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 deleted file mode 100644 index c127783e5..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/InputStreamRequestBody.java +++ /dev/null @@ -1,53 +0,0 @@ - -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 final InputStream inputStream; - private final MediaType mediaType; - private final 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 deleted file mode 100644 index b75872eb4..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/MissingConceptDoiException.java +++ /dev/null @@ -1,8 +0,0 @@ - -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 deleted file mode 100644 index 544da78f5..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java +++ /dev/null @@ -1,365 +0,0 @@ - -package eu.dnetlib.dhp.common.api; - -import java.io.*; -import java.io.IOException; -import java.net.HttpURLConnection; -import java.net.URL; -import java.util.concurrent.TimeUnit; - -import org.apache.http.HttpHeaders; -import org.apache.http.entity.ContentType; -import org.jetbrains.annotations.NotNull; - -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) { - - 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 = "{}"; - - URL url = new URL(urlString); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()); - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setRequestMethod("POST"); - conn.setDoOutput(true); - try (OutputStream os = conn.getOutputStream()) { - byte[] input = json.getBytes("utf-8"); - os.write(input, 0, input.length); - } - - String body = getBody(conn); - - int responseCode = conn.getResponseCode(); - conn.disconnect(); - - if (!checkOKStatus(responseCode)) - throw new IOException("Unexpected code " + responseCode + body); - - ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class); - this.bucket = newSubmission.getLinks().getBucket(); - this.deposition_id = newSubmission.getId(); - - return responseCode; - } - - /** - * 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 - * @return the response code - */ - public int uploadIS(InputStream is, String file_name) throws IOException { - - URL url = new URL(bucket + "/" + file_name); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, "application/zip"); - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setDoOutput(true); - conn.setRequestMethod("PUT"); - - byte[] buf = new byte[8192]; - int length; - try (OutputStream os = conn.getOutputStream()) { - while ((length = is.read(buf)) != -1) { - os.write(buf, 0, length); - } - - } - int responseCode = conn.getResponseCode(); - if (!checkOKStatus(responseCode)) { - throw new IOException("Unexpected code " + responseCode + getBody(conn)); - } - - return responseCode; - } - - @NotNull - private String getBody(HttpURLConnection conn) throws IOException { - String body = "{}"; - try (BufferedReader br = new BufferedReader( - new InputStreamReader(conn.getInputStream(), "utf-8"))) { - StringBuilder response = new StringBuilder(); - String responseLine = null; - while ((responseLine = br.readLine()) != null) { - response.append(responseLine.trim()); - } - - body = response.toString(); - - } - return body; - } - - /** - * Associates metadata information to the current deposition - * - * @param metadata the metadata - * @return response code - * @throws IOException - */ - public int sendMretadata(String metadata) throws IOException { - - URL url = new URL(urlString + "/" + deposition_id); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()); - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setDoOutput(true); - conn.setRequestMethod("PUT"); - - try (OutputStream os = conn.getOutputStream()) { - byte[] input = metadata.getBytes("utf-8"); - os.write(input, 0, input.length); - - } - - final int responseCode = conn.getResponseCode(); - conn.disconnect(); - if (!checkOKStatus(responseCode)) - throw new IOException("Unexpected code " + responseCode + getBody(conn)); - - return responseCode; - - } - - private boolean checkOKStatus(int responseCode) { - - if (HttpURLConnection.HTTP_OK != responseCode || - HttpURLConnection.HTTP_CREATED != responseCode) - return true; - return false; - } - - /** - * To publish the current deposition. It works for both new deposition or new version of an old deposition - * - * @return response code - * @throws IOException - */ - @Deprecated - public int publish() throws IOException { - - String json = "{}"; - - OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build(); - - RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON); - - Request request = new Request.Builder() - .url(urlString + "/" + deposition_id + "/actions/publish") - .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()); - - 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, 1); - String json = "{}"; - - URL url = new URL(urlString + "/" + deposition_id + "/actions/newversion"); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setDoOutput(true); - conn.setRequestMethod("POST"); - - try (OutputStream os = conn.getOutputStream()) { - byte[] input = json.getBytes("utf-8"); - os.write(input, 0, input.length); - - } - - String body = getBody(conn); - - int responseCode = conn.getResponseCode(); - - conn.disconnect(); - if (!checkOKStatus(responseCode)) - throw new IOException("Unexpected code " + responseCode + body); - - ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class); - String latest_draft = zenodoModel.getLinks().getLatest_draft(); - deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1); - bucket = getBucket(latest_draft); - - return responseCode; - - } - - /** - * To finish uploading a version or new deposition not published - * It sets the deposition_id and the bucket to be used - * - * - * @param deposition_id the deposition id of the not yet published upload - * concept_rec_id = 656930 - * @return response code - * @throws IOException - * @throws MissingConceptDoiException - */ - public int uploadOpenDeposition(String deposition_id) throws IOException, MissingConceptDoiException { - - this.deposition_id = deposition_id; - - String json = "{}"; - - URL url = new URL(urlString + "/" + deposition_id); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setRequestMethod("POST"); - conn.setDoOutput(true); - try (OutputStream os = conn.getOutputStream()) { - byte[] input = json.getBytes("utf-8"); - os.write(input, 0, input.length); - } - - String body = getBody(conn); - - int responseCode = conn.getResponseCode(); - conn.disconnect(); - - if (!checkOKStatus(responseCode)) - throw new IOException("Unexpected code " + responseCode + body); - - ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class); - bucket = zenodoModel.getLinks().getBucket(); - - return responseCode; - - } - - private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException { - - ZenodoModelList zenodoModelList = new Gson() - .fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class); - - for (ZenodoModel zm : zenodoModelList) { - if (zm.getConceptrecid().equals(concept_rec_id)) { - deposition_id = zm.getId(); - return; - } - } - if (zenodoModelList.size() == 0) - throw new MissingConceptDoiException( - "The concept record id specified was missing in the list of depositions"); - setDepositionId(concept_rec_id, page + 1); - - } - - private String getPrevDepositions(String page) throws IOException { - - HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder(); - urlBuilder.addQueryParameter("page", page); - - URL url = new URL(urlBuilder.build().toString()); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()); - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setDoOutput(true); - conn.setRequestMethod("GET"); - - String body = getBody(conn); - - int responseCode = conn.getResponseCode(); - - conn.disconnect(); - if (!checkOKStatus(responseCode)) - throw new IOException("Unexpected code " + responseCode + body); - - return body; - - } - - private String getBucket(String inputUurl) throws IOException { - - URL url = new URL(inputUurl); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()); - conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token); - conn.setDoOutput(true); - conn.setRequestMethod("GET"); - - String body = getBody(conn); - - int responseCode = conn.getResponseCode(); - - conn.disconnect(); - if (!checkOKStatus(responseCode)) - throw new IOException("Unexpected code " + responseCode + body); - - ZenodoModel zenodoModel = new Gson().fromJson(body, 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 deleted file mode 100644 index a02224383..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Community.java +++ /dev/null @@ -1,14 +0,0 @@ - -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 deleted file mode 100644 index c14af55b6..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java +++ /dev/null @@ -1,47 +0,0 @@ - -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 deleted file mode 100644 index 509f444b9..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java +++ /dev/null @@ -1,44 +0,0 @@ - -package eu.dnetlib.dhp.common.api.zenodo; - -import java.io.Serializable; - -public class File implements Serializable { - private String checksum; - private String filename; - private long filesize; - private String id; - - 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; - } - -} 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 deleted file mode 100644 index 476f1d9d8..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Grant.java +++ /dev/null @@ -1,23 +0,0 @@ - -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 deleted file mode 100644 index bdf8e5d2c..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Links.java +++ /dev/null @@ -1,92 +0,0 @@ - -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 deleted file mode 100644 index b161adb9b..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Metadata.java +++ /dev/null @@ -1,153 +0,0 @@ - -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 deleted file mode 100644 index aa088ef31..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/PrereserveDoi.java +++ /dev/null @@ -1,25 +0,0 @@ - -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 deleted file mode 100644 index 15a349636..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/RelatedIdentifier.java +++ /dev/null @@ -1,43 +0,0 @@ - -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 deleted file mode 100644 index 9843ea0f9..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModel.java +++ /dev/null @@ -1,118 +0,0 @@ - -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 deleted file mode 100644 index b3b150714..000000000 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/ZenodoModelList.java +++ /dev/null @@ -1,7 +0,0 @@ - -package eu.dnetlib.dhp.common.api.zenodo; - -import java.util.ArrayList; - -public class ZenodoModelList extends ArrayList { -} 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 deleted file mode 100644 index 92c1dcda3..000000000 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java +++ /dev/null @@ -1,109 +0,0 @@ - -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 -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"; - - private final String depositionId = "674915"; - - @Test - void testUploadOldDeposition() throws IOException, MissingConceptDoiException { - ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING, - ACCESS_TOKEN); - Assertions.assertEquals(200, client.uploadOpenDeposition(depositionId)); - - 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")); - - 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 - 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")); - - 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 - 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")); - - Assertions.assertEquals(202, client.publish()); - - } - - @Test - 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")); - - Assertions.assertEquals(202, client.publish()); - - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java new file mode 100644 index 000000000..23be515eb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java @@ -0,0 +1,272 @@ + +package eu.dnetlib.dhp.actionmanager.webcrawl; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.io.compress.GzipCodec; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.sql.*; +import org.apache.spark.sql.types.StructType; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; +import scala.Tuple2; + +/** + * @author miriam.baglioni + * @Date 18/04/24 + */ +public class CreateActionSetFromWebEntries implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class); + private static final String DOI_PREFIX = "50|doi_________::"; + + private static final String ROR_PREFIX = "20|ror_________::"; + + private static final String PMID_PREFIX = "50|pmid________::"; + + private static final String PMCID_PREFIX = "50|pmc_________::"; + private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b"; + private static final String WEB_CRAWL_NAME = "Web Crawl"; + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + CreateActionSetFromWebEntries.