merging from bulkTag branch

This commit is contained in:
Claudio Atzori 2023-11-03 12:51:37 +01:00
commit 5f1ed61c1f
38 changed files with 783 additions and 1430 deletions

View File

@ -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);
}
}
}

View File

@ -1,8 +0,0 @@
package eu.dnetlib.dhp.common.api;
public class MissingConceptDoiException extends Throwable {
public MissingConceptDoiException(String message) {
super(message);
}
}

View File

@ -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();
}
}

View File

@ -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;
}
}

View File

@ -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;
}
}

View File

@ -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;
}
}

View File

@ -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;
}
}

View File

@ -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;
}
}

View File

@ -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<Community> communities;
private List<Creator> creators;
private String description;
private String doi;
private List<Grant> grants;
private List<String> keywords;
private String language;
private String license;
private PrereserveDoi prereserve_doi;
private String publication_date;
private List<String> references;
private List<RelatedIdentifier> 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<Community> getCommunities() {
return communities;
}
public void setCommunities(List<Community> communities) {
this.communities = communities;
}
public List<Creator> getCreators() {
return creators;
}
public void setCreators(List<Creator> 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<Grant> getGrants() {
return grants;
}
public void setGrants(List<Grant> grants) {
this.grants = grants;
}
public List<String> getKeywords() {
return keywords;
}
public void setKeywords(List<String> 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<String> getReferences() {
return references;
}
public void setReferences(List<String> references) {
this.references = references;
}
public List<RelatedIdentifier> getRelated_identifiers() {
return related_identifiers;
}
public void setRelated_identifiers(List<RelatedIdentifier> related_identifiers) {
this.related_identifiers = related_identifiers;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
}

View File

@ -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;
}
}

View File

@ -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;
}
}

View File

@ -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<File> 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<File> getFiles() {
return files;
}
public void setFiles(List<File> 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;
}
}

View File

@ -1,7 +0,0 @@
package eu.dnetlib.dhp.common.api.zenodo;
import java.util.ArrayList;
public class ZenodoModelList extends ArrayList<ZenodoModel> {
}

View File

@ -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());
}
}

View File

@ -1,6 +1,24 @@
package eu.dnetlib.pace.util; package eu.dnetlib.pace.util;
/*
* Diff Match and Patch
* Copyright 2018 The diff-match-patch Authors.
* https://github.com/google/diff-match-patch
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
/* /*
* Diff Match and Patch * Diff Match and Patch
* Copyright 2018 The diff-match-patch Authors. * Copyright 2018 The diff-match-patch Authors.

View File

@ -0,0 +1,83 @@
package eu.dnetlib.dhp.api;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.URL;
import org.jetbrains.annotations.NotNull;
/**
* @author miriam.baglioni
* @Date 06/10/23
*/
public class QueryCommunityAPI {
private static final String PRODUCTION_BASE_URL = "https://services.openaire.eu/openaire/";
private static final String BETA_BASE_URL = "https://beta.services.openaire.eu/openaire/";
private static String get(String geturl) throws IOException {
URL url = new URL(geturl);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setDoOutput(true);
conn.setRequestMethod("GET");
int responseCode = conn.getResponseCode();
String body = getBody(conn);
conn.disconnect();
if (responseCode != HttpURLConnection.HTTP_OK)
throw new IOException("Unexpected code " + responseCode + body);
return body;
}
public static String communities(boolean production) throws IOException {
if (production)
return get(PRODUCTION_BASE_URL + "community/communities");
return get(BETA_BASE_URL + "community/communities");
}
public static String community(String id, boolean production) throws IOException {
if (production)
return get(PRODUCTION_BASE_URL + "community/" + id);
return get(BETA_BASE_URL + "community/" + id);
}
public static String communityDatasource(String id, boolean production) throws IOException {
if (production)
return get(PRODUCTION_BASE_URL + "community/" + id + "/contentproviders");
return (BETA_BASE_URL + "community/" + id + "/contentproviders");
}
public static String communityPropagationOrganization(String id, boolean production) throws IOException {
if (production)
return get(PRODUCTION_BASE_URL + "community/" + id + "/propagationOrganizations");
return get(BETA_BASE_URL + "community/" + id + "/propagationOrganizations");
}
public static String communityProjects(String id, String page, String size, boolean production) throws IOException {
if (production)
return get(PRODUCTION_BASE_URL + "community/" + id + "/projects/" + page + "/" + size);
return get(BETA_BASE_URL + "community/" + id + "/projects/" + page + "/" + size);
}
@NotNull
private static 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;
}
}

