSession spark = SparkSession.builder().config(conf).getOrCreate(); final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); - JavaRDD inputRdd; - - if ("summary".equalsIgnoreCase(type)) - inputRdd = spark - .read() - .load(sourcePath) - .as(Encoders.bean(ScholixSummary.class)) - .map( - (MapFunction) f -> { - final ObjectMapper mapper = new ObjectMapper(); - return mapper.writeValueAsString(f); - }, - Encoders.STRING()) - .javaRDD(); - else - inputRdd = sc.textFile(sourcePath); + JavaRDD inputRdd = sc.textFile(sourcePath); Map esCfg = new HashMap<>(); - // esCfg.put("es.nodes", "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54"); - esCfg.put("es.nodes", indexHost); + esCfg.put("es.nodes", clusterMap.get(cluster)); esCfg.put("es.mapping.id", idPath); esCfg.put("es.batch.write.retry.count", "8"); esCfg.put("es.batch.write.retry.wait", "60s"); diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java index e5ea8b9f5a..3b808ba519 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/summary/ScholixSummary.java @@ -12,6 +12,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.provision.RelatedItemInfo; import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.StructuredProperty; import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset; import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication; @@ -138,54 +140,20 @@ public class ScholixSummary implements Serializable { this.datasources = datasources; } - public static ScholixSummary fromJsonOAF(final Typology oafType, final String oafJson) { + public static ScholixSummary fromOAF(final Oaf oaf) { try { - final ObjectMapper mapper = new ObjectMapper(); final RelatedItemInfo relatedItemInfo = new RelatedItemInfo(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - switch (oafType) { - case dataset: - return summaryFromDataset(mapper.readValue(oafJson, DLIDataset.class), relatedItemInfo); - case publication: - return summaryFromPublication( - mapper.readValue(oafJson, DLIPublication.class), relatedItemInfo); - case unknown: - return summaryFromUnknown(mapper.readValue(oafJson, DLIUnknown.class), relatedItemInfo); - } - } catch (Throwable e) { - throw new RuntimeException(e); - } - return null; - } - public static String fromJsonOAF( - final Typology oafType, final String oafJson, final String relEntityJson) { - try { - final ObjectMapper mapper = new ObjectMapper(); - mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false); - - RelatedItemInfo relatedItemInfo = mapper.readValue(relEntityJson, RelatedItemInfo.class); - - switch (oafType) { - case dataset: - return mapper - .writeValueAsString( - summaryFromDataset(mapper.readValue(oafJson, DLIDataset.class), relatedItemInfo)); - case publication: - return mapper - .writeValueAsString( - summaryFromPublication( - mapper.readValue(oafJson, DLIPublication.class), relatedItemInfo)); - case unknown: - return mapper - .writeValueAsString( - summaryFromUnknown(mapper.readValue(oafJson, DLIUnknown.class), relatedItemInfo)); - } + if (oaf instanceof DLIPublication) + return summaryFromPublication((DLIPublication) oaf, relatedItemInfo); + if (oaf instanceof DLIDataset) + return summaryFromDataset((DLIDataset) oaf, relatedItemInfo); + if (oaf instanceof DLIUnknown) + return summaryFromUnknown((DLIUnknown) oaf, relatedItemInfo); } catch (Throwable e) { throw new RuntimeException(e); } - return null; } diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/cluster.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/cluster.json new file mode 100644 index 0000000000..1cea6a8b92 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/cluster.json @@ -0,0 +1,4 @@ +{ + "cluster1": "10.19.65.51, 10.19.65.52, 10.19.65.53, 10.19.65.54", + "cluster2": "10.19.65.55, 10.19.65.56, 10.19.65.57, 10.19.65.58" +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dataset2Json.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dataset2Json.json new file mode 100644 index 0000000000..41db00cbf3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dataset2Json.json @@ -0,0 +1,14 @@ +[ + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "master should be local or yarn", + "paramRequired": true + }, + { + "paramName": "w", + "paramLongName": "workingPath", + "paramDescription": "the working path", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dropAndCreateIndex.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dropAndCreateIndex.json new file mode 100644 index 0000000000..242aca8c5e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/dropAndCreateIndex.json @@ -0,0 +1,14 @@ +[ +{ + "paramName": "c", + "paramLongName": "cluster", + "paramDescription": "should be cluster1 or cluster2", + "paramRequired": true +}, + { + "paramName": "i", + "paramLongName": "index", + "paramDescription": "index name", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json index f70f7dd799..51b001a0de 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/provision/index_on_es.json @@ -18,19 +18,12 @@ "paramRequired": true }, { - "paramName": "h", - "paramLongName": "esHost", - "paramDescription": "the index host name", + "paramName": "c", + "paramLongName": "cluster", + "paramDescription": "the index cluster", "paramRequired": true }, - - { - "paramName": "t", - "paramLongName": "type", - "paramDescription": "should be scholix or summary", - "paramRequired": true - }, { "paramName": "id", "paramLongName": "idPath", diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/config-default.xml index 6fb2a1253c..7c1a43e513 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/config-default.xml @@ -7,4 +7,8 @@ oozie.action.sharelib.for.spark spark2 + + oozie.launcher.mapreduce.user.classpath.first + true + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml index 68543e3f23..83c70fa255 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml @@ -8,6 +8,14 @@ graphPath the graph path + + index + the index name + + + esCluster + the Index cluster + sparkDriverMemory memory for driver process @@ -16,18 +24,6 @@ sparkExecutorMemory memory for individual executor - - - - - - - - - - - - @@ -53,7 +49,7 @@ calculate for each ID the number of related Dataset, publication and Unknown eu.dnetlib.dhp.provision.SparkExtractRelationCount dhp-graph-provision-scholexplorer-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} + --executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} -mt yarn-cluster --workingDirPath${workingDirPath} --relationPath${graphPath}/relation @@ -69,9 +65,9 @@ yarn-cluster cluster generate Summary - eu.dnetlib.dhp.provision.SparkGenerateSummary + eu.dnetlib.dhp.provision.SparkGenerateSummaryIndex dhp-graph-provision-scholexplorer-${projectVersion}.jar - --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} + --executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=4000 ${sparkExtraOPT} -mt yarn-cluster --workingDirPath${workingDirPath} --graphPath${graphPath} @@ -87,56 +83,88 @@ yarn-cluster cluster generate Scholix - eu.dnetlib.dhp.provision.SparkGenerateScholix + eu.dnetlib.dhp.provision.SparkGenerateScholixIndex dhp-graph-provision-scholexplorer-${projectVersion}.jar - --executor-memory 6G --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} + --executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=4000 ${sparkExtraOPT} -mt yarn-cluster --workingDirPath${workingDirPath} --graphPath${graphPath} + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + generate Scholix + eu.dnetlib.dhp.provision.SparkConvertDatasetToJson + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.sql.shuffle.partitions=4000 ${sparkExtraOPT} + -m yarn-cluster + --workingPath${workingDirPath} + + + + + + + + + ${jobTracker} + ${nameNode} + eu.dnetlib.dhp.provision.DropAndCreateESIndex + -i${index} + -c${esCluster} + + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + index summary + eu.dnetlib.dhp.provision.SparkIndexCollectionOnES + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" + -mt yarn-cluster + --sourcePath${workingDirPath}/summary_json + --index${index}_object + --idPathid + --cluster${esCluster} + + + + + + + + ${jobTracker} + ${nameNode} + yarn-cluster + cluster + index scholix + eu.dnetlib.dhp.provision.SparkIndexCollectionOnES + dhp-graph-provision-scholexplorer-${projectVersion}.jar + --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" + -mt yarn-cluster + --sourcePath${workingDirPath}/scholix_json + --index${index}_scholix + --idPathidentifier + --cluster${esCluster} + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala index c9d33dbe47..0bd746cffc 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/export/ExportDLITOOAFTest.scala @@ -4,7 +4,7 @@ import java.time.LocalDateTime import java.time.format.DateTimeFormatter import eu.dnetlib.dhp.schema.oaf.Relation -import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation} +import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication} import org.apache.spark.SparkConf import org.apache.spark.rdd.RDD import org.apache.spark.sql.SparkSession @@ -65,7 +65,7 @@ class ExportDLITOOAFTest { val json = Source.fromInputStream(getClass.getResourceAsStream("relation.json")).mkString - val oaf =DLIToOAF.convertDLIRelation(mapper.readValue(json, classOf[DLIRelation])) + val oaf =mapper.readValue(json, classOf[Relation]) println(mapper.writeValueAsString(oaf)) diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DropAndCreateESIndexTest.java b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DropAndCreateESIndexTest.java new file mode 100644 index 0000000000..19e8aa6990 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/java/eu/dnetlib/dhp/provision/DropAndCreateESIndexTest.java @@ -0,0 +1,13 @@ + +package eu.dnetlib.dhp.provision; + +import org.junit.jupiter.api.Test; + +public class DropAndCreateESIndexTest { + + public void testDropAndCreate() throws Exception { + DropAndCreateESIndex.main("-c localhost -i dli_shadow".split(" ")); + + } + +} diff --git a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json index cdb0cfa1d5..7aa25525ee 100644 --- a/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json +++ b/dhp-workflows/dhp-graph-provision-scholexplorer/src/test/resources/eu/dnetlib/dhp/export/relation.json @@ -13,7 +13,7 @@ "lastupdatetimestamp": null, "relType": "IsReferencedBy", "source": "60|4ee78ab329b49416b45c3774c132f244", - "collectedFrom": [ + "collectedfrom": [ { "dataInfo": null, "value": "Europe PMC", diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index fa19647730..8194d4d016 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -48,6 +48,80 @@ spark-solr + + org.apache.solr + solr-test-framework + test + + + com.carrotsearch + * + + + com.carrotsearch.randomizedtesting + * + + + + com.fasterxml.jackson.core + * + + + com.fasterxml.jackson.dataformat + * + + + org.codehaus.jackson + * + + + org.codehaus.janino + * + + + org.codehaus.woodstox + * + + + + + + com.github.ben-manes.caffeine + * + + + com.google.guava + * + + + com.google.protobuf + * + + + com.lmax + * + + + com.tdunning + * + + + org.apache.hadoop + * + + + + + + + + + + io.dropwizard.metrics + metrics-core + test + + org.apache.httpcomponents httpclient diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java new file mode 100644 index 0000000000..8c8947298c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java @@ -0,0 +1,101 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.Closeable; +import java.io.IOException; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.solr.client.solrj.SolrResponse; +import org.apache.solr.client.solrj.SolrServerException; +import org.apache.solr.client.solrj.impl.CloudSolrClient; +import org.apache.solr.client.solrj.response.UpdateResponse; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.provision.utils.ZkServers; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class SolrAdminApplication extends SolrApplication implements Closeable { + + private static final Logger log = LoggerFactory.getLogger(SolrAdminApplication.class); + + enum Action { + DELETE_BY_QUERY, COMMIT + } + + private CloudSolrClient solrClient; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + SolrAdminApplication.class + .getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json"))); + parser.parseArgument(args); + + final String isLookupUrl = parser.get("isLookupUrl"); + log.info("isLookupUrl: {}", isLookupUrl); + + final String format = parser.get("format"); + log.info("format: {}", format); + + final Action action = Action.valueOf(parser.get("action")); + log.info("action: {}", action); + + final String query = parser.get("query"); + log.info("query: {}", query); + + final boolean commit = Optional + .ofNullable(parser.get("commit")) + .map(Boolean::valueOf) + .orElse(false); + log.info("commit: {}", commit); + + final ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); + + final String zkHost = getZkHost(isLookup); + log.info("zkHost: {}", zkHost); + + final String collection = format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION; + log.info("collection: {}", collection); + + try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) { + app.execute(action, collection, query, commit); + } + } + + public SolrAdminApplication(String zkHost) { + final ZkServers zk = ZkServers.newInstance(zkHost); + this.solrClient = new CloudSolrClient.Builder(zk.getHosts(), zk.getChroot()).build(); + } + + public SolrResponse commit(String collection) throws IOException, SolrServerException { + return execute(Action.COMMIT, collection, null, true); + } + + public SolrResponse execute(Action action, String collection, String query, boolean commit) + throws IOException, SolrServerException { + switch (action) { + + case DELETE_BY_QUERY: + UpdateResponse rsp = solrClient.deleteByQuery(collection, query); + if (commit) { + solrClient.commit(collection); + } + return rsp; + case COMMIT: + return solrClient.commit(collection); + default: + throw new IllegalArgumentException("action not managed: " + action.toString()); + } + } + + @Override + public void close() throws IOException { + solrClient.close(); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrApplication.java new file mode 100644 index 0000000000..a824c6c2c8 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrApplication.java @@ -0,0 +1,40 @@ + +package eu.dnetlib.dhp.oa.provision; + +import org.apache.commons.lang3.StringUtils; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public abstract class SolrApplication { + + private static final Logger log = LoggerFactory.getLogger(SolrApplication.class); + + protected static final String LAYOUT = "index"; + protected static final String INTERPRETATION = "openaire"; + protected static final String SEPARATOR = "-"; + protected static final String DATE_FORMAT = "yyyy-MM-dd'T'hh:mm:ss'Z'"; + + /** + * Method retrieves from the information system the zookeeper quorum of the Solr server + * + * @param isLookup + * @return the zookeeper quorum of the Solr server + * @throws ISLookUpException + */ + protected static String getZkHost(ISLookUpService isLookup) throws ISLookUpException { + return doLookup( + isLookup, + "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()"); + } + + protected static String doLookup(ISLookUpService isLookup, String xquery) throws ISLookUpException { + log.info(String.format("running xquery: %s", xquery)); + final String res = isLookup.getResourceProfileByQuery(xquery); + log.info(String.format("got response (100 chars): %s", StringUtils.left(res, 100) + " ...")); + return res; + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java index ede7aa7b48..5b55961621 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java @@ -35,17 +35,12 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpDocumentNotFoundException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; -public class XmlIndexingJob { +public class XmlIndexingJob extends SolrApplication { private static final Logger log = LoggerFactory.getLogger(XmlIndexingJob.class); private static final Integer DEFAULT_BATCH_SIZE = 1000; - private static final String LAYOUT = "index"; - private static final String INTERPRETATION = "openaire"; - private static final String SEPARATOR = "-"; - public static final String DATE_FORMAT = "yyyy-MM-dd'T'hh:mm:ss'Z'"; - public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -208,23 +203,4 @@ public class XmlIndexingJob { format)); } - /** - * Method retrieves from the information system the zookeeper quorum of the Solr server - * - * @param isLookup - * @return the zookeeper quorum of the Solr server - * @throws ISLookUpException - */ - private static String getZkHost(ISLookUpService isLookup) throws ISLookUpException { - return doLookup( - isLookup, - "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='IndexServiceResourceType'] return $x//PROTOCOL[./@name='solr']/@address/string()"); - } - - private static String doLookup(ISLookUpService isLookup, String xquery) throws ISLookUpException { - log.info(String.format("running xquery: %s", xquery)); - final String res = isLookup.getResourceProfileByQuery(xquery); - log.info(String.format("got response (100 chars): %s", StringUtils.left(res, 100) + " ...")); - return res; - } } diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ZkServers.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ZkServers.java new file mode 100644 index 0000000000..6cec3ed53e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/ZkServers.java @@ -0,0 +1,59 @@ + +package eu.dnetlib.dhp.oa.provision.utils; + +import java.util.List; +import java.util.Optional; + +import org.apache.commons.lang3.StringUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import com.google.common.base.Splitter; +import com.google.common.collect.Lists; + +public class ZkServers { + + private static final Log log = LogFactory.getLog(ZkServers.class); + public static final String SEPARATOR = "/"; + + private List hosts; + + private Optional chroot; + + public static ZkServers newInstance(final String zkUrl) { + + // quorum0:2182,quorum1:2182,quorum2:2182,quorum3:2182,quorum4:2182/solr-dev-openaire + String urls = zkUrl; + final Optional chRoot = Optional.of(SEPARATOR + StringUtils.substringAfterLast(zkUrl, SEPARATOR)); + if (chRoot.isPresent() && StringUtils.isNotBlank(chRoot.get())) { + log.debug(String.format("found zk chroot %s", chRoot)); + urls = zkUrl.replace(chRoot.get(), ""); + } + + final List urlList = Lists.newArrayList(Splitter.on(",").omitEmptyStrings().split(urls)); + log.debug(String.format("zk urls %s", zkUrl)); + + return new ZkServers(urlList, chRoot); + } + + public ZkServers(List hosts, Optional chroot) { + this.hosts = hosts; + this.chroot = chroot; + } + + public List getHosts() { + return hosts; + } + + public void setHosts(List hosts) { + this.hosts = hosts; + } + + public Optional getChroot() { + return chroot; + } + + public void setChroot(Optional chroot) { + this.chroot = chroot; + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json new file mode 100644 index 0000000000..23eca2f7b4 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "isu", + "paramLongName": "isLookupUrl", + "paramDescription": "the URL to the ISLookUp Service", + "paramRequired": true + }, + { + "paramName": "f", + "paramLongName": "format", + "paramDescription": "metadata format profile name", + "paramRequired": true + }, + { + "paramName": "a", + "paramLongName": "action", + "paramDescription": "the action to be performed by the application", + "paramRequired": true + }, + { + "paramName": "q", + "paramLongName": "query", + "paramDescription": "the query", + "paramRequired": false + }, + { + "paramName": "c", + "paramLongName": "commit", + "paramDescription": "should the action be followed by a commit?", + "paramRequired": false + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml index 91ced378ca..e2b74b9aa5 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml @@ -37,7 +37,11 @@ batchSize number of records to be included in each indexing request - + + solrDeletionQuery + *:* + query used in the deleted by query operation + sparkDriverMemoryForJoining memory for driver process @@ -109,6 +113,7 @@ ${wf:conf('resumeFrom') eq 'fork_join_related_entities'} ${wf:conf('resumeFrom') eq 'fork_join_all_entities'} ${wf:conf('resumeFrom') eq 'convert_to_xml'} + ${wf:conf('resumeFrom') eq 'drop_solr_collection'} ${wf:conf('resumeFrom') eq 'to_solr_index'} @@ -584,12 +589,31 @@ - ${wf:conf('shouldIndex') eq 'true'} + ${wf:conf('shouldIndex') eq 'true'} ${wf:conf('shouldIndex') eq 'false'} - + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.oa.provision.SolrAdminApplication + --isLookupUrl${isLookupUrl} + --format${format} + --actionDELETE_BY_QUERY + --query${solrDeletionQuery} + --committrue + + + + + yarn @@ -615,6 +639,23 @@ --format${format} --batchSize${batchSize} + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.oa.provision.SolrAdminApplication + --isLookupUrl${isLookupUrl} + --format${format} + --actionCOMMIT + diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java index 528532eddd..6818cf6a51 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJobTest.java @@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.provision; import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; +import java.util.List; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; @@ -20,8 +21,6 @@ import org.junit.jupiter.api.io.TempDir; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import com.fasterxml.jackson.databind.ObjectMapper; - import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -31,7 +30,8 @@ public class PrepareRelationsJobTest { public static final String SUBRELTYPE = "subRelType"; public static final String OUTCOME = "outcome"; - public static final String SUPPLEMENT = "supplement"; + public static final String PARTICIPATION = "participation"; + public static final String AFFILIATION = "affiliation"; private static SparkSession spark; @@ -64,7 +64,7 @@ public class PrepareRelationsJobTest { @Test public void testRunPrepareRelationsJob(@TempDir Path testPath) throws Exception { - final int maxRelations = 10; + final int maxRelations = 20; PrepareRelationsJob .main( new String[] { @@ -73,7 +73,8 @@ public class PrepareRelationsJobTest { "-outputPath", testPath.toString(), "-relPartitions", "10", "-relationFilter", "asd", - "-maxRelations", String.valueOf(maxRelations) + "-sourceMaxRelations", String.valueOf(maxRelations), + "-targetMaxRelations", String.valueOf(maxRelations * 100) }); Dataset out = spark @@ -82,19 +83,31 @@ public class PrepareRelationsJobTest { .as(Encoders.bean(Relation.class)) .cache(); - Assertions.assertEquals(10, out.count()); + Assertions.assertEquals(maxRelations, out.count()); Dataset freq = out .toDF() .cube(SUBRELTYPE) .count() .filter((FilterFunction) value -> !value.isNullAt(0)); - long outcome = freq.filter(freq.col(SUBRELTYPE).equalTo(OUTCOME)).collectAsList().get(0).getAs("count"); - long supplement = freq.filter(freq.col(SUBRELTYPE).equalTo(SUPPLEMENT)).collectAsList().get(0).getAs("count"); - Assertions.assertTrue(outcome > supplement); + log.info(freq.collectAsList().toString()); + + long outcome = getRows(freq, OUTCOME).get(0).getAs("count"); + long participation = getRows(freq, PARTICIPATION).get(0).getAs("count"); + long affiliation = getRows(freq, AFFILIATION).get(0).getAs("count"); + + Assertions.assertTrue(participation == outcome); + Assertions.assertTrue(outcome > affiliation); + Assertions.assertTrue(participation > affiliation); + Assertions.assertEquals(7, outcome); - Assertions.assertEquals(3, supplement); + Assertions.assertEquals(7, participation); + Assertions.assertEquals(6, affiliation); + } + + protected List getRows(Dataset freq, String col) { + return freq.filter(freq.col(SUBRELTYPE).equalTo(col)).collectAsList(); } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java new file mode 100644 index 0000000000..cbd7b2de29 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java @@ -0,0 +1,130 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.File; +import java.nio.file.Path; + +import org.apache.solr.client.solrj.SolrResponse; +import org.apache.solr.client.solrj.embedded.JettyConfig; +import org.apache.solr.client.solrj.impl.CloudSolrClient; +import org.apache.solr.client.solrj.impl.XMLResponseParser; +import org.apache.solr.client.solrj.request.CollectionAdminRequest; +import org.apache.solr.client.solrj.request.ConfigSetAdminRequest; +import org.apache.solr.client.solrj.request.QueryRequest; +import org.apache.solr.client.solrj.request.RequestWriter; +import org.apache.solr.client.solrj.response.CollectionAdminResponse; +import org.apache.solr.client.solrj.response.ConfigSetAdminResponse; +import org.apache.solr.client.solrj.response.SolrPingResponse; +import org.apache.solr.client.solrj.response.UpdateResponse; +import org.apache.solr.cloud.MiniSolrCloudCluster; +import org.apache.solr.common.params.CollectionParams; +import org.apache.solr.common.params.CoreAdminParams; +import org.apache.solr.common.params.ModifiableSolrParams; +import org.apache.solr.common.util.NamedList; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.io.TempDir; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import junit.framework.Assert; + +public class SolrAdminApplicationTest { + + private static final Logger log = LoggerFactory.getLogger(SolrAdminApplicationTest.class); + public static final String DEFAULT_COLLECTION = "testCollection"; + public static final String CONFIG_NAME = "testConfig"; + + private static MiniSolrCloudCluster miniCluster; + private static CloudSolrClient cloudSolrClient; + + @TempDir + public static Path tempDir; + + @BeforeAll + public static void setup() throws Exception { + + // random unassigned HTTP port + final int jettyPort = 0; + + final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build(); + + // create a MiniSolrCloudCluster instance + miniCluster = new MiniSolrCloudCluster(2, tempDir, jettyConfig); + + // Upload Solr configuration directory to ZooKeeper + String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig"; + File configDir = new File(solrZKConfigDir); + + miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME); + + // override settings in the solrconfig include + System.setProperty("solr.tests.maxBufferedDocs", "100000"); + System.setProperty("solr.tests.maxIndexingThreads", "-1"); + System.setProperty("solr.tests.ramBufferSizeMB", "100"); + + // use non-test classes so RandomizedRunner isn't necessary + System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler"); + System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory"); + + cloudSolrClient = miniCluster.getSolrClient(); + cloudSolrClient.setRequestWriter(new RequestWriter()); + cloudSolrClient.setParser(new XMLResponseParser()); + cloudSolrClient.setDefaultCollection(DEFAULT_COLLECTION); + cloudSolrClient.connect(); + + log.info(new ConfigSetAdminRequest.List().process(cloudSolrClient).toString()); + log.info(CollectionAdminRequest.ClusterStatus.getClusterStatus().process(cloudSolrClient).toString()); + + createCollection(cloudSolrClient, DEFAULT_COLLECTION, 2, 1, CONFIG_NAME); + } + + @AfterAll + public static void shutDown() throws Exception { + miniCluster.shutdown(); + } + + protected static NamedList createCollection(CloudSolrClient client, String name, int numShards, + int replicationFactor, String configName) throws Exception { + ModifiableSolrParams modParams = new ModifiableSolrParams(); + modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name()); + modParams.set("name", name); + modParams.set("numShards", numShards); + modParams.set("replicationFactor", replicationFactor); + modParams.set("collection.configName", configName); + QueryRequest request = new QueryRequest(modParams); + request.setPath("/admin/collections"); + return client.request(request); + } + + @Test + public void testPing() throws Exception { + SolrPingResponse pingResponse = cloudSolrClient.ping(); + log.info("pingResponse: '{}'", pingResponse.getStatus()); + Assert.assertTrue(pingResponse.getStatus() == 0); + } + + @Test + public void testAdminApplication_DELETE() throws Exception { + + SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost()); + + UpdateResponse rsp = (UpdateResponse) admin + .execute(SolrAdminApplication.Action.DELETE_BY_QUERY, DEFAULT_COLLECTION, "*:*", false); + + Assertions.assertTrue(rsp.getStatus() == 0); + } + + @Test + public void testAdminApplication_COMMIT() throws Exception { + + SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost()); + + UpdateResponse rsp = (UpdateResponse) admin.commit(DEFAULT_COLLECTION); + + Assertions.assertTrue(rsp.getStatus() == 0); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_ca.