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/webcrawl/as_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 -> { + + createActionSet(spark, inputPath, outputPath + "actionSet"); + createPlainRelations(spark, inputPath, outputPath + "relations"); + }); + } + + private static void createPlainRelations(SparkSession spark, String inputPath, String outputPath) { + final Dataset dataset = readWebCrawl(spark, inputPath); + + dataset.flatMap((FlatMapFunction>) row -> { + List> ret = new ArrayList<>(); + + final String ror = row.getAs("ror"); + ret.addAll(createAffiliationRelationPairDOI(row.getAs("publication_year"), row.getAs("doi"), ror)); + ret.addAll(createAffiliationRelationPairPMID(row.getAs("publication_year"), row.getAs("pmid"), ror)); + ret.addAll(createAffiliationRelationPairPMCID(row.getAs("publication_year"), row.getAs("pmcid"), ror)); + + return ret + .iterator(); + }, Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class))) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + + private static Collection> createAffiliationRelationPairPMCID( + String publication_year, String pmcid, String ror) { + if (pmcid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair("PMC" + pmcid, ror) + .stream() + .map(r -> new Tuple2(publication_year, r)) + .collect(Collectors.toList()); + } + + private static Collection> createAffiliationRelationPairPMID( + String publication_year, String pmid, String ror) { + if (pmid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair(pmid, ror) + .stream() + .map(r -> new Tuple2(publication_year, r)) + .collect(Collectors.toList()); + } + + private static Collection> createAffiliationRelationPairDOI( + String publication_year, String doi, String ror) { + if (doi == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair(doi, ror) + .stream() + .map(r -> new Tuple2(publication_year, r)) + .collect(Collectors.toList()); + } + + public static void createActionSet(SparkSession spark, String inputPath, + String outputPath) { + + final Dataset dataset = readWebCrawl(spark, inputPath) + .filter("publication_year <= 2020 or country_code=='IE'") + .drop("publication_year"); + + dataset.flatMap((FlatMapFunction) row -> { + List ret = new ArrayList<>(); + final String ror = ROR_PREFIX + + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror"))); + ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror)); + ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror)); + ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror)); + + return ret + .iterator(); + }, Encoders.bean(Relation.class)) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); + + } + + private static Dataset readWebCrawl(SparkSession spark, String inputPath) { + StructType webInfo = StructType + .fromDDL( + "`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, " + + + "`authorships` ARRAY>>>"); + + return spark + .read() + .schema(webInfo) + .json(inputPath) + .withColumn( + "authors", functions + .explode( + functions.col("authorships"))) + .selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions") + .withColumn( + "institution", functions + .explode( + functions.col("institutions"))) + .selectExpr( + "id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror", + "institution.country_code as country_code", "publication_year") + // .where("country_code == 'IE'") + .distinct(); + + } + + private static List createAffiliationRelationPairPMCID(String pmcid, String ror) { + if (pmcid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair( + PMCID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), "PMC" + pmcid.substring(43))), + ror); + } + + private static List createAffiliationRelationPairPMID(String pmid, String ror) { + if (pmid == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair( + PMID_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pmid.substring(33))), + ror); + } + + private static List createAffiliationRelationPairDOI(String doi, String ror) { + if (doi == null) + return new ArrayList<>(); + + return createAffiliatioRelationPair( + DOI_PREFIX + + IdentifierFactory + .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), doi.substring(16))), + ror); + + } + + private static List createAffiliatioRelationPair(String resultId, String orgId) { + ArrayList newRelations = new ArrayList(); + + newRelations + .add( + OafMapperUtils + .getRelation( + orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, + ModelConstants.IS_AUTHOR_INSTITUTION_OF, + Arrays + .asList( + OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null)); + + newRelations + .add( + OafMapperUtils + .getRelation( + resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION, + ModelConstants.HAS_AUTHOR_INSTITUTION, + Arrays + .asList( + OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)), + OafMapperUtils + .dataInfo( + false, null, false, false, + OafMapperUtils + .qualifier( + "sysimport:crasswalk:webcrawl", "Imported from Webcrawl", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"), + null)); + + return newRelations; + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json new file mode 100644 index 000000000..3f056edf7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "sp", + "paramLongName": "sourcePath", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + } +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties new file mode 100644 index 000000000..f616baea7 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties @@ -0,0 +1,2 @@ +sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/ +outputPath=/tmp/miriam/webcrawlComplete/ diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml new file mode 100644 index 000000000..a1755f329 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/config-default.xml @@ -0,0 +1,58 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + + + spark2EventLogDir + /user/spark/spark2ApplicationHistory + + + sparkDriverMemory + 15G + + + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml new file mode 100644 index 000000000..653a7d384 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml @@ -0,0 +1,53 @@ + + + + ${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())}] + + + + + yarn + cluster + Produces the AS for WC + eu.dnetlib.dhp.actionmanager.webcrawl.CreateActionSetFromWebEntries + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${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${sourcePath} + --outputPath${outputPath} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml index 071d202b6..b2432ea7b 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml @@ -1,4 +1,4 @@ - + sourcePath @@ -8,19 +8,40 @@ database the PDB Database Working Path - - targetPath - the Target Working dir path + mdStoreOutputId + the identifier of the cleaned MDStore + + + mdStoreManagerURI + the path of the cleaned mdstore - + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionNEW_VERSION + --mdStoreID${mdStoreOutputId} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + yarn @@ -41,11 +62,48 @@ --masteryarn --dbPath${sourcePath} --database${database} - --targetPath${targetPath} + --mdstoreOutputVersion${wf:actionData('StartTransaction')['mdStoreVersion']} - - + + + - + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionCOMMIT + --namenode${nameNode} + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionROLLBACK + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json index 76d0bfd6d..e205926ec 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json @@ -2,5 +2,5 @@ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, {"paramName":"db", "paramLongName":"database", "paramDescription": "should be PDB or UNIPROT", "paramRequired": true}, {"paramName":"p", "paramLongName":"dbPath", "paramDescription": "the path of the database to transform", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the OAF target path ", "paramRequired": true} + {"paramName":"mo", "paramLongName":"mdstoreOutputVersion", "paramDescription": "the oaf path ", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json index 8039131b2..04d976a69 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json @@ -1,5 +1,20 @@ [ - {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"s", "paramLongName":"sourcePath","paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"t", "paramLongName":"targetPath","paramDescription": "the oaf path ", "paramRequired": true} + { + "paramName": "mt", + "paramLongName": "master", + "paramDescription": "should be local or yarn", + "paramRequired": true + }, + { + "paramName": "s", + "paramLongName": "sourcePath", + "paramDescription": "the source Path", + "paramRequired": true + }, + { + "paramName": "mo", + "paramLongName": "mdstoreOutputVersion", + "paramDescription": "the oaf path ", + "paramRequired": true + } ] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml index 4b47ae38e..047a037dd 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml @@ -9,34 +9,26 @@ the Working Path - targetPath - the OAF MDStore Path + mdStoreOutputId + the identifier of the cleaned MDStore - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor + mdStoreManagerURI + the path of the cleaned mdstore resumeFrom - DownloadEBILinks + CreateEBIDataSet node to start - + ${wf:conf('resumeFrom') eq 'DownloadEBILinks'} - ${wf:conf('resumeFrom') eq 'CreateEBIDataSet'} + ${wf:conf('resumeFrom') eq 'CreateEBIDataSet'} @@ -77,9 +69,29 @@ - + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionNEW_VERSION + --mdStoreID${mdStoreOutputId} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + yarn-cluster @@ -95,11 +107,49 @@ ${sparkExtraOPT} --sourcePath${sourcePath}/ebi_links_dataset - --targetPath${targetPath} + --mdstoreOutputVersion${wf:actionData('StartTransaction')['mdStoreVersion']} --masteryarn + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionCOMMIT + --namenode${nameNode} + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionROLLBACK + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index df356548a..65c348062 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -231,7 +231,7 @@ object BioDBToOAF { def uniprotToOAF(input: String): List[Oaf] = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) - val pid = (json \ "pid").extract[String] + val pid = (json \ "pid").extract[String].trim() val d = new Dataset diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala index 96075b4f3..2b1aa0963 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -2,12 +2,15 @@ package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.collection.CollectionUtils +import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} +import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion import eu.dnetlib.dhp.schema.oaf.Oaf import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.slf4j.{Logger, LoggerFactory} +import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile} object SparkTransformBioDatabaseToOAF { @@ -25,8 +28,13 @@ object SparkTransformBioDatabaseToOAF { val dbPath: String = parser.get("dbPath") log.info("dbPath: {}", database) - val targetPath: String = parser.get("targetPath") - log.info("targetPath: {}", database) + + val mdstoreOutputVersion = parser.get("mdstoreOutputVersion") + log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion) + + val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) + val outputBasePath = cleanedMdStoreVersion.getHdfsPath + log.info("outputBasePath: {}", outputBasePath) val spark: SparkSession = SparkSession @@ -43,24 +51,28 @@ object SparkTransformBioDatabaseToOAF { case "UNIPROT" => CollectionUtils.saveDataset( spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))), - targetPath + s"$outputBasePath/$MDSTORE_DATA_PATH" ) case "PDB" => CollectionUtils.saveDataset( spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))), - targetPath + s"$outputBasePath/$MDSTORE_DATA_PATH" ) case "SCHOLIX" => CollectionUtils.saveDataset( spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)), - targetPath + s"$outputBasePath/$MDSTORE_DATA_PATH" ) case "CROSSREF_LINKS" => CollectionUtils.saveDataset( spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))), - targetPath + s"$outputBasePath/$MDSTORE_DATA_PATH" ) } + + val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH") + val mdStoreSize = df.count + writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH") } } diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala index 7cb6153ff..227dccf14 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala @@ -9,6 +9,9 @@ import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql._ import org.slf4j.{Logger, LoggerFactory} +import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} +import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion +import eu.dnetlib.dhp.utils.DHPUtils.