View File

@ -0,0 +1,166 @@
package eu.dnetlib.dhp.api;
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.stream.Collectors;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.amazonaws.util.StringUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.api.model.*;
import eu.dnetlib.dhp.bulktag.community.Community;
import eu.dnetlib.dhp.bulktag.community.CommunityConfiguration;
import eu.dnetlib.dhp.bulktag.community.Provider;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolverFactory;
/**
* @author miriam.baglioni
* @Date 09/10/23
*/
public class Utils implements Serializable {
private static final ObjectMapper MAPPER = new ObjectMapper();
private static final VerbResolver resolver = VerbResolverFactory.newInstance();
private static final Logger log = LoggerFactory.getLogger(Utils.class);
public static CommunityConfiguration getCommunityConfiguration(boolean production) throws IOException {
final Map<String, Community> communities = Maps.newHashMap();
List<Community> validCommunities = new ArrayList<>();
getValidCommunities(production)
.forEach(community -> {
try {
CommunityModel cm = MAPPER
.readValue(QueryCommunityAPI.community(community.getId(), production), CommunityModel.class);
validCommunities.add(getCommunity(cm));
} catch (IOException e) {
throw new RuntimeException(e);
}
});
validCommunities.forEach(community -> {
try {
DatasourceList dl = MAPPER
.readValue(
QueryCommunityAPI.communityDatasource(community.getId(), production), DatasourceList.class);
community.setProviders(dl.stream().map(d -> {
if (d.getEnabled() == null || Boolean.FALSE.equals(d.getEnabled()))
return null;
Provider p = new Provider();
p.setOpenaireId("10|" + d.getOpenaireId());
p.setSelectionConstraints(d.getSelectioncriteria());
if (p.getSelectionConstraints() != null)
p.getSelectionConstraints().setSelection(resolver);
return p;
})
.filter(Objects::nonNull)
.collect(Collectors.toList()));
} catch (IOException e) {
throw new RuntimeException(e);
}
});
validCommunities.forEach(community -> {
if (community.isValid())
communities.put(community.getId(), community);
});
return new CommunityConfiguration(communities);
}
private static Community getCommunity(CommunityModel cm) {
Community c = new Community();
c.setId(cm.getId());
c.setZenodoCommunities(cm.getOtherZenodoCommunities());
if (!StringUtils.isNullOrEmpty(cm.getZenodoCommunity()))
c.getZenodoCommunities().add(cm.getZenodoCommunity());
c.setSubjects(cm.getSubjects());
c.getSubjects().addAll(cm.getFos());
c.getSubjects().addAll(cm.getSdg());
if (cm.getAdvancedConstraints() != null) {
c.setConstraints(cm.getAdvancedConstraints());
c.getConstraints().setSelection(resolver);
}
if (cm.getRemoveConstraints() != null) {
c.setRemoveConstraints(cm.getRemoveConstraints());
c.getRemoveConstraints().setSelection(resolver);
}
return c;
}
public static List<CommunityModel> getValidCommunities(boolean production) throws IOException {
return MAPPER
.readValue(QueryCommunityAPI.communities(production), CommunitySummary.class)
.stream()
.filter(
community -> !community.getStatus().equals("hidden") &&
(community.getType().equals("ri") || community.getType().equals("community")))
.collect(Collectors.toList());
}
/**
* it returns for each organization the list of associated communities
*/
public static CommunityEntityMap getCommunityOrganization(boolean production) throws IOException {
CommunityEntityMap organizationMap = new CommunityEntityMap();
getValidCommunities(production)
.forEach(community -> {
String id = community.getId();
try {
List<String> associatedOrgs = MAPPER
.readValue(
QueryCommunityAPI.communityPropagationOrganization(id, production), OrganizationList.class);
associatedOrgs.forEach(o -> {
if (!organizationMap
.keySet()
.contains(
"20|" + o))
organizationMap.put("20|" + o, new ArrayList<>());
organizationMap.get("20|" + o).add(community.getId());
});
} catch (IOException e) {
throw new RuntimeException(e);
}
});
return organizationMap;
}
public static CommunityEntityMap getCommunityProjects(boolean production) throws IOException {
CommunityEntityMap projectMap = new CommunityEntityMap();
getValidCommunities(production)
.forEach(community -> {
int page = -1;
int size = 100;
ContentModel cm = new ContentModel();
do {
page++;
try {
cm = MAPPER
.readValue(
QueryCommunityAPI
.communityProjects(
community.getId(), String.valueOf(page), String.valueOf(size), production),
ContentModel.class);
if (cm.getContent().size() > 0) {
cm.getContent().forEach(p -> {
if (!projectMap.keySet().contains("40|" + p.getOpenaireId()))
projectMap.put("40|" + p.getOpenaireId(), new ArrayList<>());
projectMap.get("40|" + p.getOpenaireId()).add(community.getId());
});
}
} catch (IOException e) {
throw new RuntimeException(e);
}
} while (!cm.getLast());
});
return projectMap;
}
}