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_ca.txt new file mode 100644 index 0000000000..307a85f913 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_ca.txt @@ -0,0 +1,8 @@ +# Set of Catalan contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +d +l +m +n +s +t diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_fr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_fr.txt new file mode 100644 index 0000000000..f1bba51b23 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_fr.txt @@ -0,0 +1,15 @@ +# Set of French contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +l +m +t +qu +n +s +j +d +c +jusqu +quoiqu +lorsqu +puisqu diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_ga.txt new file mode 100644 index 0000000000..9ebe7fa349 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_ga.txt @@ -0,0 +1,5 @@ +# Set of Irish contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +d +m +b diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_it.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_it.txt new file mode 100644 index 0000000000..cac0409537 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/contractions_it.txt @@ -0,0 +1,23 @@ +# Set of Italian contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +c +l +all +dall +dell +nell +sull +coll +pell +gl +agl +dagl +degl +negl +sugl +un +m +t +s +v +d diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/hyphenations_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/hyphenations_ga.txt new file mode 100644 index 0000000000..4d2642cc5a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/hyphenations_ga.txt @@ -0,0 +1,5 @@ +# Set of Irish hyphenations for StopFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +h +n +t diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stemdict_nl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stemdict_nl.txt new file mode 100644 index 0000000000..441072971d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stemdict_nl.txt @@ -0,0 +1,6 @@ +# Set of overrides for the dutch stemmer +# TODO: load this as a resource from the analyzer and sync it in build.xml +fiets fiets +bromfiets bromfiets +ei eier +kind kinder diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stoptags_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stoptags_ja.txt new file mode 100644 index 0000000000..71b750845e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stoptags_ja.txt @@ -0,0 +1,420 @@ +# +# This file defines a Japanese stoptag set for JapanesePartOfSpeechStopFilter. +# +# Any token with a part-of-speech tag that exactly matches those defined in this +# file are removed from the token stream. +# +# Set your own stoptags by uncommenting the lines below. Note that comments are +# not allowed on the same line as a stoptag. See LUCENE-3745 for frequency lists, +# etc. that can be useful for building you own stoptag set. +# +# The entire possible tagset is provided below for convenience. +# +##### +# noun: unclassified nouns +#名詞 +# +# noun-common: Common nouns or nouns where the sub-classification is undefined +#名詞-一般 +# +# noun-proper: Proper nouns where the sub-classification is undefined +#名詞-固有名詞 +# +# noun-proper-misc: miscellaneous proper nouns +#名詞-固有名詞-一般 +# +# noun-proper-person: Personal names where the sub-classification is undefined +#名詞-固有名詞-人名 +# +# noun-proper-person-misc: names that cannot be divided into surname and +# given name; foreign names; names where the surname or given name is unknown. +# e.g. お市の方 +#名詞-固有名詞-人名-一般 +# +# noun-proper-person-surname: Mainly Japanese surnames. +# e.g. 山田 +#名詞-固有名詞-人名-姓 +# +# noun-proper-person-given_name: Mainly Japanese given names. +# e.g. 太郎 +#名詞-固有名詞-人名-名 +# +# noun-proper-organization: Names representing organizations. +# e.g. 通産省, NHK +#名詞-固有名詞-組織 +# +# noun-proper-place: Place names where the sub-classification is undefined +#名詞-固有名詞-地域 +# +# noun-proper-place-misc: Place names excluding countries. +# e.g. アジア, バルセロナ, 京都 +#名詞-固有名詞-地域-一般 +# +# noun-proper-place-country: Country names. +# e.g. 日本, オーストラリア +#名詞-固有名詞-地域-国 +# +# noun-pronoun: Pronouns where the sub-classification is undefined +#名詞-代名詞 +# +# noun-pronoun-misc: miscellaneous pronouns: +# e.g. それ, ここ, あいつ, あなた, あちこち, いくつ, どこか, なに, みなさん, みんな, わたくし, われわれ +#名詞-代名詞-一般 +# +# noun-pronoun-contraction: Spoken language contraction made by combining a +# pronoun and the particle 'wa'. +# e.g. ありゃ, こりゃ, こりゃあ, そりゃ, そりゃあ +#名詞-代名詞-縮約 +# +# noun-adverbial: Temporal nouns such as names of days or months that behave +# like adverbs. Nouns that represent amount or ratios and can be used adverbially, +# e.g. 金曜, 一月, 午後, 少量 +#名詞-副詞可能 +# +# noun-verbal: Nouns that take arguments with case and can appear followed by +# 'suru' and related verbs (する, できる, なさる, くださる) +# e.g. インプット, 愛着, 悪化, 悪戦苦闘, 一安心, 下取り +#名詞-サ変接続 +# +# noun-adjective-base: The base form of adjectives, words that appear before な ("na") +# e.g. 健康, 安易, 駄目, だめ +#名詞-形容動詞語幹 +# +# noun-numeric: Arabic numbers, Chinese numerals, and counters like 何 (回), 数. +# e.g. 0, 1, 2, 何, 数, 幾 +#名詞-数 +# +# noun-affix: noun affixes where the sub-classification is undefined +#名詞-非自立 +# +# noun-affix-misc: Of adnominalizers, the case-marker の ("no"), and words that +# attach to the base form of inflectional words, words that cannot be classified +# into any of the other categories below. This category includes indefinite nouns. +# e.g. あかつき, 暁, かい, 甲斐, 気, きらい, 嫌い, くせ, 癖, こと, 事, ごと, 毎, しだい, 次第, +# 順, せい, 所為, ついで, 序で, つもり, 積もり, 点, どころ, の, はず, 筈, はずみ, 弾み, +# 拍子, ふう, ふり, 振り, ほう, 方, 旨, もの, 物, 者, ゆえ, 故, ゆえん, 所以, わけ, 訳, +# わり, 割り, 割, ん-口語/, もん-口語/ +#名詞-非自立-一般 +# +# noun-affix-adverbial: noun affixes that that can behave as adverbs. +# e.g. あいだ, 間, あげく, 挙げ句, あと, 後, 余り, 以外, 以降, 以後, 以上, 以前, 一方, うえ, +# 上, うち, 内, おり, 折り, かぎり, 限り, きり, っきり, 結果, ころ, 頃, さい, 際, 最中, さなか, +# 最中, じたい, 自体, たび, 度, ため, 為, つど, 都度, とおり, 通り, とき, 時, ところ, 所, +# とたん, 途端, なか, 中, のち, 後, ばあい, 場合, 日, ぶん, 分, ほか, 他, まえ, 前, まま, +# 儘, 侭, みぎり, 矢先 +#名詞-非自立-副詞可能 +# +# noun-affix-aux: noun affixes treated as 助動詞 ("auxiliary verb") in school grammars +# with the stem よう(だ) ("you(da)"). +# e.g. よう, やう, 様 (よう) +#名詞-非自立-助動詞語幹 +# +# noun-affix-adjective-base: noun affixes that can connect to the indeclinable +# connection form な (aux "da"). +# e.g. みたい, ふう +#名詞-非自立-形容動詞語幹 +# +# noun-special: special nouns where the sub-classification is undefined. +#名詞-特殊 +# +# noun-special-aux: The そうだ ("souda") stem form that is used for reporting news, is +# treated as 助動詞 ("auxiliary verb") in school grammars, and attach to the base +# form of inflectional words. +# e.g. そう +#名詞-特殊-助動詞語幹 +# +# noun-suffix: noun suffixes where the sub-classification is undefined. +#名詞-接尾 +# +# noun-suffix-misc: Of the nouns or stem forms of other parts of speech that connect +# to ガル or タイ and can combine into compound nouns, words that cannot be classified into +# any of the other categories below. In general, this category is more inclusive than +# 接尾語 ("suffix") and is usually the last element in a compound noun. +# e.g. おき, かた, 方, 甲斐 (がい), がかり, ぎみ, 気味, ぐるみ, (～した) さ, 次第, 済 (ず) み, +# よう, (でき)っこ, 感, 観, 性, 学, 類, 面, 用 +#名詞-接尾-一般 +# +# noun-suffix-person: Suffixes that form nouns and attach to person names more often +# than other nouns. +# e.g. 君, 様, 著 +#名詞-接尾-人名 +# +# noun-suffix-place: Suffixes that form nouns and attach to place names more often +# than other nouns. +# e.g. 町, 市, 県 +#名詞-接尾-地域 +# +# noun-suffix-verbal: Of the suffixes that attach to nouns and form nouns, those that +# can appear before スル ("suru"). +# e.g. 化, 視, 分け, 入り, 落ち, 買い +#名詞-接尾-サ変接続 +# +# noun-suffix-aux: The stem form of そうだ (様態) that is used to indicate conditions, +# is treated as 助動詞 ("auxiliary verb") in school grammars, and attach to the +# conjunctive form of inflectional words. +# e.g. そう +#名詞-接尾-助動詞語幹 +# +# noun-suffix-adjective-base: Suffixes that attach to other nouns or the conjunctive +# form of inflectional words and appear before the copula だ ("da"). +# e.g. 的, げ, がち +#名詞-接尾-形容動詞語幹 +# +# noun-suffix-adverbial: Suffixes that attach to other nouns and can behave as adverbs. +# e.g. 後 (ご), 以後, 以降, 以前, 前後, 中, 末, 上, 時 (じ) +#名詞-接尾-副詞可能 +# +# noun-suffix-classifier: Suffixes that attach to numbers and form nouns. This category +# is more inclusive than 助数詞 ("classifier") and includes common nouns that attach +# to numbers. +# e.g. 個, つ, 本, 冊, パーセント, cm, kg, カ月, か国, 区画, 時間, 時半 +#名詞-接尾-助数詞 +# +# noun-suffix-special: Special suffixes that mainly attach to inflecting words. +# e.g. (楽し) さ, (考え) 方 +#名詞-接尾-特殊 +# +# noun-suffix-conjunctive: Nouns that behave like conjunctions and join two words +# together. +# e.g. (日本) 対 (アメリカ), 対 (アメリカ), (3) 対 (5), (女優) 兼 (主婦) +#名詞-接続詞的 +# +# noun-verbal_aux: Nouns that attach to the conjunctive particle て ("te") and are +# semantically verb-like. +# e.g. ごらん, ご覧, 御覧, 頂戴 +#名詞-動詞非自立的 +# +# noun-quotation: text that cannot be segmented into words, proverbs, Chinese poetry, +# dialects, English, etc. Currently, the only entry for 名詞 引用文字列 ("noun quotation") +# is いわく ("iwaku"). +#名詞-引用文字列 +# +# noun-nai_adjective: Words that appear before the auxiliary verb ない ("nai") and +# behave like an adjective. +# e.g. 申し訳, 仕方, とんでも, 違い +#名詞-ナイ形容詞語幹 +# +##### +# prefix: unclassified prefixes +#接頭詞 +# +# prefix-nominal: Prefixes that attach to nouns (including adjective stem forms) +# excluding numerical expressions. +# e.g. お (水), 某 (氏), 同 (社), 故 (～氏), 高 (品質), お (見事), ご (立派) +#接頭詞-名詞接続 +# +# prefix-verbal: Prefixes that attach to the imperative form of a verb or a verb +# in conjunctive form followed by なる/なさる/くださる. +# e.g. お (読みなさい), お (座り) +#接頭詞-動詞接続 +# +# prefix-adjectival: Prefixes that attach to adjectives. +# e.g. お (寒いですねえ), バカ (でかい) +#接頭詞-形容詞接続 +# +# prefix-numerical: Prefixes that attach to numerical expressions. +# e.g. 約, およそ, 毎時 +#接頭詞-数接続 +# +##### +# verb: unclassified verbs +#動詞 +# +# verb-main: +#動詞-自立 +# +# verb-auxiliary: +#動詞-非自立 +# +# verb-suffix: +#動詞-接尾 +# +##### +# adjective: unclassified adjectives +#形容詞 +# +# adjective-main: +#形容詞-自立 +# +# adjective-auxiliary: +#形容詞-非自立 +# +# adjective-suffix: +#形容詞-接尾 +# +##### +# adverb: unclassified adverbs +#副詞 +# +# adverb-misc: Words that can be segmented into one unit and where adnominal +# modification is not possible. +# e.g. あいかわらず, 多分 +#副詞-一般 +# +# adverb-particle_conjunction: Adverbs that can be followed by の, は, に, +# な, する, だ, etc. +# e.g. こんなに, そんなに, あんなに, なにか, なんでも +#副詞-助詞類接続 +# +##### +# adnominal: Words that only have noun-modifying forms. +# e.g. この, その, あの, どの, いわゆる, なんらかの, 何らかの, いろんな, こういう, そういう, ああいう, +# どういう, こんな, そんな, あんな, どんな, 大きな, 小さな, おかしな, ほんの, たいした, +# 「(, も) さる (ことながら)」, 微々たる, 堂々たる, 単なる, いかなる, 我が」「同じ, 亡き +#連体詞 +# +##### +# conjunction: Conjunctions that can occur independently. +# e.g. が, けれども, そして, じゃあ, それどころか +接続詞 +# +##### +# particle: unclassified particles. +助詞 +# +# particle-case: case particles where the subclassification is undefined. +助詞-格助詞 +# +# particle-case-misc: Case particles. +# e.g. から, が, で, と, に, へ, より, を, の, にて +助詞-格助詞-一般 +# +# particle-case-quote: the "to" that appears after nouns, a person’s speech, +# quotation marks, expressions of decisions from a meeting, reasons, judgements, +# conjectures, etc. +# e.g. ( だ) と (述べた.), ( である) と (して執行猶予...) +助詞-格助詞-引用 +# +# particle-case-compound: Compounds of particles and verbs that mainly behave +# like case particles. +# e.g. という, といった, とかいう, として, とともに, と共に, でもって, にあたって, に当たって, に当って, +# にあたり, に当たり, に当り, に当たる, にあたる, において, に於いて,に於て, における, に於ける, +# にかけ, にかけて, にかんし, に関し, にかんして, に関して, にかんする, に関する, に際し, +# に際して, にしたがい, に従い, に従う, にしたがって, に従って, にたいし, に対し, にたいして, +# に対して, にたいする, に対する, について, につき, につけ, につけて, につれ, につれて, にとって, +# にとり, にまつわる, によって, に依って, に因って, により, に依り, に因り, による, に依る, に因る, +# にわたって, にわたる, をもって, を以って, を通じ, を通じて, を通して, をめぐって, をめぐり, をめぐる, +# って-口語/, ちゅう-関西弁「という」/, (何) ていう (人)-口語/, っていう-口語/, といふ, とかいふ +助詞-格助詞-連語 +# +# particle-conjunctive: +# e.g. から, からには, が, けれど, けれども, けど, し, つつ, て, で, と, ところが, どころか, とも, ども, +# ながら, なり, ので, のに, ば, ものの, や ( した), やいなや, (ころん) じゃ(いけない)-口語/, +# (行っ) ちゃ(いけない)-口語/, (言っ) たって (しかたがない)-口語/, (それがなく)ったって (平気)-口語/ +助詞-接続助詞 +# +# particle-dependency: +# e.g. こそ, さえ, しか, すら, は, も, ぞ +助詞-係助詞 +# +# particle-adverbial: +# e.g. がてら, かも, くらい, 位, ぐらい, しも, (学校) じゃ(これが流行っている)-口語/, +# (それ)じゃあ (よくない)-口語/, ずつ, (私) なぞ, など, (私) なり (に), (先生) なんか (大嫌い)-口語/, +# (私) なんぞ, (先生) なんて (大嫌い)-口語/, のみ, だけ, (私) だって-口語/, だに, +# (彼)ったら-口語/, (お茶) でも (いかが), 等 (とう), (今後) とも, ばかり, ばっか-口語/, ばっかり-口語/, +# ほど, 程, まで, 迄, (誰) も (が)([助詞-格助詞] および [助詞-係助詞] の前に位置する「も」) +助詞-副助詞 +# +# particle-interjective: particles with interjective grammatical roles. +# e.g. (松島) や +助詞-間投助詞 +# +# particle-coordinate: +# e.g. と, たり, だの, だり, とか, なり, や, やら +助詞-並立助詞 +# +# particle-final: +# e.g. かい, かしら, さ, ぜ, (だ)っけ-口語/, (とまってる) で-方言/, な, ナ, なあ-口語/, ぞ, ね, ネ, +# ねぇ-口語/, ねえ-口語/, ねん-方言/, の, のう-口語/, や, よ, ヨ, よぉ-口語/, わ, わい-口語/ +助詞-終助詞 +# +# particle-adverbial/conjunctive/final: The particle "ka" when unknown whether it is +# adverbial, conjunctive, or sentence final. For example: +# (a) 「A か B か」. Ex:「(国内で運用する) か,(海外で運用する) か (.)」 +# (b) Inside an adverb phrase. Ex:「(幸いという) か (, 死者はいなかった.)」 +# 「(祈りが届いたせい) か (, 試験に合格した.)」 +# (c) 「かのように」. Ex:「(何もなかった) か (のように振る舞った.)」 +# e.g. か +助詞-副助詞／並立助詞／終助詞 +# +# particle-adnominalizer: The "no" that attaches to nouns and modifies +# non-inflectional words. +助詞-連体化 +# +# particle-adnominalizer: The "ni" and "to" that appear following nouns and adverbs +# that are giongo, giseigo, or gitaigo. +# e.g. に, と +助詞-副詞化 +# +# particle-special: A particle that does not fit into one of the above classifications. +# This includes particles that are used in Tanka, Haiku, and other poetry. +# e.g. かな, けむ, ( しただろう) に, (あんた) にゃ(わからん), (俺) ん (家) +助詞-特殊 +# +##### +# auxiliary-verb: +助動詞 +# +##### +# interjection: Greetings and other exclamations. +# e.g. おはよう, おはようございます, こんにちは, こんばんは, ありがとう, どうもありがとう, ありがとうございます, +# いただきます, ごちそうさま, さよなら, さようなら, はい, いいえ, ごめん, ごめんなさい +#感動詞 +# +##### +# symbol: unclassified Symbols. +記号 +# +# symbol-misc: A general symbol not in one of the categories below. +# e.g. [○◎@$〒→+] +記号-一般 +# +# symbol-comma: Commas +# e.g. [,、] +記号-読点 +# +# symbol-period: Periods and full stops. +# e.g. [.．。] +記号-句点 +# +# symbol-space: Full-width whitespace. +記号-空白 +# +# symbol-open_bracket: +# e.g. [({‘“『【] +記号-括弧開 +# +# symbol-close_bracket: +# e.g. [)}’”』」】] +記号-括弧閉 +# +# symbol-alphabetic: +#記号-アルファベット +# +##### +# other: unclassified other +#その他 +# +# other-interjection: Words that are hard to classify as noun-suffixes or +# sentence-final particles. +# e.g. (だ)ァ +その他-間投 +# +##### +# filler: Aizuchi that occurs during a conversation or sounds inserted as filler. +# e.g. あの, うんと, えと +フィラー +# +##### +# non-verbal: non-verbal sound. +非言語音 +# +##### +# fragment: +#語断片 +# +##### +# unknown: unknown part of speech. +#未知語 +# +##### End of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ar.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ar.txt new file mode 100644 index 0000000000..046829db6a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ar.txt @@ -0,0 +1,125 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +# Cleaned on October 11, 2009 (not normalized, so use before normalization) +# This means that when modifying this list, you might need to add some +# redundant entries, for example containing forms with both أ and ا +من +ومن +منها +منه +في +وفي +فيها +فيه +و +ف +ثم +او +أو +ب +بها +به +ا +أ +اى +اي +أي +أى +لا +ولا +الا +ألا +إلا +لكن +ما +وما +كما +فما +عن +مع +اذا +إذا +ان +أن +إن +انها +أنها +إنها +انه +أنه +إنه +بان +بأن +فان +فأن +وان +وأن +وإن +التى +التي +الذى +الذي +الذين +الى +الي +إلى +إلي +على +عليها +عليه +اما +أما +إما +ايضا +أيضا +كل +وكل +لم +ولم +لن +ولن +هى +هي +هو +وهى +وهي +وهو +فهى +فهي +فهو +انت +أنت +لك +لها +له +هذه +هذا +تلك +ذلك +هناك +كانت +كان +يكون +تكون +وكانت +وكان +غير +بعض +قد +نحو +بين +بينما +منذ +ضمن +حيث +الان +الآن +خلال +بعد +قبل +حتى +عند +عندما +لدى +جميع diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_bg.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_bg.txt new file mode 100644 index 0000000000..1ae4ba2ae3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_bg.txt @@ -0,0 +1,193 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +а +аз +ако +ала +бе +без +беше +би +бил +била +били +било +близо +бъдат +бъде +бяха +в +вас +ваш +ваша +вероятно +вече +взема +ви +вие +винаги +все +всеки +всички +всичко +всяка +във +въпреки +върху +г +ги +главно +го +д +да +дали +до +докато +докога +дори +досега +доста +е +едва +един +ето +за +зад +заедно +заради +засега +затова +защо +защото +и +из +или +им +има +имат +иска +й +каза +как +каква +какво +както +какъв +като +кога +когато +което +които +кой +който +колко +която +къде +където +към +ли +м +ме +между +мен +ми +мнозина +мога +могат +може +моля +момента +му +н +на +над +назад +най +направи +напред +например +нас +не +него +нея +ни +ние +никой +нито +но +някои +някой +няма +обаче +около +освен +особено +от +отгоре +отново +още +пак +по +повече +повечето +под +поне +поради +после +почти +прави +пред +преди +през +при +пък +първо +с +са +само +се +сега +си +скоро +след +сме +според +сред +срещу +сте +съм +със +също +т +тази +така +такива +такъв +там +твой +те +тези +ти +тн +то +това +тогава +този +той +толкова +точно +трябва +тук +тъй +тя +тях +у +харесва +ч +че +често +чрез +ще +щом +я diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ca.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ca.txt new file mode 100644 index 0000000000..3da65deafe --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ca.txt @@ -0,0 +1,220 @@ +# Catalan stopwords from http://github.com/vcl/cue.language (Apache 2 Licensed) +a +abans +ací +ah +així +això +al +als +aleshores +algun +alguna +algunes +alguns +alhora +allà +allí +allò +altra +altre +altres +amb +ambdós +ambdues +apa +aquell +aquella +aquelles +aquells +aquest +aquesta +aquestes +aquests +aquí +baix +cada +cadascú +cadascuna +cadascunes +cadascuns +com +contra +d'un +d'una +d'unes +d'uns +dalt +de +del +dels +des +després +dins +dintre +donat +doncs +durant +e +eh +el +els +em +en +encara +ens +entre +érem +eren +éreu +es +és +esta +està +estàvem +estaven +estàveu +esteu +et +etc +ets +fins +fora +gairebé +ha +han +has +havia +he +hem +heu +hi +ho +i +igual +iguals +ja +l'hi +la +les +li +li'n +llavors +m'he +ma +mal +malgrat +mateix +mateixa +mateixes +mateixos +me +mentre +més +meu +meus +meva +meves +molt +molta +moltes +molts +mon +mons +n'he +n'hi +ne +ni +no +nogensmenys +només +nosaltres +nostra +nostre +nostres +o +oh +oi +on +pas +pel +pels +per +però +perquè +poc +poca +pocs +poques +potser +propi +qual +quals +quan +quant +que +què +quelcom +qui +quin +quina +quines +quins +s'ha +s'han +sa +semblant +semblants +ses +seu +seus +seva +seva +seves +si +sobre +sobretot +sóc +solament +sols +son +són +sons +sota +sou +t'ha +t'han +t'he +ta +tal +també +tampoc +tan +tant +tanta +tantes +teu +teus +teva +teves +ton +tons +tot +tota +totes +tots +un +una +unes +uns +us +va +vaig +vam +van +vas +veu +vosaltres +vostra +vostre +vostres diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_cz.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_cz.txt new file mode 100644 index 0000000000..53c6097dac --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_cz.txt @@ -0,0 +1,172 @@ +a +s +k +o +i +u +v +z +dnes +cz +tímto +budeš +budem +byli +jseš +můj +svým +ta +tomto +tohle +tuto +tyto +jej +zda +proč +máte +tato +kam +tohoto +kdo +kteří +mi +nám +tom +tomuto +mít +nic +proto +kterou +byla +toho +protože +asi +ho +naši +napište +re +což +tím +takže +svých +její +svými +jste +aj +tu +tedy +teto +bylo +kde +ke +pravé +ji +nad +nejsou +či +pod +téma +mezi +přes +ty +pak +vám +ani +když +však +neg +jsem +tento +článku +články +aby +jsme +před +pta +jejich +byl +ještě +až +bez +také +pouze +první +vaše +která +nás +nový +tipy +pokud +může +strana +jeho +své +jiné +zprávy +nové +není +vás +jen +podle +zde +už +být +více +bude +již +než +který +by +které +co +nebo +ten +tak +má +při +od +po +jsou +jak +další +ale +si +se +ve +to +jako +za +zpět +ze +do +pro +je +na +atd +atp +jakmile +přičemž +já +on +ona +ono +oni +ony +my +vy +jí +ji +mě +mne +jemu +tomu +těm +těmu +němu +němuž +jehož +jíž +jelikož +jež +jakož +načež diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_da.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_da.txt new file mode 100644 index 0000000000..42e6145b98 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_da.txt @@ -0,0 +1,110 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/danish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Danish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + +og | and +i | in +jeg | I +det | that (dem. pronoun)/it (pers. pronoun) +at | that (in front of a sentence)/to (with infinitive) +en | a/an +den | it (pers. pronoun)/that (dem. pronoun) +til | to/at/for/until/against/by/of/into, more +er | present tense of "to be" +som | who, as +på | on/upon/in/on/at/to/after/of/with/for, on +de | they +med | with/by/in, along +han | he +af | of/by/from/off/for/in/with/on, off +for | at/for/to/from/by/of/ago, in front/before, because +ikke | not +der | who/which, there/those +var | past tense of "to be" +mig | me/myself +sig | oneself/himself/herself/itself/themselves +men | but +et | a/an/one, one (number), someone/somebody/one +har | present tense of "to have" +om | round/about/for/in/a, about/around/down, if +vi | we +min | my +havde | past tense of "to have" +ham | him +hun | she +nu | now +over | over/above/across/by/beyond/past/on/about, over/past +da | then, when/as/since +fra | from/off/since, off, since +du | you +ud | out +sin | his/her/its/one's +dem | them +os | us/ourselves +op | up +man | you/one +hans | his +hvor | where +eller | or +hvad | what +skal | must/shall etc. +selv | myself/youself/herself/ourselves etc., even +her | here +alle | all/everyone/everybody etc. +vil | will (verb) +blev | past tense of "to stay/to remain/to get/to become" +kunne | could +ind | in +når | when +være | present tense of "to be" +dog | however/yet/after all +noget | something +ville | would +jo | you know/you see (adv), yes +deres | their/theirs +efter | after/behind/according to/for/by/from, later/afterwards +ned | down +skulle | should +denne | this +end | than +dette | this +mit | my/mine +også | also +under | under/beneath/below/during, below/underneath +have | have +dig | you +anden | other +hende | her +mine | my +alt | everything +meget | much/very, plenty of +sit | his, her, its, one's +sine | his, her, its, one's +vor | our +mod | against +disse | these +hvis | if +din | your/yours +nogle | some +hos | by/at +blive | be/become +mange | many +ad | by/through +bliver | present tense of "to be/to become" +hendes | her/hers +været | be +thi | for (conj) +jer | you +sådan | such, like this/like that diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_de.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_de.txt new file mode 100644 index 0000000000..86525e7ae0 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_de.txt @@ -0,0 +1,294 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/german/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A German stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | The number of forms in this list is reduced significantly by passing it + | through the German stemmer. + + +aber | but + +alle | all +allem +allen +aller +alles + +als | than, as +also | so +am | an + dem +an | at + +ander | other +andere +anderem +anderen +anderer +anderes +anderm +andern +anderr +anders + +auch | also +auf | on +aus | out of +bei | by +bin | am +bis | until +bist | art +da | there +damit | with it +dann | then + +der | the +den +des +dem +die +das + +daß | that + +derselbe | the same +derselben +denselben +desselben +demselben +dieselbe +dieselben +dasselbe + +dazu | to that + +dein | thy +deine +deinem +deinen +deiner +deines + +denn | because + +derer | of those +dessen | of him + +dich | thee +dir | to thee +du | thou + +dies | this +diese +diesem +diesen +dieser +dieses + + +doch | (several meanings) +dort | (over) there + + +durch | through + +ein | a +eine +einem +einen +einer +eines + +einig | some +einige +einigem +einigen +einiger +einiges + +einmal | once + +er | he +ihn | him +ihm | to him + +es | it +etwas | something + +euer | your +eure +eurem +euren +eurer +eures + +für | for +gegen | towards +gewesen | p.p. of sein +hab | have +habe | have +haben | have +hat | has +hatte | had +hatten | had +hier | here +hin | there +hinter | behind + +ich | I +mich | me +mir | to me + + +ihr | you, to her +ihre +ihrem +ihren +ihrer +ihres +euch | to you + +im | in + dem +in | in +indem | while +ins | in + das +ist | is + +jede | each, every +jedem +jeden +jeder +jedes + +jene | that +jenem +jenen +jener +jenes + +jetzt | now +kann | can + +kein | no +keine +keinem +keinen +keiner +keines + +können | can +könnte | could +machen | do +man | one + +manche | some, many a +manchem +manchen +mancher +manches + +mein | my +meine +meinem +meinen +meiner +meines + +mit | with +muss | must +musste | had to +nach | to(wards) +nicht | not +nichts | nothing +noch | still, yet +nun | now +nur | only +ob | whether +oder | or +ohne | without +sehr | very + +sein | his +seine +seinem +seinen +seiner +seines + +selbst | self +sich | herself + +sie | they, she +ihnen | to them + +sind | are +so | so + +solche | such +solchem +solchen +solcher +solches + +soll | shall +sollte | should +sondern | but +sonst | else +über | over +um | about, around +und | and + +uns | us +unse +unsem +unsen +unser +unses + +unter | under +viel | much +vom | von + dem +von | from +vor | before +während | while +war | was +waren | were +warst | wast +was | what +weg | away, off +weil | because +weiter | further + +welche | which +welchem +welchen +welcher +welches + +wenn | when +werde | will +werden | will +wie | how +wieder | again +will | want +wir | we +wird | will +wirst | willst +wo | where +wollen | want +wollte | wanted +würde | would +würden | would +zu | to +zum | zu + dem +zur | zu + der +zwar | indeed +zwischen | between + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_el.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_el.txt new file mode 100644 index 0000000000..232681f5bd --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_el.txt @@ -0,0 +1,78 @@ +# Lucene Greek Stopwords list +# Note: by default this file is used after GreekLowerCaseFilter, +# so when modifying this file use 'σ' instead of 'ς' +ο +η +το +οι +τα +του +τησ +των +τον +την +και +κι +κ +ειμαι +εισαι +ειναι +ειμαστε +ειστε +στο +στον +στη +στην +μα +αλλα +απο +για +προσ +με +σε +ωσ +παρα +αντι +κατα +μετα +θα +να +δε +δεν +μη +μην +επι +ενω +εαν +αν +τοτε +που +πωσ +ποιοσ +ποια +ποιο +ποιοι +ποιεσ +ποιων +ποιουσ +αυτοσ +αυτη +αυτο +αυτοι +αυτων +αυτουσ +αυτεσ +αυτα +εκεινοσ +εκεινη +εκεινο +εκεινοι +εκεινεσ +εκεινα +εκεινων +εκεινουσ +οπωσ +ομωσ +ισωσ +οσο +οτι diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_en.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_en.txt new file mode 100644 index 0000000000..2c164c0b2a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_en.txt @@ -0,0 +1,54 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +# a couple of test stopwords to test that the words are really being +# configured from this file: +stopworda +stopwordb + +# Standard english stop words taken from Lucene's StopAnalyzer +a +an +and +are +as +at +be +but +by +for +if +in +into +is +it +no +not +of +on +or +such +that +the +their +then +there +these +they +this +to +was +will +with diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_es.