{MAPPER, writeHdfsFile} object SparkEBILinksToOaf { @@ -32,8 +35,13 @@ object SparkEBILinksToOaf { import spark.implicits._ val sourcePath = parser.get("sourcePath") log.info(s"sourcePath -> $sourcePath") - val targetPath = parser.get("targetPath") - log.info(s"targetPath -> $targetPath") + val mdstoreOutputVersion = parser.get("mdstoreOutputVersion") + log.info("mdstoreOutputVersion: {}", mdstoreOutputVersion) + + val cleanedMdStoreVersion = MAPPER.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) + val outputBasePath = cleanedMdStoreVersion.getHdfsPath + log.info("outputBasePath: {}", outputBasePath) + implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) val ebLinks: Dataset[EBILinkItem] = spark.read @@ -46,7 +54,10 @@ object SparkEBILinksToOaf { .flatMap(j => BioDBToOAF.parse_ebi_links(j.links)) .filter(p => BioDBToOAF.EBITargetLinksFilter(p)) .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)), - targetPath + s"$outputBasePath/$MDSTORE_DATA_PATH" ) + val df = spark.read.text(s"$outputBasePath/$MDSTORE_DATA_PATH") + val mdStoreSize = df.count + writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$mdStoreSize", s"$outputBasePath/$MDSTORE_SIZE_PATH") } } diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java new file mode 100644 index 000000000..4a0cd273b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java @@ -0,0 +1,349 @@ + +package eu.dnetlib.dhp.actionmanager.webcrawl; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +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.FilterFunction; +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.actionmanager.opencitations.CreateActionSetSparkJob; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; + +public class CreateASTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(CreateASTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateASTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CreateASTest.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(CreateASTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testNumberofRelations() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl/") + .getPath(); + + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + Assertions.assertEquals(64, tmp.count()); + + } + +// https://ror.org/04c6bry31 "openalex":"https://openalex.org/W2115261608", +// "doi":"https://doi.org/10.1056/nejmoa0908721", +// "mag":"2115261608", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20375404" +// +// +// https://ror.org/03bea9k73 "openalex":"https://openalex.org/W2157622195", +// "doi":"https://doi.org/10.1016/s0140-6736(10)60834-3", +// "mag":"2157622195", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20561675" +// +// +// https://ror.org/008te2062 "openalex":"https://openalex.org/W2104948944", +// "doi":"https://doi.org/10.1056/nejmoa0909494", +// "mag":"2104948944", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20089952" +// +// +// +// https://ror.org/05m7pjf47 , https://ror.org/02tyrky19 "openalex":"https://openalex.org/W2071754162", +// "doi":"https://doi.org/10.1371/journal.pone.0009672", +// "mag":"2071754162", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20300637", +// "pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2837382" +// +// +// +// https://ror.org/05m7pjf47 "openalex":"https://openalex.org/W2144543496", +// "doi":"https://doi.org/10.1086/649858", +// "mag":"2144543496", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20047480", +// "pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5826644" +// +// +// https://ror.org/04q107642", "openalex":"https://openalex.org/W2115169717", +// "doi":"https://doi.org/10.1016/s0140-6736(09)61965-6", +// "mag":"2115169717", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20167359" +// +// +// https://ror.org/03265fv13 "openalex":"https://openalex.org/W2119378720", +// "doi":"https://doi.org/10.1038/nnano.2010.15", +// "mag":"2119378720", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20173755" +// +// +// https://ror.org/02tyrky19 "openalex":"https://openalex.org/W2140206763", +// "doi":"https://doi.org/10.1038/nature08900", +// "mag":"2140206763", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20200518", +// "pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2862165" +// +// +// +// https://ror.org/05m7pjf47 https://ror.org/02tyrky19 "openalex":"https://openalex.org/W2110374888", +// "doi":"https://doi.org/10.1038/nature09146", +// "mag":"2110374888", +// "pmid":"https://pubmed.ncbi.nlm.nih.gov/20531469", +// "pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3021798" + @Test + void testRelations() throws Exception { + +// , "doi":"https://doi.org/10.1126/science.1188021", "pmid":"https://pubmed.ncbi.nlm.nih.gov/20448178", https://www.ncbi.nlm.nih.gov/pmc/articles/5100745 + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl/") + .getPath(); + + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getSource() + .equals( + "50|doi_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "50|doi_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023")))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getSource() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03argrj65")))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03argrj65")))) + .count()); + + Assertions + .assertEquals( + 5, tmp + .filter( + r -> r + .getSource() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03265fv13")))) + .count()); + + Assertions + .assertEquals( + 5, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue("ROR", "https://ror.org/03265fv13")))) + .count()); + + Assertions + .assertEquals( + 2, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|doi")) + .count()); + + Assertions + .assertEquals( + 2, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|pmid")) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter( + r -> r + .getTarget() + .equals( + "20|ror_________::" + IdentifierFactory + .md5( + PidCleaner + .normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13"))) + && r.getSource().startsWith("50|pmc")) + .count()); + } + + @Test + void testRelationsCollectedFrom() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/webcrawl") + .getPath(); + + CreateActionSetFromWebEntries + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-sourcePath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet1" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("Web Crawl", r.getCollectedfrom().get(0).getValue()); + assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey()); + }); + + } + + + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 new file mode 100644 index 000000000..a94baacb4 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/part-00000 @@ -0,0 +1 @@ +{"id": "https://openalex.org/W4214628335", "doi": "https://doi.org/10.1098/rstl.1684.0023", "title": "A letter from the learned and ingenious Mr. Will. Molyneux Secrctary to the Society of Dublin, to Will. Musgrave LL. B. Fellow of New Colledge, and Secretary to the Philosophical Society of Oxford, for advertisement of natural Knowledge; concerning Lough Neagh in Ireland, and its petrifying Qualitys", "display_name": "A letter from the learned and ingenious Mr. Will. Molyneux Secrctary to the Society of Dublin, to Will. Musgrave LL. B. Fellow of New Colledge, and Secretary to the Philosophical Society of Oxford, for advertisement of natural Knowledge; concerning Lough Neagh in Ireland, and its petrifying Qualitys", "publication_year": 1684, "publication_date": "1684-04-20", "ids": {"openalex": "https://openalex.org/W4214628335", "doi": "https://doi.org/10.1098/rstl.1684.0023"}, "language": "en", "primary_location": {"is_oa": true, "landing_page_url": "https://doi.org/10.1098/rstl.1684.0023", "pdf_url": "https://royalsocietypublishing.org/doi/pdf/10.1098/rstl.1684.0023", "source": {"id": "https://openalex.org/S4210177916", "display_name": "Philosophical transactions of the Royal Society of London", "issn_l": "0261-0523", "issn": ["0261-0523", "2053-9223"], "is_oa": false, "is_in_doaj": false, "host_organization": "https://openalex.org/P4310319787", "host_organization_name": "Royal Society", "host_organization_lineage": ["https://openalex.org/P4310319787"], "host_organization_lineage_names": ["Royal Society"], "type": 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Abrahams", "orcid": null}, "institutions": [{"id": "https://openalex.org/I94690351", "display_name": "Center for Autism and Related Disorders", "ror": "https://ror.org/00t7r5h51", "country_code": "US", "type": "other", "lineage": ["https://openalex.org/I94690351"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Brett S. 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Bader", "raw_affiliation_string": "Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,", "raw_affiliation_strings": ["Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5034194945", "display_name": "Anthony Bailey", "orcid": null}, "institutions": [{"id": "https://openalex.org/I2803066836", "display_name": "Warneford Hospital", "ror": "https://ror.org/03we1zb10", "country_code": "GB", "type": "healthcare", "lineage": ["https://openalex.org/I2802171185", "https://openalex.org/I2803066836"]}, {"id": "https://openalex.org/I40120149", "display_name": "University of Oxford", "ror": "https://ror.org/052gg0110", "country_code": "GB", "type": "education", "lineage": ["https://openalex.org/I40120149"]}], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Anthony J. Bailey", "raw_affiliation_string": "Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford OX3 7JX, UK.,", "raw_affiliation_strings": ["Department of Psychiatry, University of Oxford, Warneford Hospital, Headington, Oxford OX3 7JX, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5067210442", "display_name": "Gillian Baird", "orcid": "https://orcid.org/0000-0002-7601-7074"}, "institutions": [{"id": "https://openalex.org/I1298207432", "display_name": "Guy's Hospital", "ror": "https://ror.org/04r33pf22", "country_code": "GB", "type": "healthcare", "lineage": ["https://openalex.org/I1298207432", "https://openalex.org/I200166805", "https://openalex.org/I4210111135"]}], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Gillian Baird", "raw_affiliation_string": "Newcomen Centre, Guy’s Hospital, London SE1 9RT, UK.,", "raw_affiliation_strings": ["Newcomen Centre, Guy’s Hospital, London SE1 9RT, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5044044440", "display_name": "Agatino Battaglia", "orcid": "https://orcid.org/0000-0002-7128-7606"}, "institutions": [{"id": "https://openalex.org/I4210126460", "display_name": "Fondazione Stella Maris", "ror": "https://ror.org/02w8ez808", "country_code": "IT", "type": "healthcare", "lineage": ["https://openalex.org/I4210126460", "https://openalex.org/I4210153126"]}], "countries": ["IT"], "is_corresponding": false, "raw_author_name": "Agatino Battaglia", "raw_affiliation_string": "Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone (Pisa), Italy.,", "raw_affiliation_strings": ["Stella Maris Institute for Child and Adolescent Neuropsychiatry, 56128 Calambrone (Pisa), Italy.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5008688186", "display_name": "T. 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Berney", "orcid": null}, "institutions": [{"id": "https://openalex.org/I84884186", "display_name": "Newcastle University", "ror": "https://ror.org/01kj2bm70", "country_code": "GB", "type": "education", "lineage": ["https://openalex.org/I84884186"]}], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Tom Berney", "raw_affiliation_string": "Child and Adolescent Mental Health, University of Newcastle, Sir James Spence Institute, Newcastle upon Tyne NE1 4LP, UK.,", "raw_affiliation_strings": ["Child and Adolescent Mental Health, University of Newcastle, Sir James Spence Institute, Newcastle upon Tyne NE1 4LP, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5016075120", "display_name": "Nadia Bolshakova", "orcid": "https://orcid.org/0000-0003-2173-6562"}, "institutions": [{"id": "https://openalex.org/I205274468", "display_name": "Trinity College Dublin", "ror": "https://ror.org/02tyrky19", "country_code": "IE", "type": "education", "lineage": ["https://openalex.org/I205274468"]}], "countries": ["IE"], "is_corresponding": false, "raw_author_name": "Nadia Bolshakova", "raw_affiliation_string": "Department of Psychiatry, Autism Genetics Group, School of Medicine, Trinity College, Dublin 8, Ireland.,", "raw_affiliation_strings": ["Department of Psychiatry, Autism Genetics Group, School of Medicine, Trinity College, Dublin 8, Ireland.