View File

@ -0,0 +1,43 @@
package eu.dnetlib.dhp.api.model;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.google.gson.Gson;
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
@JsonAutoDetect
@JsonIgnoreProperties(ignoreUnknown = true)
public class CommunityContentprovider {
private String openaireId;
private SelectionConstraints selectioncriteria;
private String enabled;
public String getEnabled() {
return enabled;
}
public void setEnabled(String enabled) {
this.enabled = enabled;
}
public String getOpenaireId() {
return openaireId;
}
public void setOpenaireId(final String openaireId) {
this.openaireId = openaireId;
}
public SelectionConstraints getSelectioncriteria() {
return this.selectioncriteria;
}
public void setSelectioncriteria(SelectionConstraints selectioncriteria) {
this.selectioncriteria = selectioncriteria;
}
}

View File

@ -0,0 +1,21 @@
package eu.dnetlib.dhp.api.model;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
public class CommunityEntityMap extends HashMap<String, List<String>> {
public CommunityEntityMap() {
super();
}
public List<String> get(String key) {
if (super.get(key) == null) {
return new ArrayList<>();
}
return super.get(key);
}
}

View File

@ -0,0 +1,108 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import eu.dnetlib.dhp.bulktag.community.SelectionConstraints;
/**
* @author miriam.baglioni
* @Date 06/10/23
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class CommunityModel implements Serializable {
private String id;
private String type;
private String status;
private String zenodoCommunity;
private List<String> subjects;
private List<String> otherZenodoCommunities;
private List<String> fos;
private List<String> sdg;
private SelectionConstraints advancedConstraints;
private SelectionConstraints removeConstraints;
public String getZenodoCommunity() {
return zenodoCommunity;
}
public void setZenodoCommunity(String zenodoCommunity) {
this.zenodoCommunity = zenodoCommunity;
}
public List<String> getSubjects() {
return subjects;
}
public void setSubjects(List<String> subjects) {
this.subjects = subjects;
}
public List<String> getOtherZenodoCommunities() {
return otherZenodoCommunities;
}
public void setOtherZenodoCommunities(List<String> otherZenodoCommunities) {
this.otherZenodoCommunities = otherZenodoCommunities;
}
public List<String> getFos() {
return fos;
}
public void setFos(List<String> fos) {
this.fos = fos;
}
public List<String> getSdg() {
return sdg;
}
public void setSdg(List<String> sdg) {
this.sdg = sdg;
}
public SelectionConstraints getRemoveConstraints() {
return removeConstraints;
}
public void setRemoveConstraints(SelectionConstraints removeConstraints) {
this.removeConstraints = removeConstraints;
}
public SelectionConstraints getAdvancedConstraints() {
return advancedConstraints;
}
public void setAdvancedConstraints(SelectionConstraints advancedConstraints) {
this.advancedConstraints = advancedConstraints;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public String getStatus() {
return status;
}
public void setStatus(String status) {
this.status = status;
}
}

View File

@ -0,0 +1,15 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import java.util.ArrayList;
/**
* @author miriam.baglioni
* @Date 06/10/23
*/
public class CommunitySummary extends ArrayList<CommunityModel> implements Serializable {
public CommunitySummary() {
super();
}
}

View File

@ -0,0 +1,51 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import java.util.List;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* @author miriam.baglioni
* @Date 09/10/23
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class ContentModel implements Serializable {
private List<ProjectModel> content;
private Integer totalPages;
private Boolean last;
private Integer number;
public List<ProjectModel> getContent() {
return content;
}
public void setContent(List<ProjectModel> content) {
this.content = content;
}
public Integer getTotalPages() {
return totalPages;
}
public void setTotalPages(Integer totalPages) {
this.totalPages = totalPages;
}
public Boolean getLast() {
return last;
}
public void setLast(Boolean last) {
this.last = last;
}
public Integer getNumber() {
return number;
}
public void setNumber(Integer number) {
this.number = number;
}
}

View File

@ -0,0 +1,13 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import java.util.ArrayList;
import eu.dnetlib.dhp.api.model.CommunityContentprovider;
public class DatasourceList extends ArrayList<CommunityContentprovider> implements Serializable {
public DatasourceList() {
super();
}
}

View File

@ -0,0 +1,16 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import java.util.ArrayList;
/**
* @author miriam.baglioni
* @Date 09/10/23
*/
public class OrganizationList extends ArrayList<String> implements Serializable {
public OrganizationList() {
super();
}
}

View File

@ -0,0 +1,24 @@
package eu.dnetlib.dhp.api.model;
import java.io.Serializable;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
/**
* @author miriam.baglioni
* @Date 09/10/23
*/
@JsonIgnoreProperties(ignoreUnknown = true)
public class ProjectModel implements Serializable {
private String openaireId;
public String getOpenaireId() {
return openaireId;
}
public void setOpenaireId(String openaireId) {
this.openaireId = openaireId;
}
}