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_es.txt new file mode 100644 index 0000000000..487d78c8d5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_es.txt @@ -0,0 +1,356 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/spanish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Spanish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + + | The following is a ranked list (commonest to rarest) of stopwords + | deriving from a large sample of text. + + | Extra words have been added at the end. + +de | from, of +la | the, her +que | who, that +el | the +en | in +y | and +a | to +los | the, them +del | de + el +se | himself, from him etc +las | the, them +por | for, by, etc +un | a +para | for +con | with +no | no +una | a +su | his, her +al | a + el + | es from SER +lo | him +como | how +más | more +pero | pero +sus | su plural +le | to him, her +ya | already +o | or + | fue from SER +este | this + | ha from HABER +sí | himself etc +porque | because +esta | this + | son from SER +entre | between + | está from ESTAR +cuando | when +muy | very +sin | without +sobre | on + | ser from SER + | tiene from TENER +también | also +me | me +hasta | until +hay | there is/are +donde | where + | han from HABER +quien | whom, that + | están from ESTAR + | estado from ESTAR +desde | from +todo | all +nos | us +durante | during + | estados from ESTAR +todos | all +uno | a +les | to them +ni | nor +contra | against +otros | other + | fueron from SER +ese | that +eso | that + | había from HABER +ante | before +ellos | they +e | and (variant of y) +esto | this +mí | me +antes | before +algunos | some +qué | what? +unos | a +yo | I +otro | other +otras | other +otra | other +él | he +tanto | so much, many +esa | that +estos | these +mucho | much, many +quienes | who +nada | nothing +muchos | many +cual | who + | sea from SER +poco | few +ella | she +estar | to be + | haber from HABER +estas | these + | estaba from ESTAR + | estamos from ESTAR +algunas | some +algo | something +nosotros | we + + | other forms + +mi | me +mis | mi plural +tú | thou +te | thee +ti | thee +tu | thy +tus | tu plural +ellas | they +nosotras | we +vosotros | you +vosotras | you +os | you +mío | mine +mía | +míos | +mías | +tuyo | thine +tuya | +tuyos | +tuyas | +suyo | his, hers, theirs +suya | +suyos | +suyas | +nuestro | ours +nuestra | +nuestros | +nuestras | +vuestro | yours +vuestra | +vuestros | +vuestras | +esos | those +esas | those + + | forms of estar, to be (not including the infinitive): +estoy +estás +está +estamos +estáis +están +esté +estés +estemos +estéis +estén +estaré +estarás +estará +estaremos +estaréis +estarán +estaría +estarías +estaríamos +estaríais +estarían +estaba +estabas +estábamos +estabais +estaban +estuve +estuviste +estuvo +estuvimos +estuvisteis +estuvieron +estuviera +estuvieras +estuviéramos +estuvierais +estuvieran +estuviese +estuvieses +estuviésemos +estuvieseis +estuviesen +estando +estado +estada +estados +estadas +estad + + | forms of haber, to have (not including the infinitive): +he +has +ha +hemos +habéis +han +haya +hayas +hayamos +hayáis +hayan +habré +habrás +habrá +habremos +habréis +habrán +habría +habrías +habríamos +habríais +habrían +había +habías +habíamos +habíais +habían +hube +hubiste +hubo +hubimos +hubisteis +hubieron +hubiera +hubieras +hubiéramos +hubierais +hubieran +hubiese +hubieses +hubiésemos +hubieseis +hubiesen +habiendo +habido +habida +habidos +habidas + + | forms of ser, to be (not including the infinitive): +soy +eres +es +somos +sois +son +sea +seas +seamos +seáis +sean +seré +serás +será +seremos +seréis +serán +sería +serías +seríamos +seríais +serían +era +eras +éramos +erais +eran +fui +fuiste +fue +fuimos +fuisteis +fueron +fuera +fueras +fuéramos +fuerais +fueran +fuese +fueses +fuésemos +fueseis +fuesen +siendo +sido + | sed also means 'thirst' + + | forms of tener, to have (not including the infinitive): +tengo +tienes +tiene +tenemos +tenéis +tienen +tenga +tengas +tengamos +tengáis +tengan +tendré +tendrás +tendrá +tendremos +tendréis +tendrán +tendría +tendrías +tendríamos +tendríais +tendrían +tenía +tenías +teníamos +teníais +tenían +tuve +tuviste +tuvo +tuvimos +tuvisteis +tuvieron +tuviera +tuvieras +tuviéramos +tuvierais +tuvieran +tuviese +tuvieses +tuviésemos +tuvieseis +tuviesen +teniendo +tenido +tenida +tenidos +tenidas +tened + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_eu.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_eu.txt new file mode 100644 index 0000000000..25f1db9346 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_eu.txt @@ -0,0 +1,99 @@ +# example set of basque stopwords +al +anitz +arabera +asko +baina +bat +batean +batek +bati +batzuei +batzuek +batzuetan +batzuk +bera +beraiek +berau +berauek +bere +berori +beroriek +beste +bezala +da +dago +dira +ditu +du +dute +edo +egin +ere +eta +eurak +ez +gainera +gu +gutxi +guzti +haiei +haiek +haietan +hainbeste +hala +han +handik +hango +hara +hari +hark +hartan +hau +hauei +hauek +hauetan +hemen +hemendik +hemengo +hi +hona +honek +honela +honetan +honi +hor +hori +horiei +horiek +horietan +horko +horra +horrek +horrela +horretan +horri +hortik +hura +izan +ni +noiz +nola +non +nondik +nongo +nor +nora +ze +zein +zen +zenbait +zenbat +zer +zergatik +ziren +zituen +zu +zuek +zuen +zuten diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fa.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fa.txt new file mode 100644 index 0000000000..723641c6da --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fa.txt @@ -0,0 +1,313 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +# Note: by default this file is used after normalization, so when adding entries +# to this file, use the arabic 'ي' instead of 'ی' +انان +نداشته +سراسر +خياه +ايشان +وي +تاكنون +بيشتري +دوم +پس +ناشي +وگو +يا +داشتند +سپس +هنگام +هرگز +پنج +نشان +امسال +ديگر +گروهي +شدند +چطور +ده +و +دو +نخستين +ولي +چرا +چه +وسط +ه +كدام +قابل +يك +رفت +هفت +همچنين +در +هزار +بله +بلي +شايد +اما +شناسي +گرفته +دهد +داشته +دانست +داشتن +خواهيم +ميليارد +وقتيكه +امد +خواهد +جز +اورده +شده +بلكه +خدمات +شدن +برخي +نبود +بسياري +جلوگيري +حق +كردند +نوعي +بعري +نكرده +نظير +نبايد +بوده +بودن +داد +اورد +هست +جايي +شود +دنبال +داده +بايد +سابق +هيچ +همان +انجا +كمتر +كجاست +گردد +كسي +تر +مردم +تان +دادن +بودند +سري +جدا +ندارند +مگر +يكديگر +دارد +دهند +بنابراين +هنگامي +سمت +جا +انچه +خود +دادند +زياد +دارند +اثر +بدون +بهترين +بيشتر +البته +به +براساس +بيرون +كرد +بعضي +گرفت +توي +اي +ميليون +او +جريان +تول +بر +مانند +برابر +باشيم +مدتي +گويند +اكنون +تا +تنها +جديد +چند +بي +نشده +كردن +كردم +گويد +كرده +كنيم +نمي +نزد +روي +قصد +فقط +بالاي +ديگران +اين +ديروز +توسط +سوم +ايم +دانند +سوي +استفاده +شما +كنار +داريم +ساخته +طور +امده +رفته +نخست +بيست +نزديك +طي +كنيد +از +انها +تمامي +داشت +يكي +طريق +اش +چيست +روب +نمايد +گفت +چندين +چيزي +تواند +ام +ايا +با +ان +ايد +ترين +اينكه +ديگري +راه +هايي +بروز +همچنان +پاعين +كس +حدود +مختلف +مقابل +چيز +گيرد +ندارد +ضد +همچون +سازي +شان +مورد +باره +مرسي +خويش +برخوردار +چون +خارج +شش +هنوز +تحت +ضمن +هستيم +گفته +فكر +بسيار +پيش +براي +روزهاي +انكه +نخواهد +بالا +كل +وقتي +كي +چنين +كه +گيري +نيست +است +كجا +كند +نيز +يابد +بندي +حتي +توانند +عقب +خواست +كنند +بين +تمام +همه +ما +باشند +مثل +شد +اري +باشد +اره +طبق +بعد +اگر +صورت +غير +جاي +بيش +ريزي +اند +زيرا +چگونه +بار +لطفا +مي +درباره +من +ديده +همين +گذاري +برداري +علت +گذاشته +هم +فوق +نه +ها +شوند +اباد +همواره +هر +اول +خواهند +چهار +نام +امروز +مان +هاي +قبل +كنم +سعي +تازه +را +هستند +زير +جلوي +عنوان +بود diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fi.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fi.txt new file mode 100644 index 0000000000..4372c9a055 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fi.txt @@ -0,0 +1,97 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/finnish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + +| forms of BE + +olla +olen +olet +on +olemme +olette +ovat +ole | negative form + +oli +olisi +olisit +olisin +olisimme +olisitte +olisivat +olit +olin +olimme +olitte +olivat +ollut +olleet + +en | negation +et +ei +emme +ette +eivät + +|Nom Gen Acc Part Iness Elat Illat Adess Ablat Allat Ess Trans +minä minun minut minua minussa minusta minuun minulla minulta minulle | I +sinä sinun sinut sinua sinussa sinusta sinuun sinulla sinulta sinulle | you +hän hänen hänet häntä hänessä hänestä häneen hänellä häneltä hänelle | he she +me meidän meidät meitä meissä meistä meihin meillä meiltä meille | we +te teidän teidät teitä teissä teistä teihin teillä teiltä teille | you +he heidän heidät heitä heissä heistä heihin heillä heiltä heille | they + +tämä tämän tätä tässä tästä tähän tallä tältä tälle tänä täksi | this +tuo tuon tuotä tuossa tuosta tuohon tuolla tuolta tuolle tuona tuoksi | that +se sen sitä siinä siitä siihen sillä siltä sille sinä siksi | it +nämä näiden näitä näissä näistä näihin näillä näiltä näille näinä näiksi | these +nuo noiden noita noissa noista noihin noilla noilta noille noina noiksi | those +ne niiden niitä niissä niistä niihin niillä niiltä niille niinä niiksi | they + +kuka kenen kenet ketä kenessä kenestä keneen kenellä keneltä kenelle kenenä keneksi| who +ketkä keiden ketkä keitä keissä keistä keihin keillä keiltä keille keinä keiksi | (pl) +mikä minkä minkä mitä missä mistä mihin millä miltä mille minä miksi | which what +mitkä | (pl) + +joka jonka jota jossa josta johon jolla jolta jolle jona joksi | who which +jotka joiden joita joissa joista joihin joilla joilta joille joina joiksi | (pl) + +| conjunctions + +että | that +ja | and +jos | if +koska | because +kuin | than +mutta | but +niin | so +sekä | and +sillä | for +tai | or +vaan | but +vai | or +vaikka | although + + +| prepositions + +kanssa | with +mukaan | according to +noin | about +poikki | across +yli | over, across + +| other + +kun | when +niin | so +nyt | now +itse | self + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fr.txt new file mode 100644 index 0000000000..749abae684 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_fr.txt @@ -0,0 +1,186 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/french/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A French stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + +au | a + le +aux | a + les +avec | with +ce | this +ces | these +dans | with +de | of +des | de + les +du | de + le +elle | she +en | `of them' etc +et | and +eux | them +il | he +je | I +la | the +le | the +leur | their +lui | him +ma | my (fem) +mais | but +me | me +même | same; as in moi-même (myself) etc +mes | me (pl) +moi | me +mon | my (masc) +ne | not +nos | our (pl) +notre | our +nous | we +on | one +ou | where +par | by +pas | not +pour | for +qu | que before vowel +que | that +qui | who +sa | his, her (fem) +se | oneself +ses | his (pl) +son | his, her (masc) +sur | on +ta | thy (fem) +te | thee +tes | thy (pl) +toi | thee +ton | thy (masc) +tu | thou +un | a +une | a +vos | your (pl) +votre | your +vous | you + + | single letter forms + +c | c' +d | d' +j | j' +l | l' +à | to, at +m | m' +n | n' +s | s' +t | t' +y | there + + | forms of être (not including the infinitive): +été +étée +étées +étés +étant +suis +es +est +sommes +êtes +sont +serai +seras +sera +serons +serez +seront +serais +serait +serions +seriez +seraient +étais +était +étions +étiez +étaient +fus +fut +fûmes +fûtes +furent +sois +soit +soyons +soyez +soient +fusse +fusses +fût +fussions +fussiez +fussent + + | forms of avoir (not including the infinitive): +ayant +eu +eue +eues +eus +ai +as +avons +avez +ont +aurai +auras +aura +aurons +aurez +auront +aurais +aurait +aurions +auriez +auraient +avais +avait +avions +aviez +avaient +eut +eûmes +eûtes +eurent +aie +aies +ait +ayons +ayez +aient +eusse +eusses +eût +eussions +eussiez +eussent + + | Later additions (from Jean-Christophe Deschamps) +ceci | this +cela | that +celà | that +cet | this +cette | this +ici | here +ils | they +les | the (pl) +leurs | their (pl) +quel | which +quels | which +quelle | which +quelles | which +sans | without +soi | oneself + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ga.txt new file mode 100644 index 0000000000..9ff88d747e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ga.txt @@ -0,0 +1,110 @@ + +a +ach +ag +agus +an +aon +ar +arna +as +b' +ba +beirt +bhúr +caoga +ceathair +ceathrar +chomh +chtó +chuig +chun +cois +céad +cúig +cúigear +d' +daichead +dar +de +deich +deichniúr +den +dhá +do +don +dtí +dá +dár +dó +faoi +faoin +faoina +faoinár +fara +fiche +gach +gan +go +gur +haon +hocht +i +iad +idir +in +ina +ins +inár +is +le +leis +lena +lenár +m' +mar +mo +mé +na +nach +naoi +naonúr +ná +ní +níor +nó +nócha +ocht +ochtar +os +roimh +sa +seacht +seachtar +seachtó +seasca +seisear +siad +sibh +sinn +sna +sé +sí +tar +thar +thú +triúr +trí +trína +trínár +tríocha +tú +um +ár +é +éis +í +ó +ón +óna +ónár diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_gl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_gl.txt new file mode 100644 index 0000000000..d8760b12c1 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_gl.txt @@ -0,0 +1,161 @@ +# galican stopwords +a +aínda +alí +aquel +aquela +aquelas +aqueles +aquilo +aquí +ao +aos +as +así +á +ben +cando +che +co +coa +comigo +con +connosco +contigo +convosco +coas +cos +cun +cuns +cunha +cunhas +da +dalgunha +dalgunhas +dalgún +dalgúns +das +de +del +dela +delas +deles +desde +deste +do +dos +dun +duns +dunha +dunhas +e +el +ela +elas +eles +en +era +eran +esa +esas +ese +eses +esta +estar +estaba +está +están +este +estes +estiven +estou +eu +é +facer +foi +foron +fun +había +hai +iso +isto +la +las +lle +lles +lo +los +mais +me +meu +meus +min +miña +miñas +moi +na +nas +neste +nin +no +non +nos +nosa +nosas +noso +nosos +nós +nun +nunha +nuns +nunhas +o +os +ou +ó +ós +para +pero +pode +pois +pola +polas +polo +polos +por +que +se +senón +ser +seu +seus +sexa +sido +sobre +súa +súas +tamén +tan +te +ten +teñen +teño +ter +teu +teus +ti +tido +tiña +tiven +túa +túas +un +unha +unhas +uns +vos +vosa +vosas +voso +vosos +vós diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hi.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hi.txt new file mode 100644 index 0000000000..86286bb083 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hi.txt @@ -0,0 +1,235 @@ +# Also see http://www.opensource.org/licenses/bsd-license.html +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# This file was created by Jacques Savoy and is distributed under the BSD license. +# Note: by default this file also contains forms normalized by HindiNormalizer +# for spelling variation (see section below), such that it can be used whether or +# not you enable that feature. When adding additional entries to this list, +# please add the normalized form as well. +अंदर +अत +अपना +अपनी +अपने +अभी +आदि +आप +इत्यादि +इन +इनका +इन्हीं +इन्हें +इन्हों +इस +इसका +इसकी +इसके +इसमें +इसी +इसे +उन +उनका +उनकी +उनके +उनको +उन्हीं +उन्हें +उन्हों +उस +उसके +उसी +उसे +एक +एवं +एस +ऐसे +और +कई +कर +करता +करते +करना +करने +करें +कहते +कहा +का +काफ़ी +कि +कितना +किन्हें +किन्हों +किया +किर +किस +किसी +किसे +की +कुछ +कुल +के +को +कोई +कौन +कौनसा +गया +घर +जब +जहाँ +जा +जितना +जिन +जिन्हें +जिन्हों +जिस +जिसे +जीधर +जैसा +जैसे +जो +तक +तब +तरह +तिन +तिन्हें +तिन्हों +तिस +तिसे +तो +था +थी +थे +दबारा +दिया +दुसरा +दूसरे +दो +द्वारा +न +नहीं +ना +निहायत +नीचे +ने +पर +पर +पहले +पूरा +पे +फिर +बनी +बही +बहुत +बाद +बाला +बिलकुल +भी +भीतर +मगर +मानो +मे +में +यदि +यह +यहाँ +यही +या +यिह +ये +रखें +रहा +रहे +ऱ्वासा +लिए +लिये +लेकिन +व +वर्ग +वह +वह +वहाँ +वहीं +वाले +वुह +वे +वग़ैरह +संग +सकता +सकते +सबसे +सभी +साथ +साबुत +साभ +सारा +से +सो +ही +हुआ +हुई +हुए +है +हैं +हो +होता +होती +होते +होना +होने +# additional normalized forms of the above +अपनि +जेसे +होति +सभि +तिंहों +इंहों +दवारा +इसि +किंहें +थि +उंहों +ओर +जिंहें +वहिं +अभि +बनि +हि +उंहिं +उंहें +हें +वगेरह +एसे +रवासा +कोन +निचे +काफि +उसि +पुरा +भितर +हे +बहि +वहां +कोइ +यहां +जिंहों +तिंहें +किसि +कइ +यहि +इंहिं +जिधर +इंहें +अदि +इतयादि +हुइ +कोनसा +इसकि +दुसरे +जहां +अप +किंहों +उनकि +भि +वरग +हुअ +जेसा +नहिं diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hu.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hu.txt new file mode 100644 index 0000000000..37526da8aa --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hu.txt @@ -0,0 +1,211 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/hungarian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + +| Hungarian stop word list +| prepared by Anna Tordai + +a +ahogy +ahol +aki +akik +akkor +alatt +által +általában +amely +amelyek +amelyekben +amelyeket +amelyet +amelynek +ami +amit +amolyan +amíg +amikor +át +abban +ahhoz +annak +arra +arról +az +azok +azon +azt +azzal +azért +aztán +azután +azonban +bár +be +belül +benne +cikk +cikkek +cikkeket +csak +de +e +eddig +egész +egy +egyes +egyetlen +egyéb +egyik +egyre +ekkor +el +elég +ellen +elő +először +előtt +első +én +éppen +ebben +ehhez +emilyen +ennek +erre +ez +ezt +ezek +ezen +ezzel +ezért +és +fel +felé +hanem +hiszen +hogy +hogyan +igen +így +illetve +ill. +ill +ilyen +ilyenkor +ison +ismét +itt +jó +jól +jobban +kell +kellett +keresztül +keressünk +ki +kívül +között +közül +legalább +lehet +lehetett +legyen +lenne +lenni +lesz +lett +maga +magát +majd +majd +már +más +másik +meg +még +mellett +mert +mely +melyek +mi +mit +míg +miért +milyen +mikor +minden +mindent +mindenki +mindig +mint +mintha +mivel +most +nagy +nagyobb +nagyon +ne +néha +nekem +neki +nem +néhány +nélkül +nincs +olyan +ott +össze +ő +ők +őket +pedig +persze +rá +s +saját +sem +semmi +sok +sokat +sokkal +számára +szemben +szerint +szinte +talán +tehát +teljes +tovább +továbbá +több +úgy +ugyanis +új +újabb +újra +után +utána +utolsó +vagy +vagyis +valaki +valami +valamint +való +vagyok +van +vannak +volt +voltam +voltak +voltunk +vissza +vele +viszont +volna diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hy.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hy.txt new file mode 100644 index 0000000000..60c1c50fbc --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_hy.txt @@ -0,0 +1,46 @@ +# example set of Armenian stopwords. +այդ +այլ +այն +այս +դու +դուք +եմ +են +ենք +ես +եք +է +էի +էին +էինք +էիր +էիք +էր +ըստ +թ +ի +ին +իսկ +իր +կամ +համար +հետ +հետո +մենք +մեջ +մի +ն +նա +նաև +նրա +նրանք +որ +որը +որոնք +որպես +ու +ում +պիտի +վրա +և diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_id.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_id.txt new file mode 100644 index 0000000000..4617f83a5c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_id.txt @@ -0,0 +1,359 @@ +# from appendix D of: A Study of Stemming Effects on Information +# Retrieval in Bahasa Indonesia +ada +adanya +adalah +adapun +agak +agaknya +agar +akan +akankah +akhirnya +aku +akulah +amat +amatlah +anda +andalah +antar +diantaranya +antara +antaranya +diantara +apa +apaan +mengapa +apabila +apakah +apalagi +apatah +atau +ataukah +ataupun +bagai +bagaikan +sebagai +sebagainya +bagaimana +bagaimanapun +sebagaimana +bagaimanakah +bagi +bahkan +bahwa +bahwasanya +sebaliknya +banyak +sebanyak +beberapa +seberapa +begini +beginian +beginikah +beginilah +sebegini +begitu +begitukah +begitulah +begitupun +sebegitu +belum +belumlah +sebelum +sebelumnya +sebenarnya +berapa +berapakah +berapalah +berapapun +betulkah +sebetulnya +biasa +biasanya +bila +bilakah +bisa +bisakah +sebisanya +boleh +bolehkah +bolehlah +buat +bukan +bukankah +bukanlah +bukannya +cuma +percuma +dahulu +dalam +dan +dapat +dari +daripada +dekat +demi +demikian +demikianlah +sedemikian +dengan +depan +di +dia +dialah +dini +diri +dirinya +terdiri +dong +dulu +enggak +enggaknya +entah +entahlah +terhadap +terhadapnya +hal +hampir +hanya +hanyalah +harus +haruslah +harusnya +seharusnya +hendak +hendaklah +hendaknya +hingga +sehingga +ia +ialah +ibarat +ingin +inginkah +inginkan +ini +inikah +inilah +itu +itukah +itulah +jangan +jangankan +janganlah +jika +jikalau +juga +justru +kala +kalau +kalaulah +kalaupun +kalian +kami +kamilah +kamu +kamulah +kan +kapan +kapankah +kapanpun +dikarenakan +karena +karenanya +ke +kecil +kemudian +kenapa +kepada +kepadanya +ketika +seketika +khususnya +kini +kinilah +kiranya +sekiranya +kita +kitalah +kok +lagi +lagian +selagi +lah +lain +lainnya +melainkan +selaku +lalu +melalui +terlalu +lama +lamanya +selama +selama +selamanya +lebih +terlebih +bermacam +macam +semacam +maka +makanya +makin +malah +malahan +mampu +mampukah +mana +manakala +manalagi +masih +masihkah +semasih +masing +mau +maupun +semaunya +memang +mereka +merekalah +meski +meskipun +semula +mungkin +mungkinkah +nah +namun +nanti +nantinya +nyaris +oleh +olehnya +seorang +seseorang +pada +padanya +padahal +paling +sepanjang +pantas +sepantasnya +sepantasnyalah +para +pasti +pastilah +per +pernah +pula +pun +merupakan +rupanya +serupa +saat +saatnya +sesaat +saja +sajalah +saling +bersama +sama +sesama +sambil +sampai +sana +sangat +sangatlah +saya +sayalah +se +sebab +sebabnya +sebuah +tersebut +tersebutlah +sedang +sedangkan +sedikit +sedikitnya +segala +segalanya +segera +sesegera +sejak +sejenak +sekali +sekalian +sekalipun +sesekali +sekaligus +sekarang +sekarang +sekitar +sekitarnya +sela +selain +selalu +seluruh +seluruhnya +semakin +sementara +sempat +semua +semuanya +sendiri +sendirinya +seolah +seperti +sepertinya +sering +seringnya +serta +siapa +siapakah +siapapun +disini +disinilah +sini +sinilah +sesuatu +sesuatunya +suatu +sesudah +sesudahnya +sudah +sudahkah +sudahlah +supaya +tadi +tadinya +tak +tanpa +setelah +telah +tentang +tentu +tentulah +tentunya +tertentu +seterusnya +tapi +tetapi +setiap +tiap +setidaknya +tidak +tidakkah +tidaklah +toh +waduh +wah +wahai +sewaktu +walau +walaupun +wong +yaitu +yakni +yang diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_it.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_it.txt new file mode 100644 index 0000000000..1219cc773a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_it.txt @@ -0,0 +1,303 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/italian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | An Italian stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + +ad | a (to) before vowel +al | a + il +allo | a + lo +ai | a + i +agli | a + gli +all | a + l' +agl | a + gl' +alla | a + la +alle | a + le +con | with +col | con + il +coi | con + i (forms collo, cogli etc are now very rare) +da | from +dal | da + il +dallo | da + lo +dai | da + i +dagli | da + gli +dall | da + l' +dagl | da + gll' +dalla | da + la +dalle | da + le +di | of +del | di + il +dello | di + lo +dei | di + i +degli | di + gli +dell | di + l' +degl | di + gl' +della | di + la +delle | di + le +in | in +nel | in + el +nello | in + lo +nei | in + i +negli | in + gli +nell | in + l' +negl | in + gl' +nella | in + la +nelle | in + le +su | on +sul | su + il +sullo | su + lo +sui | su + i +sugli | su + gli +sull | su + l' +sugl | su + gl' +sulla | su + la +sulle | su + le +per | through, by +tra | among +contro | against +io | I +tu | thou +lui | he +lei | she +noi | we +voi | you +loro | they +mio | my +mia | +miei | +mie | +tuo | +tua | +tuoi | thy +tue | +suo | +sua | +suoi | his, her +sue | +nostro | our +nostra | +nostri | +nostre | +vostro | your +vostra | +vostri | +vostre | +mi | me +ti | thee +ci | us, there +vi | you, there +lo | him, the +la | her, the +li | them +le | them, the +gli | to him, the +ne | from there etc +il | the +un | a +uno | a +una | a +ma | but +ed | and +se | if +perché | why, because +anche | also +come | how +dov | where (as dov') +dove | where +che | who, that +chi | who +cui | whom +non | not +più | more +quale | who, that +quanto | how much +quanti | +quanta | +quante | +quello | that +quelli | +quella | +quelle | +questo | this +questi | +questa | +queste | +si | yes +tutto | all +tutti | all + + | single letter forms: + +a | at +c | as c' for ce or ci +e | and +i | the +l | as l' +o | or + + | forms of avere, to have (not including the infinitive): + +ho +hai +ha +abbiamo +avete +hanno +abbia +abbiate +abbiano +avrò +avrai +avrà +avremo +avrete +avranno +avrei +avresti +avrebbe +avremmo +avreste +avrebbero +avevo +avevi +aveva +avevamo +avevate +avevano +ebbi +avesti +ebbe +avemmo +aveste +ebbero +avessi +avesse +avessimo +avessero +avendo +avuto +avuta +avuti +avute + + | forms of essere, to be (not including the infinitive): +sono +sei +è +siamo +siete +sia +siate +siano +sarò +sarai +sarà +saremo +sarete +saranno +sarei +saresti +sarebbe +saremmo +sareste +sarebbero +ero +eri +era +eravamo +eravate +erano +fui +fosti +fu +fummo +foste +furono +fossi +fosse +fossimo +fossero +essendo + + | forms of fare, to do (not including the infinitive, fa, fat-): +faccio +fai +facciamo +fanno +faccia +facciate +facciano +farò +farai +farà +faremo +farete +faranno +farei +faresti +farebbe +faremmo +fareste +farebbero +facevo +facevi +faceva +facevamo +facevate +facevano +feci +facesti +fece +facemmo +faceste +fecero +facessi +facesse +facessimo +facessero +facendo + + | forms of stare, to be (not including the infinitive): +sto +stai +sta +stiamo +stanno +stia +stiate +stiano +starò +starai +starà +staremo +starete +staranno +starei +staresti +starebbe +staremmo +stareste +starebbero +stavo +stavi +stava +stavamo +stavate +stavano +stetti +stesti +stette +stemmo +steste +stettero +stessi +stesse +stessimo +stessero +stando diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ja.txt new file mode 100644 index 0000000000..d4321be6b1 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ja.txt @@ -0,0 +1,127 @@ +# +# This file defines a stopword set for Japanese. +# +# This set is made up of hand-picked frequent terms from segmented Japanese Wikipedia. +# Punctuation characters and frequent kanji have mostly been left out. See LUCENE-3745 +# for frequency lists, etc. that can be useful for making your own set (if desired) +# +# Note that there is an overlap between these stopwords and the terms stopped when used +# in combination with the JapanesePartOfSpeechStopFilter. When editing this file, note +# that comments are not allowed on the same line as stopwords. +# +# Also note that stopping is done in a case-insensitive manner. Change your StopFilter +# configuration if you need case-sensitive stopping. Lastly, note that stopping is done +# using the same character width as the entries in this file. Since this StopFilter is +# normally done after a CJKWidthFilter in your chain, you would usually want your romaji +# entries to be in half-width and your kana entries to be in full-width. +# +の +に +は +を +た +が +で +て +と +し +れ +さ +ある +いる +も +する +から +な +こと +として +い +や +れる +など +なっ +ない +この +ため +その +あっ +よう +また +もの +という +あり +まで +られ +なる +へ +か +だ +これ +によって +により +おり +より +による +ず +なり +られる +において +ば +なかっ +なく +しかし +について +せ +だっ +その後 +できる +それ +う +ので +なお +のみ +でき +き +つ +における +および +いう +さらに +でも +ら +たり +その他 +に関する +たち +ます +ん +なら +に対して +特に +せる +及び +これら +とき +では +にて +ほか +ながら +うち +そして +とともに +ただし +かつて +それぞれ +または +お +ほど +ものの +に対する +ほとんど +と共に +といった +です +とも +ところ +ここ +##### End of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_lv.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_lv.txt new file mode 100644 index 0000000000..e21a23c06c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_lv.txt @@ -0,0 +1,172 @@ +# Set of Latvian stopwords from A Stemming Algorithm for Latvian, Karlis Kreslins +# the original list of over 800 forms was refined: +# pronouns, adverbs, interjections were removed +# +# prepositions +aiz +ap +ar +apakš +ārpus +augšpus +bez +caur +dēļ +gar +iekš +iz +kopš +labad +lejpus +līdz +no +otrpus +pa +par +pār +pēc +pie +pirms +pret +priekš +starp +šaipus +uz +viņpus +virs +virspus +zem +apakšpus +# Conjunctions +un +bet +jo +ja +ka +lai +tomēr +tikko +turpretī +arī +kaut +gan +tādēļ +tā +ne +tikvien +vien +kā +ir +te +vai +kamēr +# Particles +ar +diezin +droši +diemžēl +nebūt +ik +it +taču +nu +pat +tiklab +iekšpus +nedz +tik +nevis +turpretim +jeb +iekam +iekām +iekāms +kolīdz +līdzko +tiklīdz +jebšu +tālab +tāpēc +nekā +itin +jā +jau +jel +nē +nezin +tad +tikai +vis +tak +iekams +vien +# modal verbs +būt +biju +biji +bija +bijām +bijāt +esmu +esi +esam +esat +būšu +būsi +būs +būsim +būsiet +tikt +tiku +tiki +tika +tikām +tikāt +tieku +tiec +tiek +tiekam +tiekat +tikšu +tiks +tiksim +tiksiet +tapt +tapi +tapāt +topat +tapšu +tapsi +taps +tapsim +tapsiet +kļūt +kļuvu +kļuvi +kļuva +kļuvām +kļuvāt +kļūstu +kļūsti +kļūst +kļūstam +kļūstat +kļūšu +kļūsi +kļūs +kļūsim +kļūsiet +# verbs +varēt +varēju +varējām +varēšu +varēsim +var +varēji +varējāt +varēsi +varēsiet +varat +varēja +varēs diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_nl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_nl.txt new file mode 100644 index 0000000000..47a2aeacf6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_nl.txt @@ -0,0 +1,119 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/dutch/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Dutch stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large sample of Dutch text. + + | Dutch stop words frequently exhibit homonym clashes. These are indicated + | clearly below. + +de | the +en | and +van | of, from +ik | I, the ego +te | (1) chez, at etc, (2) to, (3) too +dat | that, which +die | that, those, who, which +in | in, inside +een | a, an, one +hij | he +het | the, it +niet | not, nothing, naught +zijn | (1) to be, being, (2) his, one's, its +is | is +was | (1) was, past tense of all persons sing. of 'zijn' (to be) (2) wax, (3) the washing, (4) rise of river +op | on, upon, at, in, up, used up +aan | on, upon, to (as dative) +met | with, by +als | like, such as, when +voor | (1) before, in front of, (2) furrow +had | had, past tense all persons sing. of 'hebben' (have) +er | there +maar | but, only +om | round, about, for etc +hem | him +dan | then +zou | should/would, past tense all persons sing. of 'zullen' +of | or, whether, if +wat | what, something, anything +mijn | possessive and noun 'mine' +men | people, 'one' +dit | this +zo | so, thus, in this way +door | through by +over | over, across +ze | she, her, they, them +zich | oneself +bij | (1) a bee, (2) by, near, at +ook | also, too +tot | till, until +je | you +mij | me +uit | out of, from +der | Old Dutch form of 'van der' still found in surnames +daar | (1) there, (2) because +haar | (1) her, their, them, (2) hair +naar | (1) unpleasant, unwell etc, (2) towards, (3) as +heb | present first person sing. of 'to have' +hoe | how, why +heeft | present third person sing. of 'to have' +hebben | 'to have' and various parts thereof +deze | this +u | you +want | (1) for, (2) mitten, (3) rigging +nog | yet, still +zal | 'shall', first and third person sing. of verb 'zullen' (will) +me | me +zij | she, they +nu | now +ge | 'thou', still used in Belgium and south Netherlands +geen | none +omdat | because +iets | something, somewhat +worden | to become, grow, get +toch | yet, still +al | all, every, each +waren | (1) 'were' (2) to wander, (3) wares, (3) +veel | much, many +meer | (1) more, (2) lake +doen | to do, to make +toen | then, when +moet | noun 'spot/mote' and present form of 'to must' +ben | (1) am, (2) 'are' in interrogative second person singular of 'to be' +zonder | without +kan | noun 'can' and present form of 'to be able' +hun | their, them +dus | so, consequently +alles | all, everything, anything +onder | under, beneath +ja | yes, of course +eens | once, one day +hier | here +wie | who +werd | imperfect third person sing. of 'become' +altijd | always +doch | yet, but etc +wordt | present third person sing. of 'become' +wezen | (1) to be, (2) 'been' as in 'been fishing', (3) orphans +kunnen | to be able +ons | us/our +zelf | self +tegen | against, towards, at +na | after, near +reeds | already +wil | (1) present tense of 'want', (2) 'will', noun, (3) fender +kon | could; past tense of 'to be able' +niets | nothing +uw | your +iemand | somebody +geweest | been; past participle of 'be' +andere | other diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_no.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_no.txt new file mode 100644 index 0000000000..a7a2c28ba5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_no.txt @@ -0,0 +1,194 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/norwegian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Norwegian stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This stop word list is for the dominant bokmål dialect. Words unique + | to nynorsk are marked *. + + | Revised by Jan Bruusgaard , Jan 2005 + +og | and +i | in +jeg | I +det | it/this/that +at | to (w. inf.) +en | a/an +et | a/an +den | it/this/that +til | to +er | is/am/are +som | who/that +på | on +de | they / you(formal) +med | with +han | he +av | of +ikke | not +ikkje | not * +der | there +så | so +var | was/were +meg | me +seg | you +men | but +ett | one +har | have +om | about +vi | we +min | my +mitt | my +ha | have +hadde | had +hun | she +nå | now +over | over +da | when/as +ved | by/know +fra | from +du | you +ut | out +sin | your +dem | them +oss | us +opp | up +man | you/one +kan | can +hans | his +hvor | where +eller | or +hva | what +skal | shall/must +selv | self (reflective) +sjøl | self (reflective) +her | here +alle | all +vil | will +bli | become +ble | became +blei | became * +blitt | have become +kunne | could +inn | in +når | when +være | be +kom | come +noen | some +noe | some +ville | would +dere | you +som | who/which/that +deres | their/theirs +kun | only/just +ja | yes +etter | after +ned | down +skulle | should +denne | this +for | for/because +deg | you +si | hers/his +sine | hers/his +sitt | hers/his +mot | against +å | to +meget | much +hvorfor | why +dette | this +disse | these/those +uten | without +hvordan | how +ingen | none +din | your +ditt | your +blir | become +samme | same +hvilken | which +hvilke | which (plural) +sånn | such a +inni | inside/within +mellom | between +vår | our +hver | each +hvem | who +vors | us/ours +hvis | whose +både | both +bare | only/just +enn | than +fordi | as/because +før | before +mange | many +også | also +slik | just +vært | been +være | to be +båe | both * +begge | both +siden | since +dykk | your * +dykkar | yours * +dei | they * +deira | them * +deires | theirs * +deim | them * +di | your (fem.) * +då | as/when * +eg | I * +ein | a/an * +eit | a/an * +eitt | a/an * +elles | or * +honom | he * +hjå | at * +ho | she * +hoe | she * +henne | her +hennar | her/hers +hennes | hers +hoss | how * +hossen | how * +ikkje | not * +ingi | noone * +inkje | noone * +korleis | how * +korso | how * +kva | what/which * +kvar | where * +kvarhelst | where * +kven | who/whom * +kvi | why * +kvifor | why * +me | we * +medan | while * +mi | my * +mine | my * +mykje | much * +no | now * +nokon | some (masc./neut.) * +noka | some (fem.) * +nokor | some * +noko | some * +nokre | some * +si | his/hers * +sia | since * +sidan | since * +so | so * +somt | some * +somme | some * +um | about* +upp | up * +vere | be * +vore | was * +verte | become * +vort | become * +varte | became * +vart | became * + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_pt.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_pt.txt new file mode 100644 index 0000000000..acfeb01af6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_pt.txt @@ -0,0 +1,253 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/portuguese/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Portuguese stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + + | The following is a ranked list (commonest to rarest) of stopwords + | deriving from a large sample of text. + + | Extra words have been added at the end. + +de | of, from +a | the; to, at; her +o | the; him +que | who, that +e | and +do | de + o +da | de + a +em | in +um | a +para | for + | é from SER +com | with +não | not, no +uma | a +os | the; them +no | em + o +se | himself etc +na | em + a +por | for +mais | more +as | the; them +dos | de + os +como | as, like +mas | but + | foi from SER +ao | a + o +ele | he +das | de + as + | tem from TER +à | a + a +seu | his +sua | her +ou | or + | ser from SER +quando | when +muito | much + | há from HAV +nos | em + os; us +já | already, now + | está from EST +eu | I +também | also +só | only, just +pelo | per + o +pela | per + a +até | up to +isso | that +ela | he +entre | between + | era from SER +depois | after +sem | without +mesmo | same +aos | a + os + | ter from TER +seus | his +quem | whom +nas | em + as +me | me +esse | that +eles | they + | estão from EST +você | you + | tinha from TER + | foram from SER +essa | that +num | em + um +nem | nor +suas | her +meu | my +às | a + as +minha | my + | têm from TER +numa | em + uma +pelos | per + os +elas | they + | havia from HAV + | seja from SER +qual | which + | será from SER +nós | we + | tenho from TER +lhe | to him, her +deles | of them +essas | those +esses | those +pelas | per + as +este | this + | fosse from SER +dele | of him + + | other words. There are many contractions such as naquele = em+aquele, + | mo = me+o, but they are rare. + | Indefinite article plural forms are also rare. + +tu | thou +te | thee +vocês | you (plural) +vos | you +lhes | to them +meus | my +minhas +teu | thy +tua +teus +tuas +nosso | our +nossa +nossos +nossas + +dela | of her +delas | of them + +esta | this +estes | these +estas | these +aquele | that +aquela | that +aqueles | those +aquelas | those +isto | this +aquilo | that + + | forms of estar, to be (not including the infinitive): +estou +está +estamos +estão +estive +esteve +estivemos +estiveram +estava +estávamos +estavam +estivera +estivéramos +esteja +estejamos +estejam +estivesse +estivéssemos +estivessem +estiver +estivermos +estiverem + + | forms of haver, to have (not including the infinitive): +hei +há +havemos +hão +houve +houvemos +houveram +houvera +houvéramos +haja +hajamos +hajam +houvesse +houvéssemos +houvessem +houver +houvermos +houverem +houverei +houverá +houveremos +houverão +houveria +houveríamos +houveriam + + | forms of ser, to be (not including the infinitive): +sou +somos +são +era +éramos +eram +fui +foi +fomos +foram +fora +fôramos +seja +sejamos +sejam +fosse +fôssemos +fossem +for +formos +forem +serei +será +seremos +serão +seria +seríamos +seriam + + | forms of ter, to have (not including the infinitive): +tenho +tem +temos +tém +tinha +tínhamos +tinham +tive +teve +tivemos +tiveram +tivera +tivéramos +tenha +tenhamos +tenham +tivesse +tivéssemos +tivessem +tiver +tivermos +tiverem +terei +terá +teremos +terão +teria +teríamos +teriam diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ro.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ro.txt new file mode 100644 index 0000000000..4fdee90a5b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ro.txt @@ -0,0 +1,233 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +acea +aceasta +această +aceea +acei +aceia +acel +acela +acele +acelea +acest +acesta +aceste +acestea +aceşti +aceştia +acolo +acum +ai +aia +aibă +aici +al +ăla +ale +alea +ălea +altceva +altcineva +am +ar +are +aş +aşadar +asemenea +asta +ăsta +astăzi +astea +ăstea +ăştia +asupra +aţi +au +avea +avem +aveţi +azi +bine +bucur +bună +ca +că +căci +când +care +cărei +căror +cărui +cât +câte +câţi +către +câtva +ce +cel +ceva +chiar +cînd +cine +cineva +cît +cîte +cîţi +cîtva +contra +cu +cum +cumva +curând +curînd +da +dă +dacă +dar +datorită +de +deci +deja +deoarece +departe +deşi +din +dinaintea +dintr +dintre +drept +după +ea +ei +el +ele +eram +este +eşti +eu +face +fără +fi +fie +fiecare +fii +fim +fiţi +iar +ieri +îi +îl +îmi +împotriva +în +înainte +înaintea +încât +încît +încotro +între +întrucât +întrucît +îţi +la +lângă +le +li +lîngă +lor +lui +mă +mâine +mea +mei +mele +mereu +meu +mi +mine +mult +multă +mulţi +ne +nicăieri +nici +nimeni +nişte +noastră +noastre +noi +noştri +nostru +nu +ori +oricând +oricare +oricât +orice +oricînd +oricine +oricît +oricum +oriunde +până +pe +pentru +peste +pînă +poate +pot +prea +prima +primul +prin +printr +sa +să +săi +sale +sau +său +se +şi +sînt +sîntem +sînteţi +spre +sub +sunt +suntem +sunteţi +ta +tăi +tale +tău +te +ţi +ţie +tine +toată +toate +tot +toţi +totuşi +tu +un +una +unde +undeva +unei +unele +uneori +unor +vă +vi +voastră +voastre +voi +voştri +vostru +vouă +vreo +vreun diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ru.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ru.txt new file mode 100644 index 0000000000..55271400c6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_ru.txt @@ -0,0 +1,243 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/russian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | a russian stop word list. comments begin with vertical bar. each stop + | word is at the start of a line. + + | this is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + | letter `ё' is translated to `е'. + +и | and +в | in/into +во | alternative form +не | not +что | what/that +он | he +на | on/onto +я | i +с | from +со | alternative form +как | how +а | milder form of `no' (but) +то | conjunction and form of `that' +все | all +она | she +так | so, thus +его | him +но | but +да | yes/and +ты | thou +к | towards, by +у | around, chez +же | intensifier particle +вы | you +за | beyond, behind +бы | conditional/subj. particle +по | up to, along +только | only +ее | her +мне | to me +было | it was +вот | here is/are, particle +от | away from +меня | me +еще | still, yet, more +нет | no, there isnt/arent +о | about +из | out of +ему | to him +теперь | now +когда | when +даже | even +ну | so, well +вдруг | suddenly +ли | interrogative particle +если | if +уже | already, but homonym of `narrower' +или | or +ни | neither +быть | to be +был | he was +него | prepositional form of его +до | up to +вас | you accusative +нибудь | indef. suffix preceded by hyphen +опять | again +уж | already, but homonym of `adder' +вам | to you +сказал | he said +ведь | particle `after all' +там | there +потом | then +себя | oneself +ничего | nothing +ей | to her +может | usually with `быть' as `maybe' +они | they +тут | here +где | where +есть | there is/are +надо | got to, must +ней | prepositional form of ей +для | for +мы | we +тебя | thee +их | them, their +чем | than +была | she was +сам | self +чтоб | in order to +без | without +будто | as if +человек | man, person, one +чего | genitive form of `what' +раз | once +тоже | also +себе | to oneself +под | beneath +жизнь | life +будет | will be +ж | short form of intensifer particle `же' +тогда | then +кто | who +этот | this +говорил | was saying +того | genitive form of `that' +потому | for that reason +этого | genitive form of `this' +какой | which +совсем | altogether +ним | prepositional form of `его', `они' +здесь | here +этом | prepositional form of `этот' +один | one +почти | almost +мой | my +тем | instrumental/dative plural of `тот', `то' +чтобы | full form of `in order that' +нее | her (acc.) +кажется | it seems +сейчас | now +были | they were +куда | where to +зачем | why +сказать | to say +всех | all (acc., gen. preposn. plural) +никогда | never +сегодня | today +можно | possible, one can +при | by +наконец | finally +два | two +об | alternative form of `о', about +другой | another +хоть | even +после | after +над | above +больше | more +тот | that one (masc.) +через | across, in +эти | these +нас | us +про | about +всего | in all, only, of all +них | prepositional form of `они' (they) +какая | which, feminine +много | lots +разве | interrogative particle +сказала | she said +три | three +эту | this, acc. fem. sing. +моя | my, feminine +впрочем | moreover, besides +хорошо | good +свою | ones own, acc. fem. sing. +этой | oblique form of `эта', fem. `this' +перед | in front of +иногда | sometimes +лучше | better +чуть | a little +том | preposn. form of `that one' +нельзя | one must not +такой | such a one +им | to them +более | more +всегда | always +конечно | of course +всю | acc. fem. sing of `all' +между | between + + + | b: some paradigms + | + | personal pronouns + | + | я меня мне мной [мною] + | ты тебя тебе тобой [тобою] + | он его ему им [него, нему, ним] + | она ее эи ею [нее, нэи, нею] + | оно его ему им [него, нему, ним] + | + | мы нас нам нами + | вы вас вам вами + | они их им ими [них, ним, ними] + | + | себя себе собой [собою] + | + | demonstrative pronouns: этот (this), тот (that) + | + | этот эта это эти + | этого эты это эти + | этого этой этого этих + | этому этой этому этим + | этим этой этим [этою] этими + | этом этой этом этих + | + | тот та то те + | того ту то те + | того той того тех + | тому той тому тем + | тем той тем [тою] теми + | том той том тех + | + | determinative pronouns + | + | (a) весь (all) + | + | весь вся все все + | всего всю все все + | всего всей всего всех + | всему всей всему всем + | всем всей всем [всею] всеми + | всем всей всем всех + | + | (b) сам (himself etc) + | + | сам сама само сами + | самого саму само самих + | самого самой самого самих + | самому самой самому самим + | самим самой самим [самою] самими + | самом самой самом самих + | + | stems of verbs `to be', `to have', `to do' and modal + | + | быть бы буд быв есть суть + | име + | дел + | мог мож мочь + | уме + | хоч хот + | долж + | можн + | нужн + | нельзя + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_sv.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_sv.txt new file mode 100644 index 0000000000..096f87f676 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_sv.txt @@ -0,0 +1,133 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/swedish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Swedish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + | Swedish stop words occasionally exhibit homonym clashes. For example + | så = so, but also seed. These are indicated clearly below. + +och | and +det | it, this/that +att | to (with infinitive) +i | in, at +en | a +jag | I +hon | she +som | who, that +han | he +på | on +den | it, this/that +med | with +var | where, each +sig | him(self) etc +för | for +så | so (also: seed) +till | to +är | is +men | but +ett | a +om | if; around, about +hade | had +de | they, these/those +av | of +icke | not, no +mig | me +du | you +henne | her +då | then, when +sin | his +nu | now +har | have +inte | inte någon = no one +hans | his +honom | him +skulle | 'sake' +hennes | her +där | there +min | my +man | one (pronoun) +ej | nor +vid | at, by, on (also: vast) +kunde | could +något | some etc +från | from, off +ut | out +när | when +efter | after, behind +upp | up +vi | we +dem | them +vara | be +vad | what +över | over +än | than +dig | you +kan | can +sina | his +här | here +ha | have +mot | towards +alla | all +under | under (also: wonder) +någon | some etc +eller | or (else) +allt | all +mycket | much +sedan | since +ju | why +denna | this/that +själv | myself, yourself etc +detta | this/that +åt | to +utan | without +varit | was +hur | how +ingen | no +mitt | my +ni | you +bli | to be, become +blev | from bli +oss | us +din | thy +dessa | these/those +några | some etc +deras | their +blir | from bli +mina | my +samma | (the) same +vilken | who, that +er | you, your +sådan | such a +vår | our +blivit | from bli +dess | its +inom | within +mellan | between +sådant | such a +varför | why +varje | each +vilka | who, that +ditt | thy +vem | who +vilket | who, that +sitta | his +sådana | such a +vart | each +dina | thy +vars | whose +vårt | our +våra | our +ert | your +era | your +vilkas | whose + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_th.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_th.txt new file mode 100644 index 0000000000..07f0fabe69 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_th.txt @@ -0,0 +1,119 @@ +# Thai stopwords from: +# "Opinion Detection in Thai Political News Columns +# Based on Subjectivity Analysis" +# Khampol Sukhum, Supot Nitsuwat, and Choochart Haruechaiyasak +ไว้ +ไม่ +ไป +ได้ +ให้ +ใน +โดย +แห่ง +แล้ว +และ +แรก +แบบ +แต่ +เอง +เห็น +เลย +เริ่ม +เรา +เมื่อ +เพื่อ +เพราะ +เป็นการ +เป็น +เปิดเผย +เปิด +เนื่องจาก +เดียวกัน +เดียว +เช่น +เฉพาะ +เคย +เข้า +เขา +อีก +อาจ +อะไร +ออก +อย่าง +อยู่ +อยาก +หาก +หลาย +หลังจาก +หลัง +หรือ +หนึ่ง +ส่วน +ส่ง +สุด +สําหรับ +ว่า +วัน +ลง +ร่วม +ราย +รับ +ระหว่าง +รวม +ยัง +มี +มาก +มา +พร้อม +พบ +ผ่าน +ผล +บาง +น่า +นี้ +นํา +นั้น +นัก +นอกจาก +ทุก +ที่สุด +ที่ +ทําให้ +ทํา +ทาง +ทั้งนี้ +ทั้ง +ถ้า +ถูก +ถึง +ต้อง +ต่างๆ +ต่าง +ต่อ +ตาม +ตั้งแต่ +ตั้ง +ด้าน +ด้วย +ดัง +ซึ่ง +ช่วง +จึง +จาก +จัด +จะ +คือ +ความ +ครั้ง +คง +ขึ้น +ของ +ขอ +ขณะ +ก่อน +ก็ +การ +กับ +กัน +กว่า +กล่าว diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_tr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_tr.txt new file mode 100644 index 0000000000..84d9408d4e --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/stopwords_tr.txt @@ -0,0 +1,212 @@ +# Turkish stopwords from LUCENE-559 +# merged with the list from "Information Retrieval on Turkish Texts" +# (http://www.users.muohio.edu/canf/papers/JASIST2008offPrint.pdf) +acaba +altmış +altı +ama +ancak +arada +aslında +ayrıca +bana +bazı +belki +ben +benden +beni +benim +beri +beş +bile +bin +bir +birçok +biri +birkaç +birkez +birşey +birşeyi +biz +bize +bizden +bizi +bizim +böyle +böylece +bu +buna +bunda +bundan +bunlar +bunları +bunların +bunu +bunun +burada +çok +çünkü +da +daha +dahi +de +defa +değil +diğer +diye +doksan +dokuz +dolayı +dolayısıyla +dört +edecek +eden +ederek +edilecek +ediliyor +edilmesi +ediyor +eğer +elli +en +etmesi +etti +ettiği +ettiğini +gibi +göre +halen +hangi +hatta +hem +henüz +hep +hepsi +her +herhangi +herkesin +hiç +hiçbir +için +iki +ile +ilgili +ise +işte +itibaren +itibariyle +kadar +karşın +katrilyon +kendi +kendilerine +kendini +kendisi +kendisine +kendisini +kez +ki +kim +kimden +kime +kimi +kimse +kırk +milyar +milyon +mu +mü +mı +nasıl +ne +neden +nedenle +nerde +nerede +nereye +niye +niçin +o +olan +olarak +oldu +olduğu +olduğunu +olduklarını +olmadı +olmadığı +olmak +olması +olmayan +olmaz +olsa +olsun +olup +olur +olursa +oluyor +on +ona +ondan +onlar +onlardan +onları +onların +onu +onun +otuz +oysa +öyle +pek +rağmen +sadece +sanki +sekiz +seksen +sen +senden +seni +senin +siz +sizden +sizi +sizin +şey +şeyden +şeyi +şeyler +şöyle +şu +şuna +şunda +şundan +şunları +şunu +tarafından +trilyon +tüm +üç +üzere +var +vardı +ve +veya +ya +yani +yapacak +yapılan +yapılması +yapıyor +yapmak +yaptı +yaptığı +yaptığını +yaptıkları +yedi +yerine +yetmiş +yine +yirmi +yoksa +yüz +zaten diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/userdict_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/userdict_ja.txt new file mode 100644 index 0000000000..6f0368e4d8 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/lang/userdict_ja.txt @@ -0,0 +1,29 @@ +# +# This is a sample user dictionary for Kuromoji (JapaneseTokenizer) +# +# Add entries to this file in order to override the statistical model in terms +# of segmentation, readings and part-of-speech tags. Notice that entries do +# not have weights since they are always used when found. This is by-design +# in order to maximize ease-of-use. +# +# Entries are defined using the following CSV format: +# , ... , ... , +# +# Notice that a single half-width space separates tokens and readings, and +# that the number tokens and readings must match exactly. +# +# Also notice that multiple entries with the same is undefined. +# +# Whitespace only lines are ignored. Comments are not allowed on entry lines. +# + +# Custom segmentation for kanji compounds +日本経済新聞,日本 経済 新聞,ニホン ケイザイ シンブン,カスタム名詞 +関西国際空港,関西 国際 空港,カンサイ コクサイ クウコウ,カスタム名詞 + +# Custom segmentation for compound katakana +トートバッグ,トート バッグ,トート バッグ,かずカナ名詞 +ショルダーバッグ,ショルダー バッグ,ショルダー バッグ,かずカナ名詞 + +# Custom reading for former sumo wrestler +朝青龍,朝青龍,アサショウリュウ,カスタム人名 diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema new file mode 100644 index 0000000000..b50c5586c4 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/managed-schema @@ -0,0 +1,1003 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + id + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/params.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/params.json new file mode 100644 index 0000000000..06114ef257 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/params.json @@ -0,0 +1,20 @@ +{"params":{ + "query":{ + "defType":"edismax", + "q.alt":"*:*", + "rows":"10", + "fl":"*,score", + "":{"v":0} + }, + "facets":{ + "facet":"on", + "facet.mincount": "1", + "":{"v":0} + }, + "velocity":{ + "wt": "velocity", + "v.template":"browse", + "v.layout": "layout", + "":{"v":0} + } +}} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/protwords.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/protwords.txt new file mode 100644 index 0000000000..1dfc0abecb --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/protwords.txt @@ -0,0 +1,21 @@ +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +#----------------------------------------------------------------------- +# Use a protected word file to protect against the stemmer reducing two +# unrelated words to the same base word. + +# Some non-words that normally won't be encountered, +# just to test that they won't be stemmed. +dontstems +zwhacky + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/solrconfig.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/solrconfig.xml new file mode 100644 index 0000000000..562b1cb555 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/solrconfig.xml @@ -0,0 +1,1364 @@ + + + + + + + + + 7.5.0 + + + + + + + + + + + + + + + + + + + + ${solr.data.dir:} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${solr.lock.type:single} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${solr.ulog.dir:} + ${solr.ulog.numVersionBuckets:65536} + + + + + ${solr.autoCommit.maxTime:15000} + false + + + + + + ${solr.autoSoftCommit.maxTime:-1} + + + + + + + + + + + + + + 1024 + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + 20 + + + 200 + + + + + + + + + + + + + + + + false + + + + + + + + + + + + + + + + + + + + + + explicit + 10 + + + + + + + + + + + + + + + + explicit + json + true + + + + + + + + explicit + + + + + + _text_ + + + + + + + true + ignored_ + _text_ + + + + + + + + + text_general + + + + + + default + _text_ + solr.DirectSolrSpellChecker + + internal + + 0.5 + + 2 + + 1 + + 5 + + 4 + + 0.01 + + + + + + + + + + + + default + on + true + 10 + 5 + 5 + true + true + 10 + 5 + + + spellcheck + + + + + + + + + + true + + + tvComponent + + + + + + + + + + + + true + false + + + terms + + + + + + + + string + + + + + + explicit + + + elevator + + + + + + + + + + + 100 + + + + + + + + 70 + + 0.5 + + [-\w ,/\n\"']{20,200} + + + + + + + ]]> + ]]> + + + + + + + + + + + + + + + + + + + + + + + + ,, + ,, + ,, + ,, + ,]]> + ]]> + + + + + + 10 + .,!? + + + + + + + WORD + + + en + US + + + + + + + + + + + + [^\w-\.] + _ + + + + + + + yyyy-MM-dd'T'HH:mm:ss.SSSZ + yyyy-MM-dd'T'HH:mm:ss,SSSZ + yyyy-MM-dd'T'HH:mm:ss.SSS + yyyy-MM-dd'T'HH:mm:ss,SSS + yyyy-MM-dd'T'HH:mm:ssZ + yyyy-MM-dd'T'HH:mm:ss + yyyy-MM-dd'T'HH:mmZ + yyyy-MM-dd'T'HH:mm + yyyy-MM-dd HH:mm:ss.SSSZ + yyyy-MM-dd HH:mm:ss,SSSZ + yyyy-MM-dd HH:mm:ss.SSS + yyyy-MM-dd HH:mm:ss,SSS + yyyy-MM-dd HH:mm:ssZ + yyyy-MM-dd HH:mm:ss + yyyy-MM-dd HH:mmZ + yyyy-MM-dd HH:mm + yyyy-MM-dd + + + + + java.lang.String + text_general + + *_str + 256 + + + true + + + java.lang.Boolean + booleans + + + java.util.Date + pdates + + + java.lang.Long + java.lang.Integer + plongs + + + java.lang.Number + pdoubles + + + + + + + + + + + + + + + + + + + + + + + + + + text/plain; charset=UTF-8 + + + + + ${velocity.template.base.dir:} + ${velocity.solr.resource.loader.enabled:true} + ${velocity.params.resource.loader.enabled:false} + + + + + 5 + + + + + + + + + + + + + + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/stopwords.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/stopwords.txt new file mode 100644 index 0000000000..ae1e83eeb3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/stopwords.txt @@ -0,0 +1,14 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/synonyms.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/synonyms.txt new file mode 100644 index 0000000000..eab4ee8753 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/testConfig/synonyms.txt @@ -0,0 +1,29 @@ +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +#----------------------------------------------------------------------- +#some test synonym mappings unlikely to appear in real input text +aaafoo => aaabar +bbbfoo => bbbfoo bbbbar +cccfoo => cccbar cccbaz +fooaaa,baraaa,bazaaa + +# Some synonym groups specific to this example +GB,gib,gigabyte,gigabytes +MB,mib,megabyte,megabytes +Television, Televisions, TV, TVs +#notice we use "gib" instead of "GiB" so any WordDelimiterGraphFilter coming +#after us won't split it into two words. + +# Synonym mappings can be used for spelling correction too +pixima => pixma + diff --git a/dhp-workflows/dhp-worfklow-profiles/pom.xml b/dhp-workflows/dhp-workflow-profiles/pom.xml similarity index 93% rename from dhp-workflows/dhp-worfklow-profiles/pom.xml rename to dhp-workflows/dhp-workflow-profiles/pom.xml index 34996a0218..54e76c1e29 100644 --- a/dhp-workflows/dhp-worfklow-profiles/pom.xml +++ b/dhp-workflows/dhp-workflow-profiles/pom.xml @@ -7,7 +7,7 @@ 4.0.0 - dhp-worfklow-profiles + dhp-workflow-profiles jar