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5054839489", "display_name": "Sven Bölte", "orcid": "https://orcid.org/0000-0002-4579-4970"}, "institutions": [{"id": "https://openalex.org/I114090438", "display_name": "Goethe University Frankfurt", "ror": "https://ror.org/04cvxnb49", "country_code": "DE", "type": "education", "lineage": ["https://openalex.org/I114090438"]}], "countries": ["DE"], "is_corresponding": false, "raw_author_name": "Sven Bölte", "raw_affiliation_string": "Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,", "raw_affiliation_strings": ["Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5030755834", "display_name": "Patrick Bolton", "orcid": null}, "institutions": [{"id": "https://openalex.org/I4210114595", "display_name": "Psychiatry Research Trust", "ror": "https://ror.org/01ywejq18", "country_code": "GB", "type": "nonprofit", "lineage": ["https://openalex.org/I4210114595"]}], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Patrick F. 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Crawford", "orcid": null}, "institutions": [{"id": "https://openalex.org/I200719446", "display_name": "Vanderbilt University", "ror": "https://ror.org/02vm5rt34", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I200719446"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Emily L. 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Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599-3366, USA.,", "raw_affiliation_strings": ["Autism Speaks, New York 10016, USA.,", "Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina 27599-3366, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5039670828", "display_name": "Maretha de Jonge", "orcid": null}, "institutions": [{"id": "https://openalex.org/I3018483916", "display_name": "University Medical Center Utrecht", "ror": "https://ror.org/0575yy874", "country_code": "NL", "type": "healthcare", "lineage": ["https://openalex.org/I3018483916"]}], "countries": ["NL"], "is_corresponding": false, "raw_author_name": "Maretha de Jonge", "raw_affiliation_string": "Department of Child Psychiatry, University Medical Center, Utrecht 3508 GA, The Netherlands.,", "raw_affiliation_strings": ["Department of Child Psychiatry, University Medical Center, Utrecht 3508 GA, The Netherlands.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5020448299", "display_name": "Richard Delorme", "orcid": null}, "institutions": [{"id": "https://openalex.org/I4210096842", "display_name": "Fondation FondaMental", "ror": "https://ror.org/00rrhf939", "country_code": "FR", "type": "other", "lineage": ["https://openalex.org/I4210096842"]}, {"id": "https://openalex.org/I154526488", "display_name": "Inserm", "ror": "https://ror.org/02vjkv261", "country_code": "FR", "type": "government", "lineage": ["https://openalex.org/I154526488"]}, {"id": "https://openalex.org/I4210126712", "display_name": "Hôpital Robert-Debré", "ror": "https://ror.org/02dcqy320", "country_code": "FR", "type": "healthcare", "lineage": ["https://openalex.org/I4210097159", "https://openalex.org/I4210126712"]}], "countries": ["FR"], "is_corresponding": false, "raw_author_name": "Richard Delorme", "raw_affiliation_string": "INSERM U 955, Fondation FondaMental, APHP, Hôpital Robert Debré, Child and Adolescent Psychiatry, 75019 Paris, France.,", "raw_affiliation_strings": ["INSERM U 955, Fondation FondaMental, APHP, Hôpital Robert Debré, Child and Adolescent Psychiatry, 75019 Paris, France.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5081523158", "display_name": "Irene Drmic", "orcid": "https://orcid.org/0000-0002-9212-4929"}, "institutions": [{"id": "https://openalex.org/I2801420703", "display_name": "Holland Bloorview Kids Rehabilitation Hospital", "ror": "https://ror.org/03qea8398", "country_code": "CA", "type": "healthcare", "lineage": ["https://openalex.org/I2801420703"]}, {"id": "https://openalex.org/I185261750", "display_name": "University of Toronto", "ror": "https://ror.org/03dbr7087", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I185261750"]}, {"id": "https://openalex.org/I2801317318", "display_name": "Hospital for Sick Children", "ror": "https://ror.org/057q4rt57", "country_code": "CA", "type": "healthcare", "lineage": ["https://openalex.org/I2801317318"]}, {"id": "https://openalex.org/I4210141030", "display_name": "SickKids Foundation", "ror": "https://ror.org/04374qe70", "country_code": "CA", "type": "nonprofit", "lineage": ["https://openalex.org/I4210141030"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Irene Drmic", "raw_affiliation_string": "Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehab, University of Toronto, Toronto, Ontario M5G 1X8, Canada.,", "raw_affiliation_strings": ["Autism Research Unit, The Hospital for Sick Children and Bloorview Kids Rehab, University of Toronto, Toronto, Ontario M5G 1X8, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5065665765", "display_name": "Eftichia Duketis", "orcid": null}, "institutions": [{"id": "https://openalex.org/I114090438", "display_name": "Goethe University Frankfurt", "ror": "https://ror.org/04cvxnb49", "country_code": "DE", "type": "education", "lineage": ["https://openalex.org/I114090438"]}], "countries": ["DE"], "is_corresponding": false, "raw_author_name": "Eftichia Duketis", "raw_affiliation_string": "Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,", "raw_affiliation_strings": ["Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, 60528 Frankfurt, Germany.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5048358192", "display_name": "Frederico Duque", "orcid": null}, "institutions": [], "countries": ["PT"], "is_corresponding": false, "raw_author_name": "Frederico Duque", "raw_affiliation_string": "Hospital Pediátrico de Coimbra, 3000 – 076 Coimbra, Portugal.,", "raw_affiliation_strings": ["Hospital Pediátrico de Coimbra, 3000 – 076 Coimbra, Portugal.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5067974738", "display_name": "Annette Estes", "orcid": "https://orcid.org/0000-0003-2687-4155"}, "institutions": [{"id": "https://openalex.org/I201448701", "display_name": "University of Washington", "ror": "https://ror.org/00cvxb145", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I201448701"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Annette Estes", "raw_affiliation_string": "Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington 98195, USA.,", "raw_affiliation_strings": ["Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington 98195, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5034071437", "display_name": "Penny Farrar", "orcid": null}, "institutions": [{"id": "https://openalex.org/I1336263701", "display_name": "Wellcome Centre for Human Genetics", "ror": "https://ror.org/01rjnta51", "country_code": "GB", "type": "facility", "lineage": ["https://openalex.org/I1336263701", "https://openalex.org/I40120149", "https://openalex.org/I87048295"]}, {"id": "https://openalex.org/I40120149", "display_name": "University of Oxford", "ror": "https://ror.org/052gg0110", "country_code": "GB", "type": "education", "lineage": ["https://openalex.org/I40120149"]}], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Penny Farrar", "raw_affiliation_string": "Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,", "raw_affiliation_strings": ["Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5003632230", "display_name": "Bridget A. Fernandez", "orcid": "https://orcid.org/0000-0003-1265-8259"}, "institutions": [{"id": "https://openalex.org/I130438778", "display_name": "Memorial University of Newfoundland", "ror": "https://ror.org/04haebc03", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I130438778"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Bridget A. Fernandez", "raw_affiliation_string": "Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John’s Newfoundland A1B 3V6, Canada.,", "raw_affiliation_strings": ["Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St John’s Newfoundland A1B 3V6, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5065212941", "display_name": "Susan E. Folstein", "orcid": null}, "institutions": [{"id": "https://openalex.org/I145608581", "display_name": "University of Miami", "ror": "https://ror.org/02dgjyy92", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I145608581"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Susan E. Folstein", "raw_affiliation_string": "The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,", "raw_affiliation_strings": ["The John P. 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Gilbert", "orcid": null}, "institutions": [{"id": "https://openalex.org/I145608581", "display_name": "University of Miami", "ror": "https://ror.org/02dgjyy92", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I145608581"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "John Gilbert", "raw_affiliation_string": "The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,", "raw_affiliation_strings": ["The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida 33101, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5028456703", "display_name": "Christopher Gillberg", "orcid": "https://orcid.org/0000-0001-8848-1934"}, "institutions": [{"id": "https://openalex.org/I881427289", "display_name": "University of Gothenburg", "ror": "https://ror.org/01tm6cn81", "country_code": "SE", "type": "education", "lineage": ["https://openalex.org/I881427289"]}], "countries": ["SE"], "is_corresponding": false, "raw_author_name": "Christopher Gillberg", "raw_affiliation_string": "Department of Child and Adolescent Psychiatry, Göteborg University, Göteborg S41345, Sweden.,", "raw_affiliation_strings": ["Department of Child and Adolescent Psychiatry, Göteborg University, Göteborg S41345, Sweden.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5066789855", "display_name": "Joseph T. Glessner", "orcid": "https://orcid.org/0000-0001-5131-2811"}, "institutions": [{"id": "https://openalex.org/I1335321130", "display_name": "Children's Hospital of Philadelphia", "ror": "https://ror.org/01z7r7q48", "country_code": "US", "type": "healthcare", "lineage": ["https://openalex.org/I1335321130"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Joseph T. Glessner", "raw_affiliation_string": "Division of Human Genetics, The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,", "raw_affiliation_strings": ["Division of Human Genetics, The Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5081908377", "display_name": "Jeremy Goldberg", "orcid": null}, "institutions": [{"id": "https://openalex.org/I98251732", "display_name": "McMaster University", "ror": "https://ror.org/02fa3aq29", "country_code": "CA", "type": "education", "lineage": ["https://openalex.org/I98251732"]}], "countries": ["CA"], "is_corresponding": false, "raw_author_name": "Jeremy Goldberg", "raw_affiliation_string": "Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,", "raw_affiliation_strings": ["Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5000005180", "display_name": "Andrew Green", "orcid": "https://orcid.org/0000-0002-0488-5913"}, "institutions": [{"id": "https://openalex.org/I100930933", "display_name": "University College Dublin", "ror": "https://ror.org/05m7pjf47", "country_code": "IE", "type": "education", "lineage": ["https://openalex.org/I100930933", "https://openalex.org/I181231927"]}], "countries": ["IE"], "is_corresponding": false, "raw_author_name": "Andrew Green", "raw_affiliation_string": "School of Medicine and Medical Science University College, Dublin 4, Ireland.,", "raw_affiliation_strings": ["School of Medicine and Medical Science University College, Dublin 4, Ireland.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5076431905", "display_name": "Jonathan Green", "orcid": "https://orcid.org/0000-0002-0143-181X"}, "institutions": [], "countries": ["GB"], "is_corresponding": false, "raw_author_name": "Jonathan Green", "raw_affiliation_string": "Academic Department of Child Psychiatry, Booth Hall of Children’s Hospital, Blackley, Manchester M9 7AA, UK.,", "raw_affiliation_strings": ["Academic Department of Child Psychiatry, Booth Hall of Children’s Hospital, Blackley, Manchester M9 7AA, UK.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5067479223", "display_name": "Stephen J. Guter", "orcid": null}, "institutions": [{"id": "https://openalex.org/I39422238", "display_name": "University of Illinois at Chicago", "ror": "https://ror.org/02mpq6x41", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I2801919071", "https://openalex.org/I39422238"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Stephen J. 