View File

@ -9,7 +9,6 @@ import java.util.*;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.ForeachFunction;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Encoders;
@ -21,8 +20,11 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.gson.Gson; import com.google.gson.Gson;
import eu.dnetlib.dhp.api.Utils;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.bulktag.community.*; import eu.dnetlib.dhp.bulktag.community.*;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@ -54,50 +56,38 @@ public class SparkBulkTagJob {
.orElse(Boolean.TRUE); .orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged); log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
Boolean isTest = Optional
.ofNullable(parser.get("isTest"))
.map(Boolean::valueOf)
.orElse(Boolean.FALSE);
log.info("isTest: {} ", isTest);
final String inputPath = parser.get("sourcePath"); final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath); log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath"); final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath); log.info("outputPath: {}", outputPath);
final boolean production = Boolean.valueOf(parser.get("production"));
log.info("production: {}", production);
ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class); ProtoMap protoMappingParams = new Gson().fromJson(parser.get("pathMap"), ProtoMap.class);
log.info("pathMap: {}", new Gson().toJson(protoMappingParams)); log.info("pathMap: {}", new Gson().toJson(protoMappingParams));
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
CommunityConfiguration cc; CommunityConfiguration cc;
String taggingConf = parser.get("taggingConf"); String taggingConf = Optional
.ofNullable(parser.get("taggingConf"))
.map(String::valueOf)
.orElse(null);
if (isTest) { if (taggingConf != null) {
cc = CommunityConfigurationFactory.newInstance(taggingConf); cc = CommunityConfigurationFactory.newInstance(taggingConf);
} else { } else {
cc = QueryInformationSystem.getCommunityConfiguration(parser.get("isLookUpUrl")); cc = Utils.getCommunityConfiguration(production);
} }
runWithSparkSession( runWithSparkSession(
conf, conf,
isSparkSessionManaged, isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputPath);
extendCommunityConfigurationForEOSC(spark, inputPath, cc); extendCommunityConfigurationForEOSC(spark, inputPath, cc);
execBulkTag(spark, inputPath, outputPath, protoMappingParams, resultClazz, cc); execBulkTag(spark, inputPath, outputPath, protoMappingParams, cc);
}); });
} }
@ -106,10 +96,7 @@ public class SparkBulkTagJob {
Dataset<String> datasources = readPath( Dataset<String> datasources = readPath(
spark, inputPath spark, inputPath
.substring( + "datasource",
0,
inputPath.lastIndexOf("/"))
+ "/datasource",
Datasource.class) Datasource.class)
.filter((FilterFunction<Datasource>) ds -> isOKDatasource(ds)) .filter((FilterFunction<Datasource>) ds -> isOKDatasource(ds))
.map((MapFunction<Datasource, String>) ds -> ds.getId(), Encoders.STRING()); .map((MapFunction<Datasource, String>) ds -> ds.getId(), Encoders.STRING());
@ -117,10 +104,10 @@ public class SparkBulkTagJob {
Map<String, List<Pair<String, SelectionConstraints>>> dsm = cc.getEoscDatasourceMap(); Map<String, List<Pair<String, SelectionConstraints>>> dsm = cc.getEoscDatasourceMap();
for (String ds : datasources.collectAsList()) { for (String ds : datasources.collectAsList()) {
final String dsId = ds.substring(3); // final String dsId = ds.substring(3);
if (!dsm.containsKey(dsId)) { if (!dsm.containsKey(ds)) {
ArrayList<Pair<String, SelectionConstraints>> eoscList = new ArrayList<>(); ArrayList<Pair<String, SelectionConstraints>> eoscList = new ArrayList<>();
dsm.put(dsId, eoscList); dsm.put(ds, eoscList);
} }
} }
@ -142,22 +129,30 @@ public class SparkBulkTagJob {
String inputPath, String inputPath,
String outputPath, String outputPath,
ProtoMap protoMappingParams, ProtoMap protoMappingParams,
Class<R> resultClazz,
CommunityConfiguration communityConfiguration) { CommunityConfiguration communityConfiguration) {
ResultTagger resultTagger = new ResultTagger(); ModelSupport.entityTypes
readPath(spark, inputPath, resultClazz) .keySet()
.map(patchResult(), Encoders.bean(resultClazz)) .parallelStream()
.filter(Objects::nonNull) .filter(e -> ModelSupport.isResult(e))
.map( .forEach(e -> {
(MapFunction<R, R>) value -> resultTagger removeOutputDir(spark, outputPath + e.name());
.enrichContextCriteria( ResultTagger resultTagger = new ResultTagger();
value, communityConfiguration, protoMappingParams), Class<R> resultClazz = ModelSupport.entityTypes.get(e);
Encoders.bean(resultClazz)) readPath(spark, inputPath + e.name(), resultClazz)
.write() .map(patchResult(), Encoders.bean(resultClazz))
.mode(SaveMode.Overwrite) .filter(Objects::nonNull)
.option("compression", "gzip") .map(
.json(outputPath); (MapFunction<R, R>) value -> resultTagger
.enrichContextCriteria(
value, communityConfiguration, protoMappingParams),
Encoders.bean(resultClazz))
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + e.name());
});
} }
public static <R> Dataset<R> readPath( public static <R> Dataset<R> readPath(