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Klauck", "raw_affiliation_string": "Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,", "raw_affiliation_strings": ["Division of Molecular Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5016983099", "display_name": "Alexander Kolevzon", "orcid": "https://orcid.org/0000-0001-8129-2671"}, "institutions": [{"id": "https://openalex.org/I98704320", "display_name": "Icahn School of Medicine at Mount Sinai", "ror": "https://ror.org/04a9tmd77", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I1320796813", "https://openalex.org/I98704320"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Alexander Kolevzon", "raw_affiliation_string": "Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York 10029, USA.,", "raw_affiliation_strings": ["Department of Psychiatry, The Seaver Autism Center for Research and Treatment, Mount Sinai School of Medicine, New York 10029, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5020224643", "display_name": "Olena Korvatska", "orcid": null}, "institutions": [{"id": "https://openalex.org/I201448701", "display_name": "University of Washington", "ror": "https://ror.org/00cvxb145", "country_code": "US", "type": "education", "lineage": ["https://openalex.org/I201448701"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Olena Korvatska", "raw_affiliation_string": "Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,", "raw_affiliation_strings": ["Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5007111212", "display_name": "Vlad Kustanovich", "orcid": null}, "institutions": [{"id": "https://openalex.org/I109266671", "display_name": "Autism Speaks", "ror": "https://ror.org/04bkad313", "country_code": "US", "type": "nonprofit", "lineage": ["https://openalex.org/I109266671"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Vlad Kustanovich", "raw_affiliation_string": "Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, California 90036-4234, USA.,", "raw_affiliation_strings": ["Autism Genetic Resource Exchange, Autism Speaks, Los Angeles, California 90036-4234, USA.,"]}, {"author_position": "middle", "author": {"id": "https://openalex.org/A5065072190", "display_name": "Clara Lajonchere", "orcid": "https://orcid.org/0000-0002-3190-4606"}, "institutions": [{"id": "https://openalex.org/I109266671", "display_name": "Autism Speaks", "ror": "https://ror.org/04bkad313", "country_code": "US", "type": "nonprofit", "lineage": ["https://openalex.org/I109266671"]}], "countries": ["US"], "is_corresponding": false, "raw_author_name": "Clara M. 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["Ibronectin type iii fold", " alternate scaffold", " de novo protein"], "authors": ["A.teplyakov", "G.obmolova", "G.l.gilliland"], "pmid": "24375666", "doi": "10.1002/PROT.24502"} +{"classification": "Isomerase", "pdb": "2Y88", "deposition_date": "2011-02-03", "title": "Crystal structure of mycobacterium tuberculosis phosphoribosyl Isomerase (variant d11n) with bound prfar", "Keywords": ["Romatic amino acid biosynthesis", " isomerase", " tim-barrel", " histidine", "Biosynthesis", "Tryptophan biosynthesis"], "authors": ["J.kuper", "A.v.due", "A.geerlof", "M.wilmanns"], "pmid": "21321225", "doi": "10.1073/PNAS.1015996108"} +{"classification": "Unknown function", "pdb": "1SR0", "deposition_date": "2004-03-22", "title": "Crystal structure of signalling protein from sheep(sps-40) at 3.0a Resolution using crystal grown in the presence of polysaccharides", "Keywords": ["Ignalling protein", " involution", " unknown function"], "authors": ["D.b.srivastava", "A.s.ethayathulla", "N.singh", "J.kumar", "S.sharma", "T.p.singh"]} +{"classification": "Dna binding protein", "pdb": "3RH2", "deposition_date": "2011-04-11", "title": "Crystal structure of a tetr-like transcriptional regulator (sama_0099) From shewanella amazonensis sb2b at 2.42 a resolution", "Keywords": ["Na/rna-binding 3-helical bundle", " structural genomics", " joint center", "For structural genomics", "Jcsg", "Protein structure initiative", "Psi-", "Biology", "Dna binding protein"], "authors": ["Joint center for structural genomics (jcsg)"]} +{"classification": "Transferase", "pdb": "2WK5", "deposition_date": "2009-06-05", "title": "Structural features of native human thymidine phosphorylase And in complex with 5-iodouracil", "Keywords": ["Lycosyltransferase", " developmental protein", " angiogenesis", "", "5-iodouracil", "Growth factor", "Enzyme kinetics", "", "Differentiation", "Disease mutation", "Thymidine", "Phosphorylase", "Chemotaxis", "Transferase", "Mutagenesis", "", "Polymorphism"], "authors": ["E.mitsiki", "A.c.papageorgiou", "S.iyer", "N.thiyagarajan", "S.h.prior", "", "D.sleep", "C.finnis", "K.r.acharya"], "pmid": "19555658", "doi": "10.1016/J.BBRC.2009.06.104"} +{"classification": "Hydrolase", "pdb": "3P9Y", "deposition_date": "2010-10-18", "title": "Crystal structure of the drosophila melanogaster ssu72-pctd complex", "Keywords": ["Hosphatase", " cis proline", " lmw ptp-like fold", " rna polymerase ii ctd", "", "Hydrolase"], "authors": ["J.w.werner-allen", "P.zhou"], "pmid": "21159777", "doi": "10.1074/JBC.M110.197129"} +{"classification": "Recombination/dna", "pdb": "6OEO", "deposition_date": "2019-03-27", "title": "Cryo-em structure of mouse rag1/2 nfc complex (dna1)", "Keywords": ["(d)j recombination", " dna transposition", " rag", " scid", " recombination", "", "Recombination-dna complex"], "authors": ["X.chen", "Y.cui", "Z.h.zhou", "W.yang", "M.gellert"], "pmid": "32015552", "doi": "10.1038/S41594-019-0363-2"} +{"classification": "Hydrolase", "pdb": "4ECA", "deposition_date": "1997-02-21", "title": "Asparaginase from e. coli, mutant t89v with covalently bound aspartate", "Keywords": ["Ydrolase", " acyl-enzyme intermediate", " threonine amidohydrolase"], "authors": ["G.j.palm", "J.lubkowski", "A.wlodawer"], "pmid": "8706862", "doi": "10.1016/0014-5793(96)00660-6"} +{"classification": "Transcription/protein binding", "pdb": "3UVX", "deposition_date": "2011-11-30", "title": "Crystal structure of the first bromodomain of human brd4 in complex With a diacetylated histone 4 peptide (h4k12ack16ac)", "Keywords": ["Romodomain", " bromodomain containing protein 4", " cap", " hunk1", " mcap", "", "Mitotic chromosome associated protein", "Peptide complex", "Structural", "Genomics consortium", "Sgc", "Transcription-protein binding complex"], "authors": ["P.filippakopoulos", "S.picaud", "T.keates", "E.ugochukwu", "F.von delft", "", "C.h.arrowsmith", "A.m.edwards", "J.weigelt", "C.bountra", "S.knapp", "Structural", "Genomics consortium (sgc)"], "pmid": "22464331", "doi": "10.1016/J.CELL.2012.02.013"} +{"classification": "Membrane protein", "pdb": "1TLZ", "deposition_date": "2004-06-10", "title": "Tsx structure complexed with uridine", "Keywords": ["Ucleoside transporter", " beta barrel", " uridine", " membrane", "Protein"], "authors": ["J.ye", "B.van den berg"], "pmid": "15272310", "doi": "10.1038/SJ.EMBOJ.7600330"} +{"classification": "Dna binding protein", "pdb": "7AZD", "deposition_date": "2020-11-16", "title": "Dna polymerase sliding clamp from escherichia coli with peptide 20 Bound", "Keywords": ["Ntibacterial drug", " dna binding protein"], "authors": ["C.monsarrat", "G.compain", "C.andre", "I.martiel", "S.engilberge", "V.olieric", "", "P.wolff", "K.brillet", "M.landolfo", "C.silva da veiga", "J.wagner", "G.guichard", "", "D.y.burnouf"], "pmid": "34806883", "doi": "10.1021/ACS.JMEDCHEM.1C00918"} +{"classification": "Transferase", "pdb": "5N3K", "deposition_date": "2017-02-08", "title": "Camp-dependent protein kinase a from cricetulus griseus in complex With fragment like molecule o-guanidino-l-homoserine", "Keywords": ["Ragment", " complex", " transferase", " serine threonine kinase", " camp", "", "Kinase", "Pka"], "authors": ["C.siefker", "A.heine", "G.klebe"]} +{"classification": "Biosynthetic protein", "pdb": "8H52", "deposition_date": "2022-10-11", "title": "Crystal structure of helicobacter pylori carboxyspermidine Dehydrogenase in complex with nadp", "Keywords": ["Arboxyspermidine dehydrogenase", " biosynthetic protein"], "authors": ["K.y.ko", "S.c.park", "S.y.cho", "S.i.yoon"], "pmid": "36283333", "doi": "10.1016/J.BBRC.2022.10.049"} +{"classification": "Metal binding protein", "pdb": "6DYC", "deposition_date": "2018-07-01", "title": "Co(ii)-bound structure of the engineered cyt cb562 variant, ch3", "Keywords": ["Esigned protein", " 4-helix bundle", " electron transport", " metal binding", "Protein"], "authors": ["F.a.tezcan", "J.rittle"], "pmid": "30778140", "doi": "10.1038/S41557-019-0218-9"} +{"classification": "Protein fibril", "pdb": "6A6B", "deposition_date": "2018-06-27", "title": "Cryo-em structure of alpha-synuclein fiber", "Keywords": ["Lpha-syn fiber", " parkinson disease", " protein fibril"], "authors": ["Y.w.li", "C.y.zhao", "F.luo", "Z.liu", "X.gui", "Z.luo", "X.zhang", "D.li", "C.liu", "X.li"], "pmid": "30065316", "doi": "10.1038/S41422-018-0075-X"} +{"classification": "Dna", "pdb": "7D5E", "deposition_date": "2020-09-25", "title": "Left-handed g-quadruplex containing two bulges", "Keywords": ["-quadruplex", " bulge", " dna", " left-handed"], "authors": ["P.das", "A.maity", "K.h.ngo", "F.r.winnerdy", "B.bakalar", "Y.mechulam", "E.schmitt", "", "A.t.phan"], "pmid": "33503265", "doi": "10.1093/NAR/GKAA1259"} +{"classification": "Transferase", "pdb": "3RSY", "deposition_date": "2011-05-02", "title": "Cellobiose phosphorylase from cellulomonas uda in complex with sulfate And glycerol", "Keywords": ["H94", " alpha barrel", " cellobiose phosphorylase", " disaccharide", "Phosphorylase", "Transferase"], "authors": ["A.van hoorebeke", "J.stout", "W.soetaert", "J.van beeumen", "T.desmet", "S.savvides"]} +{"classification": "Oxidoreductase", "pdb": "7MCI", "deposition_date": "2021-04-02", "title": "Mofe protein from azotobacter vinelandii with a sulfur-replenished Cofactor", "Keywords": ["Zotobacter vinelandii", " mofe-protein", " nitrogenase", " oxidoreductase"], "authors": ["W.kang", "C.lee", "Y.hu", "M.w.ribbe"], "doi": "10.1038/S41929-022-00782-7"} +{"classification": "Dna", "pdb": "1XUW", "deposition_date": "2004-10-26", "title": "Structural rationalization of a large difference in rna affinity Despite a small difference in chemistry between two 2'-o-modified Nucleic acid analogs", "Keywords": ["Na mimetic methylcarbamate amide analog", " dna"], "authors": ["R.pattanayek", "L.sethaphong", "C.pan", "M.prhavc", "T.p.prakash", "M.manoharan", "", "M.egli"], "pmid": "15547979", "doi": "10.1021/JA044637K"} +{"classification": "Lyase", "pdb": "7C0D", "deposition_date": "2020-05-01", "title": "Crystal structure of azospirillum brasilense l-2-keto-3-deoxyarabonate Dehydratase (hydroxypyruvate-bound form)", "Keywords": ["-2-keto-3-deoxyarabonate dehydratase", " lyase"], "authors": ["Y.watanabe", "S.watanabe"], "pmid": "32697085", "doi": "10.1021/ACS.BIOCHEM.0C00515"} +{"classification": "Signaling protein", "pdb": "5LYK", "deposition_date": "2016-09-28", "title": "Crystal structure of intracellular b30.2 domain of btn3a1 bound to Citrate", "Keywords": ["30.2", " butyrophilin", " signaling protein"], "authors": ["F.mohammed", "A.t.baker", "M.salim", "B.e.willcox"], "pmid": "28862425", "doi": "10.1021/ACSCHEMBIO.7B00694"} +{"classification": "Toxin", "pdb": "4IZL", "deposition_date": "2013-01-30", "title": "Structure of the n248a mutant of the panton-valentine leucocidin s Component from staphylococcus aureus", "Keywords": ["I-component leucotoxin", " staphylococcus aureus", " s component", "Leucocidin", "Beta-barrel pore forming toxin", "Toxin"], "authors": ["L.maveyraud", "B.j.laventie", "G.prevost", "L.mourey"], "pmid": "24643034", "doi": "10.1371/JOURNAL.PONE.0092094"} +{"classification": "Dna", "pdb": "6F3C", "deposition_date": "2017-11-28", "title": "The cytotoxic [pt(h2bapbpy)] platinum complex interacting with the Cgtacg hexamer", "Keywords": ["Rug-dna complex", " four-way junction", " dna"], "authors": ["M.ferraroni", "C.bazzicalupi", "P.gratteri", "F.papi"], "pmid": "31046177", "doi": "10.1002/ANIE.201814532"} +{"classification": "Signaling protein/inhibitor", "pdb": "4L5M", "deposition_date": "2013-06-11", "title": "Complexe of arno sec7 domain with the protein-protein interaction Inhibitor n-(4-hydroxy-2,6-dimethylphenyl)benzenesulfonamide at ph6.5", "Keywords": ["Ec-7domain", " signaling protein-inhibitor complex"], "authors": ["F.hoh", "J.rouhana"], "pmid": "24112024", "doi": "10.1021/JM4009357"} +{"classification": "Signaling protein", "pdb": "5I6J", "deposition_date": "2016-02-16", "title": "Crystal structure of srgap2 f-barx", "Keywords": ["Rgap2", " f-bar", " fx", " signaling protein"], "authors": ["M.sporny", "J.guez-haddad", "M.n.isupov", "Y.opatowsky"], "pmid": "28333212", "doi": "10.1093/MOLBEV/MSX094"} +{"classification": "Metal binding protein", "pdb": "1Q80", "deposition_date": "2003-08-20", "title": "Solution structure and dynamics of nereis sarcoplasmic calcium binding Protein", "Keywords": ["Ll-alpha", " metal binding protein"], "authors": ["G.rabah", "R.popescu", "J.a.cox", "Y.engelborghs", "C.t.craescu"], "pmid": "15819893", "doi": "10.1111/J.1742-4658.2005.04629.X"} +{"classification": "Transferase", "pdb": "1TW1", "deposition_date": "2004-06-30", "title": "Beta-1,4-galactosyltransferase mutant met344his (m344h-gal-t1) complex With udp-galactose and magnesium", "Keywords": ["Et344his mutation; closed conformation; mn binding", " transferase"], "authors": ["B.ramakrishnan", "E.boeggeman", "P.k.qasba"], "pmid": "15449940", "doi": "10.1021/BI049007+"} +{"classification": "Rna", "pdb": "2PN4", "deposition_date": "2007-04-23", "title": "Crystal structure of hepatitis c virus ires subdomain iia", "Keywords": ["Cv", " ires", " subdoamin iia", " rna", " strontium", " hepatitis"], "authors": ["Q.zhao", "Q.han", "C.r.kissinger", "P.a.thompson"], "pmid": "18391410", "doi": "10.1107/S0907444908002011"} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump index 6b8ed0d94..c4cc0fa95 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump @@ -1,6 +1,36 @@ -{"pid": "Q6GZX4", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 41."}], "title": "Putative transcription factor 001R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} -{"pid": "Q6GZX3", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 42."}], "title": "Uncharacterized protein 002L;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} -{"pid": "Q197F8", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 27."}], "title": "Uncharacterized protein 002R;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]} -{"pid": "Q197F7", "dates": [{"date": "16-JUN-2009", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "11-JUL-2006", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 23."}], "title": "Uncharacterized protein 003L;", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus."], "references": [{"PubMed": "16912294"}, {" DOI": "10.1128/jvi.00464-06"}]} -{"pid": "Q6GZX2", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 36."}], "title": "Uncharacterized protein 3R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} -{"pid": "Q6GZX1", "dates": [{"date": "28-JUN-2011", "date_info": " integrated into UniProtKB/Swiss-Prot."}, {"date": "19-JUL-2004", "date_info": " sequence version 1."}, {"date": "12-AUG-2020", "date_info": " entry version 34."}], "title": "Uncharacterized protein 004R;", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3).", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus."], "references": [{"PubMed": "15165820"}, {" DOI": "10.1016/j.virol.2004.02.019"}]} \ No newline at end of file +{"pid": " Q6GZX4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 43"}], "title": "Putative transcription factor 001R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZX3", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 45"}], "title": "Uncharacterized protein 002L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197F8", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-02-23", "date_info": "entry version 29"}], "title": "Uncharacterized protein 002R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q197F7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2020-08-12", "date_info": "entry version 23"}], "title": "Uncharacterized protein 003L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZX2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 3R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZX1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 38"}], "title": "Uncharacterized protein 004R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197F5", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-10-12", "date_info": "entry version 32"}], "title": "Uncharacterized protein 005L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZX0", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 47"}], "title": "Uncharacterized protein 005R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q91G88", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2023-06-28", "date_info": "entry version 53"}], "title": "Putative KilA-N domain-containing protein 006L", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]} +{"pid": " Q6GZW9", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 34"}], "title": "Uncharacterized protein 006R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZW8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 32"}], "title": "Uncharacterized protein 007R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197F3", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 28"}], "title": "Uncharacterized protein 007R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q197F2", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-02-23", "date_info": "entry version 22"}], "title": "Uncharacterized protein 008L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZW6", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 67"}], "title": "Putative helicase 009L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q91G85", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 38"}], "title": "Uncharacterized protein 009R", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]} +{"pid": " Q6GZW5", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 010R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197E9", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 28"}], "title": "Uncharacterized protein 011L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZW4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 011R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZW3", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 012L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197E7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 37"}], "title": "Uncharacterized protein IIV3-013L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZW2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 30"}], "title": "Uncharacterized protein 013R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZW1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 014R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZW0", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 50"}], "title": "Uncharacterized protein 015R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZV8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 017L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZV7", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 33"}], "title": "Uncharacterized protein 018L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZV6", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 87"}], "title": "Putative serine/threonine-protein kinase 019R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZV5", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 40"}], "title": "Uncharacterized protein 020R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZV4", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 35"}], "title": "Uncharacterized protein 021L", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197D8", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-12-14", "date_info": "entry version 35"}], "title": "Transmembrane protein 022L", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZV2", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 33"}], "title": "Uncharacterized protein 023R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197D7", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2023-02-22", "date_info": "entry version 25"}], "title": "Uncharacterized protein 023R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q6GZV1", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 37"}], "title": "Uncharacterized protein 024R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q197D5", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2006-07-11", "date_info": "sequence version 1"}, {"date": "2022-10-12", "date_info": "entry version 24"}], "title": "Uncharacterized protein 025R", "organism_species": "Invertebrate iridescent virus 3 (IIV-3) (Mosquito iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Chloriridovirus"], "references": [{"PubMed": "16912294"}, {"DOI": "10.1128/jvi.00464-06"}]} +{"pid": " Q91G70", "dates": [{"date": "2009-06-16", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2001-12-01", "date_info": "sequence version 1"}, {"date": "2020-08-12", "date_info": "entry version 32"}], "title": "Uncharacterized protein 026R", "organism_species": "Invertebrate iridescent virus 6 (IIV-6) (Chilo iridescent virus)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Betairidovirinae", "Iridovirus"], "references": [{"PubMed": "17239238"}, {"DOI": "10.1186/1743-422x-4-11"}]} +{"pid": " Q6GZU9", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 49"}], "title": "Uncharacterized protein 027R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} +{"pid": " Q6GZU8", "dates": [{"date": "2011-06-28", "date_info": "integrated into UniProtKB/Swiss-Prot"}, {"date": "2004-07-19", "date_info": "sequence version 1"}, {"date": "2023-09-13", "date_info": "entry version 55"}], "title": "Uncharacterized protein 028R", "organism_species": "Frog virus 3 (isolate Goorha) (FV-3)", "subjects": ["Viruses", "Varidnaviria", "Bamfordvirae", "Nucleocytoviricota", "Megaviricetes", "Pimascovirales", "Iridoviridae", "Alphairidovirinae", "Ranavirus"], "references": [{"PubMed": "15165820"}, {"DOI": "10.1016/j.virol.2004.02.019"}]} \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml index 2e0ed9aee..6d375f03f 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml @@ -15,4 +15,12 @@ oozie.action.sharelib.for.spark spark2 + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + pivotHistoryDatabase + ​ + \ No newline at end of file diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml index 6947019e8..7c633facc 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml @@ -198,6 +198,8 @@ --isLookUpUrl${isLookUpUrl} --actionSetId${actionSetId} --cutConnectedComponent${cutConnectedComponent} + --hiveMetastoreUris${hiveMetastoreUris} + --pivotHistoryDatabase${pivotHistoryDatabase} diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json index 15eb1b711..598fe2ba5 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/crossref/irish_funder.json @@ -73,12 +73,6 @@ "name": "Irish Nephrology Society", "synonym": [] }, - { - "id": "100011062", - "uri": "http://dx.doi.org/10.13039/100011062", - "name": "Asian Spinal Cord Network", - "synonym": [] - }, { "id": "100011096", "uri": "http://dx.doi.org/10.13039/100011096", @@ -223,12 +217,6 @@ "name": "Global Brain Health Institute", "synonym": [] }, - { - "id": "100015776", - "uri": "http://dx.doi.org/10.13039/100015776", - "name": "Health and Social Care Board", - "synonym": [] - }, { "id": "100015992", "uri": "http://dx.doi.org/10.13039/100015992", @@ -403,18 +391,6 @@ "name": "Irish Hospice Foundation", "synonym": [] }, - { - "id": "501100001596", - "uri": "http://dx.doi.org/10.13039/501100001596", - "name": "Irish Research Council for Science, Engineering and Technology", - "synonym": [] - }, - { - "id": "501100001597", - "uri": "http://dx.doi.org/10.13039/501100001597", - "name": "Irish Research Council for the Humanities and Social Sciences", - "synonym": [] - }, { "id": "501100001598", "uri": "http://dx.doi.org/10.13039/501100001598", @@ -515,7 +491,7 @@ "id": "501100002081", "uri": "http://dx.doi.org/10.13039/501100002081", "name": "Irish Research Council", - "synonym": [] + "synonym": ["501100001596", "501100001597"] }, { "id": "501100002736", diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index d8292a631..3afc453bf 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -560,7 +560,15 @@ case object Crossref2Oaf { "10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" | "10.13039/501100013589" | "10.13039/501100000271" => generateSimpleRelationFromAward(funder, "ukri________", a => a) - + //HFRI + case "10.13039/501100013209" => + generateSimpleRelationFromAward(funder, "hfri________", a => a) + val targetId = getProjectId("hfri________", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //ERASMUS+ + case "10.13039/501100010790" => + generateSimpleRelationFromAward(funder, "erasmusplus_", a => a) case _ => logger.debug("no match for " + funder.DOI.get) } diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraints.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraints.java index 0f6fab238..3392c0d4b 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraints.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraints.java @@ -53,6 +53,8 @@ public class Constraints implements Serializable { for (Constraint sc : constraint) { boolean verified = false; + if (!param.containsKey(sc.getField())) + return false; for (String value : param.get(sc.getField())) { if (sc.verifyCriteria(value.trim())) { verified = true; diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index a0cc4c84a..4e174fddc 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -14,6 +14,7 @@ import org.apache.spark.SparkConf; 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.Row; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; import org.slf4j.Logger; @@ -84,19 +85,26 @@ public class SparkCountryPropagationJob { Dataset res = readPath(spark, sourcePath, resultClazz); log.info("Reading prepared info: {}", preparedInfoPath); - Dataset prepared = spark + final Dataset preparedInfoRaw = spark .read() - .json(preparedInfoPath) - .as(Encoders.bean(ResultCountrySet.class)); - - res - .joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer") - .map(getCountryMergeFn(), Encoders.bean(resultClazz)) - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath); + .json(preparedInfoPath); + if (!preparedInfoRaw.isEmpty()) { + final Dataset prepared = preparedInfoRaw.as(Encoders.bean(ResultCountrySet.class)); + res + .joinWith(prepared, res.col("id").equalTo(prepared.col("resultId")), "left_outer") + .map(getCountryMergeFn(), Encoders.bean(resultClazz)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + } else { + res + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + } } private static MapFunction, R> getCountryMergeFn() { diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/communityconfiguration/tagging_conf_remove.xml b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/communityconfiguration/tagging_conf_remove.xml new file mode 100644 index 000000000..edd6c7e0a --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/communityconfiguration/tagging_conf_remove.xml @@ -0,0 +1,1555 @@ + + + + + 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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 + + + + re3data_____::9ebe127e5f3a0bf401875690f3bb6b81 + + + + doajarticles::c6cd4b532e12868c1d760a8d7cda6815 + + + + doajarticles::a6de4499bb87bf3c01add0a9e2c9ed0b + + + + doajarticles::6eb31d13b12bc06bbac06aef63cf33c9 + + + 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{"verb":"contains_caseinsensitive","field":"description","value":"Human Digital Twins"} + ]}, + {"constraint":[ + {"verb":"equals_caseinsensitive","field":"subject","value":"Human Digital Twins"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"title","value":"Virtual Human Twin"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"description","value":"Virtual Human Twin"} + ]}, + {"constraint":[ + {"verb":"equals_caseinsensitive","field":"subject","value":"Virtual Human Twin"} + ]}, + {"constraint":[ + {"verb":"equals_caseinsensitive","field":"subject","value":"digital twin"}, + {"verb":"contains_caseinsensitive","field":"subject","value":"health"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"structural"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"marine"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"avionics"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"battery"} + ]}, + {"constraint":[ + {"verb":"contains_caseinsensitive","field":"title","value":"digital twin health"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"Acoustic"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"Health Monitoring"}, + {"verb":"not_contains_caseinsensitive","field":"title","value":"Health Monitoring"}, + {"verb":"not_contains_caseinsensitive","field":"title","value":"Health Management"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"Health Assessment"}, + {"verb":"not_contains_caseinsensitive","field":"title","value":"Health Assessment"}, + {"verb":"not_contains_caseinsensitive","field":"title","value":"Health status"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"ELECTRICAL ENGINEERING"}, + {"verb":"not_contains_caseinsensitive","field":"subject","value":"Control and Systems Engineering"} + ]} + ]} + + + + 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{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + share_______::bbd802baad85d1fd440f32a7a3a2c2b1 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + opendoar____::6f4922f45568161a8cdf4ad2299f6d23 + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]}, + {"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCoV"}]}]} + + + + re3data_____::7980778c78fb4cf0fab13ce2159030dc + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCov"}]}]} + + + re3data_____::978378def740bbf2bfb420de868c460b + {"criteria":[{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"SARS-CoV-2"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"COVID-19"}]},{"constraint":[{"verb":"contains_caseinsensitive","field":"title","value":"2019-nCov"}]}]} + + + + + chicago-covid-19 + + + + covid-19-senacyt-panama-sample + + + + covid-19-tx-rct-stats-review + + + + covid_19_senacyt_abc_panama + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromproject/sample/dataset 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+ doi_dedup___::e225555a08a082ad8f53f179bc59c5d0 + 2023-01-27T05:32:10Z +
+ + + + + + + + + + + + 10.1098/rsta.2020.0257 + 50|doiboost____::e225555a08a082ad8f53f179bc59c5d0 + 3211056089 + 50|od______1064::83eb0f76b60445d72bb7428a1b68ef1a + oai:ora.ox.ac.uk:uuid:9fc4563a-07e1-41d1-8b99-31ce2f8ac027 + 50|od_______267::6d978e42c57dfc79d61a84ab5be28cb8 + oai:pubmedcentral.nih.gov:8543046 + od_______267::6d978e42c57dfc79d61a84ab5be28cb8 + 34689630 + PMC8543046 + 10.1098/rsta.2020.0257 + + PMC8543046 + + 34689630 + + + + + + + + + A completely automated pipeline for 3D reconstruction of + human heart from 2D cine magnetic resonance slices. + + A completely automated pipeline for 3D reconstruction of + human heart from 2D cine magnetic resonance slices + + + Vicente Grau + Abhirup Banerjee + + Ernesto Zacur + Robin P. Choudhury + + Blanca Rodriguez + + Julia Camps + Yoram Rudy + Christopher M. Andrews + + + 2021-10-01 + Cardiac magnetic resonance (CMR) imaging is a valuable modality in the diagnosis and + characterization of cardiovascular diseases, since it can identify abnormalities in structure + and function of the myocardium non-invasively and without the need for ionizing radiation. + However, in clinical practice, it is commonly acquired as a collection of separated and + independent 2D image planes, which limits its accuracy in 3D analysis. This paper presents a + completely automated pipeline for generating patient-specific 3D biventricular heart models from + cine magnetic resonance (MR) slices. Our pipeline automatically selects the relevant cine MR + images, segments them using a deep learning-based method to extract the heart contours, and + aligns the contours in 3D space correcting possible misalignments due to breathing or subject + motion first using the intensity and contours information from the cine data and next with the + help of a statistical shape model. Finally, the sparse 3D representation of the contours is used + to generate a smooth 3D biventricular mesh. The computational pipeline is applied and evaluated + in a CMR dataset of 20 healthy subjects. Our results show an average reduction of misalignment + artefacts from 1.82 ± 1.60 mm to 0.72 ± 0.73 mm over 20 subjects, in terms of distance from the + final reconstructed mesh. The high-resolution 3D biventricular meshes obtained with our + computational pipeline are used for simulations of electrical activation patterns, showing + agreement with non-invasive electrocardiographic imaging. The automatic methodologies presented + here for patient-specific MR imaging-based 3D biventricular representations contribute to the + efficient realization of precision medicine, enabling the enhanced interpretability of clinical + data, the digital twin vision through patient-specific image-based modelling and simulation, and + augmented reality applications. + This article is part of the theme issue ‘Advanced computation in cardiovascular physiology: new + challenges and opportunities’. + + General Physics and Astronomy + + General Engineering + + General Mathematics + + Pipeline (computing) + + Cine mri + + Structure and function + + Cardiac magnetic resonance + + Magnetic resonance imaging + + medicine.diagnostic_test + + medicine + + Human heart + + Modality (human–computer interaction) + + 3D reconstruction + + Computer science + + Nuclear magnetic resonance + + 3. Good health + + 03 medical and health sciences + + 0302 clinical medicine + + 030218 Nuclear Medicine & + Medical Imaging + + 03021801 Radiology/Image + segmentation + + 03021801 Radiology/Image + segmentation - deep learning/datum + + 030204 Cardiovascular System + & Hematology + + 03020401 Aging-associated + diseases/Heart diseases + + 030217 Neurology & + Neurosurgery + + 03021701 Brain/Neural circuits + + + Articles + + Research Articles + + cardiac mesh reconstruction + + cine MRI + + misalignment correction + + electrophysiological + simulation + + ECGI + + Heart + + Humans + + Imaging, Three-Dimensional + + Magnetic Resonance Imaging + + Magnetic Resonance Imaging, Cine + + Magnetic Resonance Spectroscopy + + + 2021-10-25 + + 2021-10-25 + + 2021-12-13 + + 2021-01-01 + + 2023-01-05 + + 2021-05-28 + + 2023-01-05 + + The Royal Society + Crossref + + Philosophical transactions. Series A, Mathematical, physical, and engineering sciences + + + + Philosophical Transactions of the Royal + Society A: Mathematical, Physical and Engineering Sciences + + + + + + + + + true + false + 0.8 + dedup-result-decisiontree-v3 + + + + + openorgs____::6a7b1b4c40a067a1f209de6867fe094d + + + University of Oxford + University of Oxford + + + + doi_dedup___::015b27b0b7c55649236bf23a5c75f817 + + 10.6084/m9.figshare.15656924.v2 + + 2021-01-01 + Implementation Details of the Reconstruction + Pipeline and Electrophysiological Inference Results from A completely automated pipeline + for 3D reconstruction of human heart from 2D cine magnetic resonance slices + + The Royal Society + + 10.6084/m9.figshare.15656924 + + + + + corda__h2020::27f89b49dee12d828cc0f90f51727204 + + 823712 + + + ec__________::EC::H2020 + ec__________::EC::H2020::RIA + + CompBioMed2 + A Centre of Excellence in Computational Biomedicine + + + + doi_dedup___::be1ef3b30a8d7aa7e4dfe1570d5febf7 + + 2021-01-01 + 10.6084/m9.figshare.15656927 + + The Royal Society + 10.6084/m9.figshare.15656927.v1 + + + Montage Video of the Stepwise Performance of 3D + Reconstruction Pipeline on All 20 Patients from A completely automated pipeline for 3D + reconstruction of human heart from 2D cine magnetic resonance slices + + + + + doi_________::9f9f2328e11d379b14cb888209e33088 + + 2021-01-01 + 10.6084/m9.figshare.15656924.v1 + + Implementation Details of the Reconstruction + Pipeline and Electrophysiological Inference Results from A completely automated pipeline + for 3D reconstruction of human heart from 2D cine magnetic resonance slices + + The Royal Society + + + + + + 2021-10-01 + 34689630 + + + 34689630 + + The Royal Society + + PMC8543046 + + A completely automated + pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices + + PMC8543046 + + + + 2023-01-05 + Royal Society + + A completely automated + pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance slices + + + + 2021-10-25 + The Royal Society + + A completely + automated pipeline for 3D reconstruction of human heart from 2D cine magnetic resonance + slices. + + + + + 10.1098/rsta.2020.0257 + + + + + + + 2023-01-05 + + 34689630 + + + 10.1098/rsta.2020.0257 + + + http://creativecommons.org/licenses/by/4.0/ + + https://ora.ox.ac.uk/objects/uuid:9fc4563a-07e1-41d1-8b99-31ce2f8ac027 + + + + + + + + 10.1098/rsta.2020.0257 + + + + https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8543046 + + + + + + + 2021-10-25 + + 10.1098/rsta.2020.0257 + + + https://royalsociety.org/journals/ethics-policies/data-sharing-mining/ + + https://doi.org/10.1098/rsta.2020.0257 + + + + + + + 2021-10-25 + + 34689630 + + PMC8543046 + + + 10.1098/rsta.2020.0257 + + + + https://pubmed.ncbi.nlm.nih.gov/34689630 + + + + + + + 2021-10-01 + + 34689630 + + PMC8543046 + + + 10.1098/rsta.2020.0257 + + + + http://europepmc.org/articles/PMC8543046 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.2196-33081-ethics.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.2196-33081-ethics.xml new file mode 100644 index 000000000..4c4443447 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.2196-33081-ethics.xml @@ -0,0 +1,238 @@ + + +
+ doi_dedup___::88a9861b26cdda1c3dd162d11f0bedbe + 2023-03-13T00:12:27+0000 + 2023-03-13T04:39:52.807Z +