View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.bulktag.community;
import java.io.Serializable; import java.io.Serializable;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
import java.util.Optional;
import com.google.gson.Gson; import com.google.gson.Gson;
@ -13,7 +14,7 @@ public class Community implements Serializable {
private String id; private String id;
private List<String> subjects = new ArrayList<>(); private List<String> subjects = new ArrayList<>();
private List<Provider> providers = new ArrayList<>(); private List<Provider> providers = new ArrayList<>();
private List<ZenodoCommunity> zenodoCommunities = new ArrayList<>(); private List<String> zenodoCommunities = new ArrayList<>();
private SelectionConstraints constraints = new SelectionConstraints(); private SelectionConstraints constraints = new SelectionConstraints();
private SelectionConstraints removeConstraints = new SelectionConstraints(); private SelectionConstraints removeConstraints = new SelectionConstraints();
@ -26,7 +27,7 @@ public class Community implements Serializable {
return !getSubjects().isEmpty() return !getSubjects().isEmpty()
|| !getProviders().isEmpty() || !getProviders().isEmpty()
|| !getZenodoCommunities().isEmpty() || !getZenodoCommunities().isEmpty()
|| getConstraints().getCriteria() != null; || (Optional.ofNullable(getConstraints()).isPresent() && getConstraints().getCriteria() != null);
} }
public String getId() { public String getId() {
@ -53,11 +54,11 @@ public class Community implements Serializable {
this.providers = providers; this.providers = providers;
} }
public List<ZenodoCommunity> getZenodoCommunities() { public List<String> getZenodoCommunities() {
return zenodoCommunities; return zenodoCommunities;
} }
public void setZenodoCommunities(List<ZenodoCommunity> zenodoCommunities) { public void setZenodoCommunities(List<String> zenodoCommunities) {
this.zenodoCommunities = zenodoCommunities; this.zenodoCommunities = zenodoCommunities;
} }

View File

@ -81,7 +81,7 @@ public class CommunityConfiguration implements Serializable {
this.removeConstraintsMap = removeConstraintsMap; this.removeConstraintsMap = removeConstraintsMap;
} }
CommunityConfiguration(final Map<String, Community> communities) { public CommunityConfiguration(final Map<String, Community> communities) {
this.communities = communities; this.communities = communities;
init(); init();
} }
@ -117,10 +117,10 @@ public class CommunityConfiguration implements Serializable {
add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap); add(d.getOpenaireId(), new Pair<>(id, d.getSelectionConstraints()), datasourceMap);
} }
// get zenodo communities // get zenodo communities
for (ZenodoCommunity zc : c.getZenodoCommunities()) { for (String zc : c.getZenodoCommunities()) {
add( add(
zc.getZenodoCommunityId(), zc,
new Pair<>(id, zc.getSelCriteria()), new Pair<>(id, null),
zenodocommunityMap); zenodocommunityMap);
} }
selectionConstraintsMap.put(id, c.getConstraints()); selectionConstraintsMap.put(id, c.getConstraints());

View File

@ -143,16 +143,16 @@ public class CommunityConfigurationFactory {
return providerList; return providerList;
} }
private static List<ZenodoCommunity> parseZenodoCommunities(final Node node) { private static List<String> parseZenodoCommunities(final Node node) {
final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity"); final List<Node> list = node.selectNodes("./zenodocommunities/zenodocommunity");
final List<ZenodoCommunity> zenodoCommunityList = new ArrayList<>(); final List<String> zenodoCommunityList = new ArrayList<>();
for (Node n : list) { for (Node n : list) {
ZenodoCommunity zc = new ZenodoCommunity(); // ZenodoCommunity zc = new ZenodoCommunity();
zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText()); // zc.setZenodoCommunityId(n.selectSingleNode("./zenodoid").getText());
zc.setSelCriteria(n.selectSingleNode("./selcriteria")); // zc.setSelCriteria(n.selectSingleNode("./selcriteria"));
zenodoCommunityList.add(zc); zenodoCommunityList.add(n.selectSingleNode("./zenodoid").getText());
} }
log.info("size of the zenodo community list " + zenodoCommunityList.size()); log.info("size of the zenodo community list " + zenodoCommunityList.size());

View File

@ -4,6 +4,8 @@ package eu.dnetlib.dhp.bulktag.community;
import java.io.Serializable; import java.io.Serializable;
import java.lang.reflect.InvocationTargetException; import java.lang.reflect.InvocationTargetException;
import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore;
import eu.dnetlib.dhp.bulktag.criteria.Selection; import eu.dnetlib.dhp.bulktag.criteria.Selection;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
@ -11,7 +13,8 @@ public class Constraint implements Serializable {
private String verb; private String verb;
private String field; private String field;
private String value; private String value;
// private String element;
@JsonIgnore
private Selection selection; private Selection selection;
public String getVerb() { public String getVerb() {
@ -38,10 +41,7 @@ public class Constraint implements Serializable {
this.value = value; this.value = value;
} }
public void setSelection(Selection sel) { @JsonIgnore
selection = sel;
}
public void setSelection(VerbResolver resolver) public void setSelection(VerbResolver resolver)
throws InvocationTargetException, NoSuchMethodException, InstantiationException, throws InvocationTargetException, NoSuchMethodException, InstantiationException,
IllegalAccessException { IllegalAccessException {
@ -52,11 +52,4 @@ public class Constraint implements Serializable {
return selection.apply(metadata); return selection.apply(metadata);
} }
// public String getElement() {
// return element;
// }
//
// public void setElement(String element) {
// this.element = element;
// }
} }

View File

@ -1,34 +0,0 @@
package eu.dnetlib.dhp.bulktag.community;
import java.io.IOException;
import java.util.List;
import org.apache.commons.io.IOUtils;
import org.dom4j.DocumentException;
import org.xml.sax.SAXException;
import com.google.common.base.Joiner;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class QueryInformationSystem {
public static CommunityConfiguration getCommunityConfiguration(final String isLookupUrl)
throws ISLookUpException, DocumentException, SAXException, IOException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
final List<String> res = isLookUp
.quickSearchProfile(
IOUtils
.toString(
QueryInformationSystem.class
.getResourceAsStream(
"/eu/dnetlib/dhp/bulktag/query.xq")));
final String xmlConf = "<communities>" + Joiner.on(" ").join(res) + "</communities>";
return CommunityConfigurationFactory.newInstance(xmlConf);
}
}

View File

@ -85,16 +85,18 @@ public class ResultTagger implements Serializable {
conf conf
.getRemoveConstraintsMap() .getRemoveConstraintsMap()
.keySet() .keySet()
.forEach(communityId -> { .forEach(
if (conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null && communityId -> {
conf if (conf.getRemoveConstraintsMap().keySet().contains(communityId) &&
.getRemoveConstraintsMap() conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
.get(communityId) conf
.getCriteria() .getRemoveConstraintsMap()
.stream() .get(communityId)
.anyMatch(crit -> crit.verifyCriteria(param))) .getCriteria()
removeCommunities.add(communityId); .stream()
}); .anyMatch(crit -> crit.verifyCriteria(param)))
removeCommunities.add(communityId);
});
// communities contains all the communities to be added as context for the result // communities contains all the communities to be added as context for the result
final Set<String> communities = new HashSet<>(); final Set<String> communities = new HashSet<>();
@ -124,10 +126,10 @@ public class ResultTagger implements Serializable {
if (Objects.nonNull(result.getInstance())) { if (Objects.nonNull(result.getInstance())) {
for (Instance i : result.getInstance()) { for (Instance i : result.getInstance()) {
if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) { if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) {
collfrom.add(StringUtils.substringAfter(i.getCollectedfrom().getKey(), "|")); collfrom.add(i.getCollectedfrom().getKey());
} }
if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) { if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) {
hostdby.add(StringUtils.substringAfter(i.getHostedby().getKey(), "|")); hostdby.add(i.getHostedby().getKey());
} }
} }

View File

@ -7,11 +7,13 @@ import java.util.Collection;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.google.gson.Gson; import com.google.gson.Gson;
import com.google.gson.reflect.TypeToken; import com.google.gson.reflect.TypeToken;
import eu.dnetlib.dhp.bulktag.criteria.VerbResolver; import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
@JsonAutoDetect
public class SelectionConstraints implements Serializable { public class SelectionConstraints implements Serializable {
private List<Constraints> criteria; private List<Constraints> criteria;

View File

@ -1,10 +1,5 @@
[ [
{
"paramName":"is",
"paramLongName":"isLookUpUrl",
"paramDescription": "URL of the isLookUp Service",
"paramRequired": true
},
{ {
"paramName":"s", "paramName":"s",
"paramLongName":"sourcePath", "paramLongName":"sourcePath",
@ -17,12 +12,7 @@
"paramDescription": "the json path associated to each selection field", "paramDescription": "the json path associated to each selection field",
"paramRequired": true "paramRequired": true
}, },
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
},
{ {
"paramName": "out", "paramName": "out",
"paramLongName": "outputPath", "paramLongName": "outputPath",
@ -35,17 +25,19 @@
"paramDescription": "true if the spark session is managed, false otherwise", "paramDescription": "true if the spark session is managed, false otherwise",
"paramRequired": false "paramRequired": false
}, },
{
"paramName": "test",
"paramLongName": "isTest",
"paramDescription": "Parameter intended for testing purposes only. True if the reun is relatesd to a test and so the taggingConf parameter should be loaded",
"paramRequired": false
},
{ {
"paramName": "tg", "paramName": "tg",
"paramLongName": "taggingConf", "paramLongName": "taggingConf",
"paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed", "paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed",
"paramRequired": false "paramRequired": false
},
{
"paramName": "p",
"paramLongName": "production",
"paramDescription": "this parameter is intended for testing purposes only. It is a possible tagging configuration obtained via the XQUERY. Intended to be removed",
"paramRequired": true
} }
] ]

View File

@ -45,10 +45,14 @@
</property> </property>
<property> <property>
<name>sparkExecutorMemory</name> <name>sparkExecutorMemory</name>
<value>6G</value> <value>5G</value>
</property> </property>
<property> <property>
<name>sparkExecutorCores</name> <name>memoryOverhead</name>
<value>1</value> <value>3g</value>
</property>
<property>
<name>partitions</name>
<value>3284</value>
</property> </property>
</configuration> </configuration>

View File

@ -4,10 +4,6 @@
<name>sourcePath</name> <name>sourcePath</name>
<description>the source path</description> <description>the source path</description>
</property> </property>
<property>
<name>isLookUpUrl</name>
<description>the isLookup service endpoint</description>
</property>
<property> <property>
<name>pathMap</name> <name>pathMap</name>
<description>the json path associated to each selection field</description> <description>the json path associated to each selection field</description>
@ -102,16 +98,9 @@
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<join name="copy_wait" to="fork_exec_bulktag"/> <join name="copy_wait" to="exec_bulktag"/>
<fork name="fork_exec_bulktag"> <action name="exec_bulktag">
<path start="bulktag_publication"/>
<path start="bulktag_dataset"/>
<path start="bulktag_otherresearchproduct"/>
<path start="bulktag_software"/>
</fork>
<action name="bulktag_publication">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
@ -122,104 +111,23 @@
--num-executors=${sparkExecutorNumber} --num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory} --executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--conf spark.executor.memoryOverhead=${memoryOverhead}
--conf spark.sql.shuffle.partitions=${partitions}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg> <arg>--sourcePath</arg><arg>${sourcePath}/</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg> <arg>--outputPath</arg><arg>${outputPath}/</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg> <arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg> <arg>--production</arg><arg>${production}</arg>
</spark> </spark>
<ok to="wait"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="bulktag_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-dataset</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--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}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="bulktag_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-orp</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--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}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="bulktag_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>bulkTagging-software</name>
<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--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}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
<arg>--pathMap</arg><arg>${pathMap}</arg>
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="End"/>
<end name="End"/> <end name="End"/>

View File

@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
import java.nio.file.Path; import java.nio.file.Path;
import java.util.HashMap;
import java.util.List; import java.util.List;
import org.apache.commons.io.FileUtils; import org.apache.commons.io.FileUtils;
@ -98,14 +99,11 @@ public class BulkTagJobTest {
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", "-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates").getPath(), getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(),
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", "-outputPath", workingDir.toString() + "/",
"-outputPath", workingDir.toString() + "/dataset",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -133,19 +131,16 @@ public class BulkTagJobTest {
@Test @Test
void bulktagBySubjectNoPreviousContextTest() throws Exception { void bulktagBySubjectNoPreviousContextTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext") .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext/")
.getPath(); .getPath();
final String pathMap = BulkTagJobTest.pathMap; final String pathMap = BulkTagJobTest.pathMap;
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset", "-outputPath", workingDir.toString() + "/",
"-outputPath", workingDir.toString() + "/dataset",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -230,19 +225,19 @@ public class BulkTagJobTest {
void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception { void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance") "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance/")
.getPath(); .getPath();
final String pathMap = BulkTagJobTest.pathMap; final String pathMap = BulkTagJobTest.pathMap;
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -311,18 +306,18 @@ public class BulkTagJobTest {
@Test @Test
void bulktagByDatasourceTest() throws Exception { void bulktagByDatasourceTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource") .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
"-outputPath", workingDir.toString() + "/publication", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -384,25 +379,25 @@ public class BulkTagJobTest {
void bulktagByZenodoCommunityTest() throws Exception { void bulktagByZenodoCommunityTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity") "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/orp", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<OtherResearchProduct> tmp = sc JavaRDD<OtherResearchProduct> tmp = sc
.textFile(workingDir.toString() + "/orp") .textFile(workingDir.toString() + "/otherresearchproduct")
.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
Assertions.assertEquals(10, tmp.count()); Assertions.assertEquals(10, tmp.count());
@ -505,18 +500,18 @@ public class BulkTagJobTest {
@Test @Test
void bulktagBySubjectDatasourceTest() throws Exception { void bulktagBySubjectDatasourceTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource") .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -636,14 +631,14 @@ public class BulkTagJobTest {
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", "-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/software_10.json.gz").getPath(), getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(),
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -732,18 +727,18 @@ public class BulkTagJobTest {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -774,19 +769,19 @@ public class BulkTagJobTest {
void bulkTagOtherJupyter() throws Exception { void bulkTagOtherJupyter() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct") "/eu/dnetlib/dhp/eosctag/jupyter/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/otherresearchproduct", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -829,18 +824,18 @@ public class BulkTagJobTest {
public void bulkTagDatasetJupyter() throws Exception { public void bulkTagDatasetJupyter() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/jupyter/dataset") "/eu/dnetlib/dhp/eosctag/jupyter/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -878,18 +873,18 @@ public class BulkTagJobTest {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/jupyter/software") "/eu/dnetlib/dhp/eosctag/jupyter/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1096,18 +1091,18 @@ public class BulkTagJobTest {
void galaxyOtherTest() throws Exception { void galaxyOtherTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct") "/eu/dnetlib/dhp/eosctag/galaxy/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/otherresearchproduct", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1214,18 +1209,18 @@ public class BulkTagJobTest {
void galaxySoftwareTest() throws Exception { void galaxySoftwareTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/galaxy/software") "/eu/dnetlib/dhp/eosctag/galaxy/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1333,19 +1328,19 @@ public class BulkTagJobTest {
void twitterDatasetTest() throws Exception { void twitterDatasetTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/twitter/dataset") "/eu/dnetlib/dhp/eosctag/twitter/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1373,19 +1368,19 @@ public class BulkTagJobTest {
void twitterOtherTest() throws Exception { void twitterOtherTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct") "/eu/dnetlib/dhp/eosctag/twitter/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
"-outputPath", workingDir.toString() + "/otherresearchproduct", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1418,19 +1413,19 @@ public class BulkTagJobTest {
void twitterSoftwareTest() throws Exception { void twitterSoftwareTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/eosctag/twitter/software") "/eu/dnetlib/dhp/eosctag/twitter/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
"-outputPath", workingDir.toString() + "/software", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1455,19 +1450,19 @@ public class BulkTagJobTest {
void EoscContextTagTest() throws Exception { void EoscContextTagTest() throws Exception {
final String sourcePath = getClass() final String sourcePath = getClass()
.getResource( .getResource(
"/eu/dnetlib/dhp/bulktag/eosc/dataset/dataset_10.json") "/eu/dnetlib/dhp/bulktag/eosc/dataset/")
.getPath(); .getPath();
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", sourcePath, "-sourcePath", sourcePath,
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
@ -1533,16 +1528,16 @@ public class BulkTagJobTest {
SparkBulkTagJob SparkBulkTagJob
.main( .main(
new String[] { new String[] {
"-isTest", Boolean.TRUE.toString(),
"-isSparkSessionManaged", Boolean.FALSE.toString(), "-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath", "-sourcePath",
getClass() getClass()
.getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints") .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints/")
.getPath(), .getPath(),
"-taggingConf", taggingConf, "-taggingConf", taggingConf,
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
"-outputPath", workingDir.toString() + "/dataset", "-outputPath", workingDir.toString() + "/",
"-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
"-pathMap", pathMap "-pathMap", pathMap
}); });
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@ -1568,4 +1563,42 @@ public class BulkTagJobTest {
} }
@Test
void newConfTest() throws Exception {
final String pathMap = BulkTagJobTest.pathMap;
SparkBulkTagJob
.main(
new String[] {
"-isSparkSessionManaged", Boolean.FALSE.toString(),
"-sourcePath",
getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/no_updates/").getPath(),
"-taggingConf", taggingConf,
"-outputPath", workingDir.toString() + "/",
"-production", Boolean.TRUE.toString(),
"-pathMap", pathMap
});
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<Dataset> tmp = sc
.textFile(workingDir.toString() + "/dataset")
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
Assertions.assertEquals(10, tmp.count());
org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
verificationDataset.createOrReplaceTempView("dataset");
String query = "select id, MyT.id community "
+ "from dataset "
+ "lateral view explode(context) c as MyT "
+ "lateral view explode(MyT.datainfo) d as MyD "
+ "where MyD.inferenceprovenance = 'bulktagging'";
Assertions.assertEquals(0, spark.sql(query).count());
}
} }

View File

@ -47,7 +47,7 @@ class CommunityConfigurationFactoryTest {
sc.setVerb("not_contains"); sc.setVerb("not_contains");
sc.setField("contributor"); sc.setField("contributor");
sc.setValue("DARIAH"); sc.setValue("DARIAH");
sc.setSelection(resolver.getSelectionCriteria(sc.getVerb(), sc.getValue())); sc.setSelection(resolver);// .getSelectionCriteria(sc.getVerb(), sc.getValue()));
String metadata = "This work has been partially supported by DARIAH-EU infrastructure"; String metadata = "This work has been partially supported by DARIAH-EU infrastructure";
Assertions.assertFalse(sc.verifyCriteria(metadata)); Assertions.assertFalse(sc.verifyCriteria(metadata));
} }