+ + + + + + + + + + + + oai:pure.eur.nl:publications/70bf9bd0-5ea6-45fd-bb62-8d79b48cd69f + 50|narcis______::3df5b8b060b819af0d439dd6751c8a77 + 10.2196/33081 + 50|doiboost____::88a9861b26cdda1c3dd162d11f0bedbe + 3212148341 + od_______267::276eb3ebee07cf1f3e8bfc43926fd0c2 + 35099399 + PMC8844982 + oai:services.nod.dans.knaw.nl:Publications/eur:oai:pure.eur.nl:publications/70bf9bd0-5ea6-45fd-bb62-8d79b48cd69f + 50|dris___00893::107e97e645cbb06fb7b454ce2569d6c2 + 10.2196/33081 + 35099399 + PMC8844982 + + + + + + Mapping the Ethical Issues of Digital Twins for Personalised Healthcare Service (Preprint) + Preliminary Mapping Study + Ethical Issues of Digital Twins for Personalized Health Care Service: Preliminary Mapping Study + + Ki-hun Kim + Pei-hua Huang + Maartje Schermer + Public Health + + 2022-01-01 + Background: The concept of digital twins has great potential for transforming the existing health care system by making it more personalized. As a convergence of health care, artificial intelligence, and information and communication technologies, personalized health care services that are developed under the concept of digital twins raise a myriad of ethical issues. Although some of the ethical issues are known to researchers working on digital health and personalized medicine, currently, there is no comprehensive review that maps the major ethical risks of digital twins for personalized health care services. Objective This study aims to fill the research gap by identifying the major ethical risks of digital twins for personalized health care services. We first propose a working definition for digital twins for personalized health care services to facilitate future discussions on the ethical issues related to these emerging digital health services. We then develop a process-oriented ethical map to identify the major ethical risks in each of the different data processing phases. MethodsWe resorted to the literature on eHealth, personalized medicine, precision medicine, and information engineering to identify potential issues and developed a process-oriented ethical map to structure the inquiry in a more systematic way. The ethical map allows us to see how each of the major ethical concerns emerges during the process of transforming raw data into valuable information. Developers of a digital twin for personalized health care service may use this map to identify ethical risks during the development stage in a more systematic way and can proactively address them. ResultsThis paper provides a working definition of digital twins for personalized health care services by identifying 3 features that distinguish the new application from other eHealth services. On the basis of the working definition, this paper further layouts 10 major operational problems and the corresponding ethical risks. ConclusionsIt is challenging to address all the major ethical risks that a digital twin for a personalized health care service might encounter proactively without a conceptual map at hand. The process-oriented ethical map we propose here can assist the developers of digital twins for personalized health care services in analyzing ethical risks in a more systematic manner. + education + Health Informatics + Ethical issues + Healthcare service + Psychology + Internet privacy + business.industry + business + Preprint + Artificial Intelligence + Delivery of Health Care + Health Services + Humans + Precision Medicine + Telemedicine + 03 medical and health sciences + 0302 clinical medicine + + 030212 General & Internal Medicine + + 03021201 Health care/Health care quality - datum/health care + + 03021201 Health care/Health care quality - datum/electronic health + + 0301 basic medicine + + 030104 Developmental Biology + + 0303 health sciences + + 030304 Developmental Biology + + 030304 Developmental Biology - datum/datum management/ethical + + 06 humanities and the arts + 0603 philosophy, ethics and religion + + 060301 Applied Ethics + + 06030101 Bioethics/Coordinates on Wikidata - intelligence/artificial intelligence/ethical + + 06030101 Bioethics/Coordinates on Wikidata - datum/ethical + + + + 2021-11-17 + 2022-01-31 + 2022-01-01 + Crossref + + Journal of Medical Internet Research, 24(1):e33081. Journal of medical Internet Research + urn:issn:1439-4456 + VOLUME=24;ISSUE=1;ISSN=1439-4456;TITLE=Journal of Medical Internet Research + application/pdf + + + + + + true + false + 0.8 + dedup-result-decisiontree-v3 + + + + + + Ethical Issues of Digital Twins for Personalized Health Care Service: Preliminary Mapping Study + + 2022-01-01 + + + PMC8844982 + + 2021-08-23 + Ethical Issues of Digital Twins for Personalized Health Care Service: Preliminary Mapping Study. + 35099399 + + + Preliminary Mapping Study + 2022-01-01 + + + + 2022-01-31 + Mapping the Ethical Issues of Digital Twins for Personalised Healthcare Service (Preprint) + + + + + 10.2196/33081 + JMIR Publications Inc. + + + + + + 2021-08-23 + + 35099399 + PMC8844982 + 10.2196/33081 + + + https://pubmed.ncbi.nlm.nih.gov/35099399 + + + + + + + + 2022-01-01 + 2022-01-31 + + 10.2196/33081 + 10.2196/33081 + urn:nbn:nl:ui:15-70bf9bd0-5ea6-45fd-bb62-8d79b48cd69f + + + https://doi.org/10.2196/33081 + + + + + + + 2022-01-01 + + 10.2196/33081 + urn:nbn:nl:ui:15-70bf9bd0-5ea6-45fd-bb62-8d79b48cd69f + + + https://pure.eur.nl/en/publications/70bf9bd0-5ea6-45fd-bb62-8d79b48cd69f + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.3390-pr9111967-covid.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.3390-pr9111967-covid.xml new file mode 100644 index 000000000..6287f90ee --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/edith-demo/10.3390-pr9111967-covid.xml @@ -0,0 +1,223 @@ + + +
+ doi_________::c166d06aeaed817937a79a400906a4b9 + 2023-03-09T00:12:02.045Z + 2023-03-09T00:24:00.8Z +
+ + + + + + + + + 50|openapc_____::c166d06aeaed817937a79a400906a4b9 + 10.3390/pr9111967 + pr9111967 + 50|doiboost____::c166d06aeaed817937a79a400906a4b9 + 3209532762 + 10.3390/pr9111967 + + + + + + + Digital Twins for Continuous mRNA Production + + + 2021-11-04 + The global coronavirus pandemic continues to restrict public life worldwide. An + effective means of limiting the pandemic is vaccination. Messenger ribonucleic acid (mRNA) + vaccines currently available on the market have proven to be a well-tolerated and effective + class of vaccine against coronavirus type 2 (CoV2). Accordingly, demand is presently + outstripping mRNA vaccine production. One way to increase productivity is to switch from the + currently performed batch to continuous in vitro transcription, which has proven to be a crucial + material-consuming step. In this article, a physico-chemical model of in vitro mRNA + transcription in a tubular reactor is presented and compared to classical batch and continuous + in vitro transcription in a stirred tank. The three models are validated based on a distinct and + quantitative validation workflow. Statistically significant parameters are identified as part of + the parameter determination concept. Monte Carlo simulations showed that the model is precise, + with a deviation of less than 1%. The advantages of continuous production are pointed out + compared to batchwise in vitro transcription by optimization of the space–time yield. + Improvements of a factor of 56 (0.011 µM/min) in the case of the continuously stirred tank + reactor (CSTR) and 68 (0.013 µM/min) in the case of the plug flow reactor (PFR) were found. + + Process Chemistry and Technology + + Chemical Engineering (miscellaneous) + + Bioengineering + + Coronavirus + + medicine.disease_cause + + medicine + + Continuous production + + Messenger RNA + + Continuous stirred-tank reactor + + Plug flow reactor model + + Mathematics + + In vitro transcription + + Biological system + + Yield (chemistry) + + Public life + + 03 medical and health sciences + + 0301 basic medicine + + 030104 Developmental Biology + + 0303 health sciences + + 030304 Developmental Biology + + 02 engineering and technology + + 0210 nano-technology + + 021001 Nanoscience & + Nanotechnology + + 01 natural sciences + + 0104 chemical sciences + + 010405 Organic Chemistry + + + 2021-11-05 + + 2021-11-04 + + Crossref + + + + 2146.08 + EUR + Processes + + + + false + false + 0.9 + null + + + + + + + + + 2021-11-04 + + 10.3390/pr9111967 + + + https://creativecommons.org/licenses/by/4.0/ + + https://doi.org/10.3390/pr9111967 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/sentinel.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/sentinel.xml new file mode 100644 index 000000000..475a375d3 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/eosc-future/sentinel.xml @@ -0,0 +1,138 @@ + + +
+ doi_dedup___::10a910f4a66b7f4bce8407d7a486a80a + 2023-04-05T00:36:27+0000 + 2023-04-05T07:33:52.185Z +
+ + + + + + 50|datacite____::10a910f4a66b7f4bce8407d7a486a80a + 10.5281/zenodo.6967373 + 50|datacite____::172969c66c312a9656fc745f0ec62ce5 + 10.5281/zenodo.6969999 + 50|datacite____::4fa8f1c89ff11e8e99f9ded870ade80d + 10.5281/zenodo.6967372 + 50|datacite____::a466b6173773d742b7a5881682748a8c + 10.5281/zenodo.6970067 + 10.5281/zenodo.6967373 + 10.5281/zenodo.6969999 + 10.5281/zenodo.6967372 + 10.5281/zenodo.6970067 + Sentinel-3 NDVI ARD and Long Term Statistics (1999-2019) from the Copernicus Global Land Service over Lombardia + + Marasco Pier Lorenzo + 2022-08-05 + Sentinel-3 NDVI Analysis Ready Data (ARD) (C_GLS_NDVI_20220101_20220701_Lombardia_S3_2.nc) product provided by the Copernicus Global Land Service [3]. The file C_GLS_NDVI_20220101_20220701_Lombardia_S3_2_masked.nc is derived from C_GLS_NDVI_20220101_20220701_Lombardia_S3_2.nc but values have been scaled (raw_value * ( 1/250) - 0.08) and values lower then -0.08 and greater than 0.92 have been removed (set to missing values). The original dataset can also be discovered through the OpenEO API[5] from the CGLS distributor VITO [4]. Access is free of charge but an EGI registration is needed. The file called Italy.geojson has been created using the Global Administrative Unit Layers GAUL G2015_2014 provided by FAO-UN (see Documentation). It only contains information related to Italy. Further info about drought indexes can be found in the Integrated Drought Management Programme [5] [1] Application of vegetation index and brightness temperature for drought detection [2] NDVI [3] Copernicus Global Land Service [4] Vito [5] OpenEO [5] Integrated Drought Management + These datasets are used for training purposes. See https://pangeo-data.github.io/foss4g-2022/intro.html + NDVI + vegetaion + Copernicus Global Land Service + pangeo + + 2022-08-05 + Zenodo + + + + + true + false + 0.8 + dedup-result-decisiontree-v3 + + + + + + Zenodo + 10.5281/zenodo.6967372 + 2022-08-05 + + Sentinel-3 NDVI ARD and Long Term Statistics (1999-2019) from the Copernicus Global Land Service over Lombardia + + + Zenodo + 10.5281/zenodo.6970067 + 2022-08-05 + + Sentinel-3 NDVI ARD and Long Term Statistics (1999-2019) from the Copernicus Global Land Service over Lombardia + + + Zenodo + 2022-08-05 + 10.5281/zenodo.6969999 + + Sentinel-3 NDVI ARD and Long Term Statistics (1999-2019) from the Copernicus Global Land Service over Lombardia + + + Zenodo + 2022-08-05 + + Sentinel-3 NDVI ARD and Long Term Statistics (1999-2019) from the Copernicus Global Land Service over Lombardia + 10.5281/zenodo.6967373 + + + + + + 2022-08-05 + + 10.5281/zenodo.6967373 + + https://creativecommons.org/licenses/by/4.0/legalcode + + https://doi.org/10.5281/zenodo.6967373 + + + + + + + 2022-08-05 + + 10.5281/zenodo.6970067 + + https://creativecommons.org/licenses/by/4.0/legalcode + + https://doi.org/10.5281/zenodo.6970067 + + + + + + + 2022-08-05 + + 10.5281/zenodo.6969999 + + https://creativecommons.org/licenses/by/4.0/legalcode + + https://doi.org/10.5281/zenodo.6969999 + + + + + + + 2022-08-05 + + 10.5281/zenodo.6967372 + + https://creativecommons.org/licenses/by/4.0/legalcode + + https://doi.org/10.5281/zenodo.6967372 + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index a89ec62d5..d25c990a1 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -1,10 +1,10 @@ { "eoscifguidelines": [ { - "code" : "EOSC::Jupyter Notebook", - "label" : "EOSC::Jupyter Notebook", - "url" : "", - "semanticRelation" : "compliesWith" + "code": "EOSC::Jupyter Notebook", + "label": "EOSC::Jupyter Notebook", + "url": "", + "semanticRelation": "compliesWith" } ], "measures": [ @@ -431,7 +431,26 @@ "value": "VIRTA" } ], - "context": [], + "context": [ + { + "id": "eosc", + "dataInfo": [ + { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.9", + "inferenceprovenance": "", + "provenanceaction": { + "classid": "sysimport:crosswalk", + "classname": "sysimport:crosswalk", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + ] + } + ], "contributor": [], "country": [], "coverage": [], diff --git a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml index e43e7cf14..6ee5860d5 100644 --- a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml @@ -48,16 +48,25 @@ ${wf:conf('resume') eq "format-results"} ${wf:conf('resume') eq "map-ids"} ${wf:conf('resume') eq "map-scores"} - ${wf:conf('resume') eq "start"} + ${wf:conf('resume') eq "start"} ${wf:conf('resume') eq "projects-impact"} ${wf:conf('resume') eq "create-actionset"} - + + + + + + + + + + @@ -606,6 +615,10 @@ Calculating project impact indicators failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + Re-create working dir failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + +