dimitris.pierrakos
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dnet-hadoop
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Merge branch 'beta' into beta

This commit is contained in:
Antonis Lempesis 2021-10-19 23:54:21 +02:00
parent 41ecb1eb61 512e7b0170
commit 241dcf6df1
628 changed files with 35057 additions and 5275 deletions
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2
README.md
View File

@ -1,2 +1,2 @@
# dnet-hadoop
Dnet-hadoop is a tool for
Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning.

12
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java
View File

@ -8,8 +8,6 @@ import java.util.List;
import org.apache.commons.lang.ArrayUtils;
import org.apache.commons.lang.StringUtils;
import org.apache.maven.plugin.AbstractMojo;
import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.plugin.MojoFailureException;
/**
* Generates oozie properties which were not provided from commandline.
@ -27,7 +25,7 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
};
@Override
public void execute() throws MojoExecutionException, MojoFailureException {
public void execute() {
if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
String generatedSandboxName = generateSandboxName(
@ -46,24 +44,24 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
/**
* Generates sandbox name from workflow source directory.
*
* @param wfSourceDir
* @param wfSourceDir workflow source directory
* @return generated sandbox name
*/
private String generateSandboxName(String wfSourceDir) {
// utilize all dir names until finding one of the limiters
List<String> sandboxNameParts = new ArrayList<String>();
List<String> sandboxNameParts = new ArrayList<>();
String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar);
ArrayUtils.reverse(tokens);
if (tokens.length > 0) {
for (String token : tokens) {
for (String limiter : limiters) {
if (limiter.equals(token)) {
return sandboxNameParts.size() > 0
return !sandboxNameParts.isEmpty()
? StringUtils.join(sandboxNameParts.toArray())
: null;
}
}
if (sandboxNameParts.size() > 0) {
if (!sandboxNameParts.isEmpty()) {
sandboxNameParts.add(0, File.separator);
}
sandboxNameParts.add(0, token);

11
dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java
View File

@ -16,6 +16,7 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
@ -289,7 +290,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
*/
protected List<String> getEscapeChars(String escapeChars) {
List<String> tokens = getListFromCSV(escapeChars);
List<String> realTokens = new ArrayList<String>();
List<String> realTokens = new ArrayList<>();
for (String token : tokens) {
String realToken = getRealToken(token);
realTokens.add(realToken);
@ -324,7 +325,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
* @return content
*/
protected String getContent(String comment, Properties properties, List<String> escapeTokens) {
List<String> names = new ArrayList<String>(properties.stringPropertyNames());
List<String> names = new ArrayList<>(properties.stringPropertyNames());
Collections.sort(names);
StringBuilder sb = new StringBuilder();
if (!StringUtils.isBlank(comment)) {
@ -352,7 +353,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
throws MojoExecutionException {
try {
String content = getContent(comment, properties, escapeTokens);
FileUtils.writeStringToFile(file, content, ENCODING_UTF8);
FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8);
} catch (IOException e) {
throw new MojoExecutionException("Error creating properties file", e);
}
@ -399,9 +400,9 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
*/
protected static final List<String> getListFromCSV(String csv) {
if (StringUtils.isBlank(csv)) {
return new ArrayList<String>();
return new ArrayList<>();
}
List<String> list = new ArrayList<String>();
List<String> list = new ArrayList<>();
String[] tokens = StringUtils.split(csv, ",");
for (String token : tokens) {
list.add(token.trim());

16
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java
View File

@ -9,18 +9,18 @@ import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
/** @author mhorst, claudio.atzori */
public class GenerateOoziePropertiesMojoTest {
class GenerateOoziePropertiesMojoTest {
private final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
@BeforeEach
public void clearSystemProperties() {
void clearSystemProperties() {
System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);
}
@Test
public void testExecuteEmpty() throws Exception {
void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
@ -29,7 +29,7 @@ public class GenerateOoziePropertiesMojoTest {
}
@Test
public void testExecuteSandboxNameAlreadySet() throws Exception {
void testExecuteSandboxNameAlreadySet() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
String sandboxName = "originalSandboxName";
@ -44,7 +44,7 @@ public class GenerateOoziePropertiesMojoTest {
}
@Test
public void testExecuteEmptyWorkflowSourceDir() throws Exception {
void testExecuteEmptyWorkflowSourceDir() throws Exception {
// given
String workflowSourceDir = "";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@ -57,7 +57,7 @@ public class GenerateOoziePropertiesMojoTest {
}
@Test
public void testExecuteNullSandboxNameGenerated() throws Exception {
void testExecuteNullSandboxNameGenerated() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@ -70,7 +70,7 @@ public class GenerateOoziePropertiesMojoTest {
}
@Test
public void testExecute() throws Exception {
void testExecute() throws Exception {
// given
String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@ -83,7 +83,7 @@ public class GenerateOoziePropertiesMojoTest {
}
@Test
public void testExecuteWithoutRoot() throws Exception {
void testExecuteWithoutRoot() throws Exception {
// given
String workflowSourceDir = "wf/transformers";
System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);

32
dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java
View File

@ -20,7 +20,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
/** @author mhorst, claudio.atzori */
@ExtendWith(MockitoExtension.class)
public class WritePredefinedProjectPropertiesTest {
class WritePredefinedProjectPropertiesTest {
@Mock
private MavenProject mavenProject;
@ -39,7 +39,7 @@ public class WritePredefinedProjectPropertiesTest {
// ----------------------------------- TESTS ---------------------------------------------
@Test
public void testExecuteEmpty() throws Exception {
void testExecuteEmpty() throws Exception {
// execute
mojo.execute();
@ -50,7 +50,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithProjectProperties() throws Exception {
void testExecuteWithProjectProperties() throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -70,7 +70,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test()
public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -84,7 +84,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -108,7 +108,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -132,7 +132,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -164,7 +164,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
@ -194,7 +194,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteIncludingPropertyKeysFromBlankLocation() {
void testExecuteIncludingPropertyKeysFromBlankLocation() {
// given
String key = "projectPropertyKey";
String value = "projectPropertyValue";
@ -214,7 +214,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
@ -247,7 +247,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
throws Exception {
// given
String key = "projectPropertyKey";
@ -273,7 +273,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
// given
mojo.setQuiet(true);
mojo.setIncludePropertyKeysFromFiles(new String[] {
@ -290,7 +290,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() {
void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given
mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
@ -301,7 +301,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
// given
mojo.setIncludeEnvironmentVariables(true);
@ -318,7 +318,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
// given
String key = "systemPropertyKey";
String value = "systemPropertyValue";
@ -337,7 +337,7 @@ public class WritePredefinedProjectPropertiesTest {
}
@Test
public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
throws Exception {
// given
String key = "systemPropertyKey ";

10
dhp-common/pom.xml
View File

@ -25,6 +25,11 @@
<groupId>com.github.sisyphsu</groupId>
<artifactId>dateparser</artifactId>
</dependency>
<dependency>
<groupId>me.xuender</groupId>
<artifactId>unidecode</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
@ -112,6 +117,11 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
</dependency>
<dependency>
<groupId>com.opencsv</groupId>
<artifactId>opencsv</artifactId>
</dependency>
</dependencies>
</project>

14
dhp-common/src/main/java/eu/dnetlib/dhp/application/ApplicationUtils.java
View File

@ -1,14 +0,0 @@
package eu.dnetlib.dhp.application;
import java.io.*;
import java.util.Map;
import java.util.Properties;
import org.apache.hadoop.conf.Configuration;
import com.google.common.collect.Maps;
public class ApplicationUtils {
}

8
dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java
View File

@ -56,13 +56,13 @@ public class ArgumentApplicationParser implements Serializable {
final StringWriter stringWriter = new StringWriter();
IOUtils.copy(gis, stringWriter);
return stringWriter.toString();
} catch (Throwable e) {
log.error("Wrong value to decompress:" + abstractCompressed);
throw new RuntimeException(e);
} catch (IOException e) {
log.error("Wrong value to decompress: {}", abstractCompressed);
throw new IllegalArgumentException(e);
}
}
public static String compressArgument(final String value) throws Exception {
public static String compressArgument(final String value) throws IOException {
ByteArrayOutputStream out = new ByteArrayOutputStream();
GZIPOutputStream gzip = new GZIPOutputStream(out);
gzip.write(value.getBytes());

3
dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java
View File

@ -9,9 +9,6 @@ public class OptionsParameter {
private boolean paramRequired;
private boolean compressed;
public OptionsParameter() {
}
public String getParamName() {
return paramName;
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/collection/ApiDescriptor.java
View File

@ -34,7 +34,7 @@ public class ApiDescriptor {
return params;
}
public void setParams(final HashMap<String, String> params) {
public void setParams(final Map<String, String> params) {
this.params = params;
}

9
dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
View File

@ -12,6 +12,9 @@ public class Constants {
public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
private Constants() {
}
static {
accessRightsCoarMap.put("OPEN", "c_abf2");
accessRightsCoarMap.put("RESTRICTED", "c_16ec");
@ -49,4 +52,10 @@ public class Constants {
public static final String CONTENT_INVALIDRECORDS = "InvalidRecords";
public static final String CONTENT_TRANSFORMEDRECORDS = "transformedItems";
// IETF Draft and used by Repositories like ZENODO , not included in APACHE HTTP java packages
// see https://ietf-wg-httpapi.github.io/ratelimit-headers/draft-ietf-httpapi-ratelimit-headers.html
public static final String HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT = "X-RateLimit-Limit";
public static final String HTTPHEADER_IETF_DRAFT_RATELIMIT_REMAINING = "X-RateLimit-Remaining";
public static final String HTTPHEADER_IETF_DRAFT_RATELIMIT_RESET = "X-RateLimit-Reset";
}

17
dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java
View File

@ -84,7 +84,7 @@ public class GraphResultMapper implements Serializable {
.setDocumentationUrl(
value
.stream()
.map(v -> v.getValue())
.map(Field::getValue)
.collect(Collectors.toList())));
Optional
@ -100,20 +100,20 @@ public class GraphResultMapper implements Serializable {
.setContactgroup(
Optional
.ofNullable(ir.getContactgroup())
.map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList()))
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
@ -123,7 +123,8 @@ public class GraphResultMapper implements Serializable {
Optional
.ofNullable(input.getAuthor())
.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList())));
.ifPresent(
ats -> out.setAuthor(ats.stream().map(GraphResultMapper::getAuthor).collect(Collectors.toList())));
// I do not map Access Right UNKNOWN or OTHER
@ -210,7 +211,7 @@ public class GraphResultMapper implements Serializable {
if (oInst.isPresent()) {
out
.setInstance(
oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList()));
oInst.get().stream().map(GraphResultMapper::getInstance).collect(Collectors.toList()));
}
@ -230,7 +231,7 @@ public class GraphResultMapper implements Serializable {
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
.collect(Collectors.toList());
if (iTitle.size() > 0) {
if (!iTitle.isEmpty()) {
out.setMaintitle(iTitle.get(0).getValue());
}
@ -239,7 +240,7 @@ public class GraphResultMapper implements Serializable {
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (iTitle.size() > 0) {
if (!iTitle.isEmpty()) {
out.setSubtitle(iTitle.get(0).getValue());
}

26
dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java
View File

@ -14,38 +14,33 @@ public class MakeTarArchive implements Serializable {
private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException {
Path hdfsWritePath = new Path(outputPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, true);
}
fsDataOutputStream = fileSystem.create(hdfsWritePath);
return new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream());
}
private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
throws IOException {
Path hdfsWritePath = new Path(outputPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, true);
}
fsDataOutputStream = fileSystem.create(hdfsWritePath);
try (TarArchiveOutputStream ar = new TarArchiveOutputStream(
fileSystem.create(hdfsWritePath).getWrappedStream())) {
TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
RemoteIterator<LocatedFileStatus> iterator = fileSystem
.listFiles(
new Path(inputPath), true);
while (fileStatusListIterator.hasNext()) {
writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, 0);
while (iterator.hasNext()) {
writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
}
ar.close();
}
}
public static void tarMaxSize(FileSystem fileSystem, String inputPath, String outputPath, String dir_name,
@ -90,6 +85,13 @@ public class MakeTarArchive implements Serializable {
String p_string = p.toString();
if (!p_string.endsWith("_SUCCESS")) {
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
if (name.startsWith("part-") & name.length() > 10) {
String tmp = name.substring(0, 10);
if (name.contains(".")) {
tmp += name.substring(name.indexOf("."));
}
name = tmp;
}
TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
entry.setSize(fileStatus.getLen());
current_size += fileStatus.getLen();

9
dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreClient.java
View File

@ -10,8 +10,6 @@ import java.util.Optional;
import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.bson.Document;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -21,6 +19,7 @@ import com.mongodb.BasicDBObject;
import com.mongodb.MongoClient;
import com.mongodb.MongoClientURI;
import com.mongodb.QueryBuilder;
import com.mongodb.client.FindIterable;
import com.mongodb.client.MongoCollection;
import com.mongodb.client.MongoDatabase;
@ -46,7 +45,7 @@ public class MdstoreClient implements Closeable {
final String currentId = Optional
.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
.map(r -> r.first())
.map(FindIterable::first)
.map(d -> d.getString("currentId"))
.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
@ -84,7 +83,7 @@ public class MdstoreClient implements Closeable {
if (!Iterables.contains(client.listDatabaseNames(), dbName)) {
final String err = String.format("Database '%s' not found in %s", dbName, client.getAddress());
log.warn(err);
throw new RuntimeException(err);
throw new IllegalArgumentException(err);
}
return client.getDatabase(dbName);
}
@ -97,7 +96,7 @@ public class MdstoreClient implements Closeable {
String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
log.warn(err);
if (abortIfMissing) {
throw new RuntimeException(err);
throw new IllegalArgumentException(err);
} else {
return null;
}

1
dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java
View File

@ -24,7 +24,6 @@ import com.google.common.hash.Hashing;
*/
public class PacePerson {
private static final String UTF8 = "UTF-8";
private List<String> name = Lists.newArrayList();
private List<String> surname = Lists.newArrayList();
private List<String> fullname = Lists.newArrayList();

8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/AggregatorReport.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/aggregation/AggregatorReport.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.aggregation.common;
package eu.dnetlib.dhp.common.aggregation;
import java.io.Closeable;
import java.io.IOException;
@ -11,8 +11,6 @@ import java.util.Objects;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import eu.dnetlib.dhp.message.MessageSender;
import eu.dnetlib.dhp.utils.DHPUtils;
@ -20,12 +18,12 @@ public class AggregatorReport extends LinkedHashMap<String, String> implements C
private static final Logger log = LoggerFactory.getLogger(AggregatorReport.class);
private MessageSender messageSender;
private transient MessageSender messageSender;
public AggregatorReport() {
}
public AggregatorReport(MessageSender messageSender) throws IOException {
public AggregatorReport(MessageSender messageSender) {
this.messageSender = messageSender;
}

27
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java
View File

@ -5,6 +5,9 @@ import java.io.*;
import java.io.IOException;
import java.util.concurrent.TimeUnit;
import org.apache.http.HttpHeaders;
import org.apache.http.entity.ContentType;
import com.google.gson.Gson;
import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
@ -43,7 +46,7 @@ public class ZenodoAPIClient implements Serializable {
this.deposition_id = deposition_id;
}
public ZenodoAPIClient(String urlString, String access_token) throws IOException {
public ZenodoAPIClient(String urlString, String access_token) {
this.urlString = urlString;
this.access_token = access_token;
@ -63,8 +66,8 @@ public class ZenodoAPIClient implements Serializable {
Request request = new Request.Builder()
.url(urlString)
.addHeader("Content-Type", "application/json") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.post(body)
.build();
@ -103,8 +106,8 @@ public class ZenodoAPIClient implements Serializable {
Request request = new Request.Builder()
.url(bucket + "/" + file_name)
.addHeader("Content-Type", "application/zip") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.addHeader(HttpHeaders.CONTENT_TYPE, "application/zip") // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.put(InputStreamRequestBody.create(MEDIA_TYPE_ZIP, is, len))
.build();
@ -130,8 +133,8 @@ public class ZenodoAPIClient implements Serializable {
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id)
.addHeader("Content-Type", "application/json") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.put(body)
.build();
@ -197,7 +200,7 @@ public class ZenodoAPIClient implements Serializable {
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id + "/actions/newversion")
.addHeader("Authorization", "Bearer " + access_token)
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.post(body)
.build();
@ -270,8 +273,8 @@ public class ZenodoAPIClient implements Serializable {
Request request = new Request.Builder()
.url(urlString)
.addHeader("Content-Type", "application/json") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.get()
.build();
@ -293,8 +296,8 @@ public class ZenodoAPIClient implements Serializable {
Request request = new Request.Builder()
.url(url)
.addHeader("Content-Type", "application/json") // add request headers
.addHeader("Authorization", "Bearer " + access_token)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.get()
.build();

6
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java
View File

@ -32,13 +32,13 @@ public class Creator {
public static Creator newInstance(String name, String affiliation, String orcid) {
Creator c = new Creator();
if (!(name == null)) {
if (name != null) {
c.name = name;
}
if (!(affiliation == null)) {
if (affiliation != null) {
c.affiliation = affiliation;
}
if (!(orcid == null)) {
if (orcid != null) {
c.orcid = orcid;
}

14
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java
View File

@ -3,17 +3,12 @@ package eu.dnetlib.dhp.common.api.zenodo;
import java.io.Serializable;
import net.minidev.json.annotate.JsonIgnore;
public class File implements Serializable {
private String checksum;
private String filename;
private long filesize;
private String id;
@JsonIgnore
// private Links links;
public String getChecksum() {
return checksum;
}
@ -46,13 +41,4 @@ public class File implements Serializable {
this.id = id;
}
// @JsonIgnore
// public Links getLinks() {
// return links;
// }
//
// @JsonIgnore
// public void setLinks(Links links) {
// this.links = links;
// }
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorException.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/CollectorException.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.collection;
package eu.dnetlib.dhp.common.collection;
public class CollectorException extends Exception {

56
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/GetCSV.java Normal file
View File

@ -0,0 +1,56 @@
package eu.dnetlib.dhp.common.collection;
import java.io.*;
import java.nio.charset.StandardCharsets;
import java.util.List;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.opencsv.bean.CsvToBeanBuilder;
public class GetCSV {
public static final char DEFAULT_DELIMITER = ',';
private GetCSV() {
}
public static void getCsv(FileSystem fileSystem, BufferedReader reader, String hdfsPath,
String modelClass) throws IOException, ClassNotFoundException {
getCsv(fileSystem, reader, hdfsPath, modelClass, DEFAULT_DELIMITER);
}
public static void getCsv(FileSystem fileSystem, Reader reader, String hdfsPath,
String modelClass, char delimiter) throws IOException, ClassNotFoundException {
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, false);
}
fsDataOutputStream = fileSystem.create(hdfsWritePath);
try (BufferedWriter writer = new BufferedWriter(
new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8))) {
final ObjectMapper mapper = new ObjectMapper();
@SuppressWarnings("unchecked")
final List lines = new CsvToBeanBuilder(reader)
.withType(Class.forName(modelClass))
.withSeparator(delimiter)
.build()
.parse();
for (Object line : lines) {
writer.write(mapper.writeValueAsString(line));
writer.newLine();
}
}
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpClientParams.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpClientParams.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.collection;
package eu.dnetlib.dhp.common.collection;
/**
* Bundles the http connection parameters driving the client behaviour.

36
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpConnector2.java → dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.collection;
package eu.dnetlib.dhp.common.collection;
import static eu.dnetlib.dhp.utils.DHPUtils.*;
@ -15,12 +15,13 @@ import org.apache.http.HttpHeaders;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.common.Constants;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
/**
* Migrated from https://svn.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-modular-collector-service/trunk/src/main/java/eu/dnetlib/data/collector/plugins/HttpConnector.java
*
* @author jochen, michele, andrea, alessia, claudio
* @author jochen, michele, andrea, alessia, claudio, andreas
*/
public class HttpConnector2 {
@ -32,7 +33,7 @@ public class HttpConnector2 {
private String responseType = null;
private final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
public HttpConnector2() {
this(new HttpClientParams());
@ -112,6 +113,17 @@ public class HttpConnector2 {
}
int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
String rateLimit = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT);
String rateRemaining = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_REMAINING);
if ((rateLimit != null) && (rateRemaining != null) && (Integer.parseInt(rateRemaining) < 2)) {
if (retryAfter > 0) {
backoffAndSleep(retryAfter);
} else {
backoffAndSleep(1000);
}
}
if (is2xx(urlConn.getResponseCode())) {
input = urlConn.getInputStream();
responseType = urlConn.getContentType();
@ -120,7 +132,7 @@ public class HttpConnector2 {
if (is3xx(urlConn.getResponseCode())) {
// REDIRECTS
final String newUrl = obtainNewLocation(urlConn.getHeaderFields());
log.info(String.format("The requested url has been moved to %s", newUrl));
log.info("The requested url has been moved to {}", newUrl);
report
.put(
REPORT_PREFIX + urlConn.getResponseCode(),
@ -140,14 +152,14 @@ public class HttpConnector2 {
if (retryAfter > 0) {
log
.warn(
requestUrl + " - waiting and repeating request after suggested retry-after "
+ retryAfter + " sec.");
"{} - waiting and repeating request after suggested retry-after {} sec.",
requestUrl, retryAfter);
backoffAndSleep(retryAfter * 1000);
} else {
log
.warn(
requestUrl + " - waiting and repeating request after default delay of "
+ getClientParams().getRetryDelay() + " sec.");
"{} - waiting and repeating request after default delay of {} sec.",
requestUrl, getClientParams().getRetryDelay());
backoffAndSleep(retryNumber * getClientParams().getRetryDelay() * 1000);
}
report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
@ -181,12 +193,12 @@ public class HttpConnector2 {
}
private void logHeaderFields(final HttpURLConnection urlConn) throws IOException {
log.debug("StatusCode: " + urlConn.getResponseMessage());
log.debug("StatusCode: {}", urlConn.getResponseMessage());
for (Map.Entry<String, List<String>> e : urlConn.getHeaderFields().entrySet()) {
if (e.getKey() != null) {
for (String v : e.getValue()) {
log.debug(" key: " + e.getKey() + " - value: " + v);
log.debug(" key: {} - value: {}", e.getKey(), v);
}
}
}
@ -204,7 +216,7 @@ public class HttpConnector2 {
private int obtainRetryAfter(final Map<String, List<String>> headerMap) {
for (String key : headerMap.keySet()) {
if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (headerMap.get(key).size() > 0)
if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (!headerMap.get(key).isEmpty())
&& NumberUtils.isCreatable(headerMap.get(key).get(0))) {
return Integer.parseInt(headerMap.get(key).get(0)) + 10;
}

19
dhp-common/src/main/java/eu/dnetlib/dhp/common/rest/DNetRestClient.java
View File

@ -1,11 +1,11 @@
package eu.dnetlib.dhp.common.rest;
import java.io.IOException;
import java.util.Arrays;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.client.methods.HttpPost;
import org.apache.http.client.methods.HttpUriRequest;
@ -23,17 +23,20 @@ public class DNetRestClient {
private static final ObjectMapper mapper = new ObjectMapper();
private DNetRestClient() {
}
public static <T> T doGET(final String url, Class<T> clazz) throws Exception {
final HttpGet httpGet = new HttpGet(url);
return doHTTPRequest(httpGet, clazz);
}
public static String doGET(final String url) throws Exception {
public static String doGET(final String url) throws IOException {
final HttpGet httpGet = new HttpGet(url);
return doHTTPRequest(httpGet);
}
public static <V> String doPOST(final String url, V objParam) throws Exception {
public static <V> String doPOST(final String url, V objParam) throws IOException {
final HttpPost httpPost = new HttpPost(url);
if (objParam != null) {
@ -45,12 +48,12 @@ public class DNetRestClient {
return doHTTPRequest(httpPost);
}
public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws Exception {
public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws IOException {
return mapper.readValue(doPOST(url, objParam), clazz);
}
private static String doHTTPRequest(final HttpUriRequest r) throws Exception {
CloseableHttpClient client = HttpClients.createDefault();
private static String doHTTPRequest(final HttpUriRequest r) throws IOException {
try (CloseableHttpClient client = HttpClients.createDefault()) {
log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
log
@ -62,8 +65,8 @@ public class DNetRestClient {
.map(h -> h.getName() + ":" + h.getValue())
.collect(Collectors.joining(",")));
CloseableHttpResponse response = client.execute(r);
return IOUtils.toString(response.getEntity().getContent());
return IOUtils.toString(client.execute(r).getEntity().getContent());
}
}
private static <T> T doHTTPRequest(final HttpUriRequest r, Class<T> clazz) throws Exception {

3
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java
View File

@ -46,7 +46,7 @@ public class Vocabulary implements Serializable {
}
public VocabularyTerm getTerm(final String id) {
return Optional.ofNullable(id).map(s -> s.toLowerCase()).map(s -> terms.get(s)).orElse(null);
return Optional.ofNullable(id).map(String::toLowerCase).map(terms::get).orElse(null);
}
protected void addTerm(final String id, final String name) {
@ -81,7 +81,6 @@ public class Vocabulary implements Serializable {
.ofNullable(getTermBySynonym(syn))
.map(term -> getTermAsQualifier(term.getId()))
.orElse(null);
// .orElse(OafMapperUtils.unknown(getId(), getName()));
}
}

13
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java
View File

@ -46,7 +46,6 @@ public class VocabularyGroup implements Serializable {
}
vocs.addTerm(vocId, termId, termName);
// vocs.addSynonyms(vocId, termId, termId);
}
}
@ -58,7 +57,6 @@ public class VocabularyGroup implements Serializable {
final String syn = arr[2].trim();
vocs.addSynonyms(vocId, termId, syn);
// vocs.addSynonyms(vocId, termId, termId);
}
}
@ -98,7 +96,7 @@ public class VocabularyGroup implements Serializable {
.getTerms()
.values()
.stream()
.map(t -> t.getId())
.map(VocabularyTerm::getId)
.collect(Collectors.toCollection(HashSet::new));
}
@ -154,16 +152,19 @@ public class VocabularyGroup implements Serializable {
return Optional
.ofNullable(vocId)
.map(String::toLowerCase)
.map(id -> vocs.containsKey(id))
.map(vocs::containsKey)
.orElse(false);
}
private void addSynonyms(final String vocId, final String termId, final String syn) {
String id = Optional
.ofNullable(vocId)
.map(s -> s.toLowerCase())
.map(String::toLowerCase)
.orElseThrow(
() -> new IllegalArgumentException(String.format("empty vocabulary id for [term:%s, synonym:%s]")));
() -> new IllegalArgumentException(
String
.format(
"empty vocabulary id for [term:%s, synonym:%s]", termId, syn)));
Optional
.ofNullable(vocs.get(id))
.orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId))

5
dhp-common/src/main/java/eu/dnetlib/dhp/message/Message.java
View File

@ -2,7 +2,6 @@
package eu.dnetlib.dhp.message;
import java.io.Serializable;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
@ -10,8 +9,8 @@ public class Message implements Serializable {
private static final long serialVersionUID = 401753881204524893L;
public static String CURRENT_PARAM = "current";
public static String TOTAL_PARAM = "total";
public static final String CURRENT_PARAM = "current";
public static final String TOTAL_PARAM = "total";
private MessageType messageType;

17
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
View File

@ -4,7 +4,6 @@ package eu.dnetlib.dhp.oa.merge;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
@ -19,6 +18,9 @@ public class AuthorMerger {
private static final Double THRESHOLD = 0.95;
private AuthorMerger() {
}
public static List<Author> merge(List<List<Author>> authors) {
authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)));
@ -36,7 +38,8 @@ public class AuthorMerger {
public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
int pa = countAuthorsPids(a);
int pb = countAuthorsPids(b);
List<Author> base, enrich;
List<Author> base;
List<Author> enrich;
int sa = authorsSize(a);
int sb = authorsSize(b);
@ -62,7 +65,7 @@ public class AuthorMerger {
// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
final Map<String, Author> basePidAuthorMap = base
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
.flatMap(
a -> a
.getPid()
@ -74,7 +77,7 @@ public class AuthorMerger {
// <pid, Author> (list of pid that are missing in the other list)
final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
.flatMap(
a -> a
.getPid()
@ -117,9 +120,9 @@ public class AuthorMerger {
}
public static String pidToComparableString(StructuredProperty pid) {
return (pid.getQualifier() != null
? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
: "")
final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
: "";
return (pid.getQualifier() != null ? classid : "")
+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
}

3
dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java
View File

@ -12,6 +12,9 @@ import com.ximpleware.VTDNav;
/** Created by sandro on 9/29/16. */
public class VtdUtilityParser {
private VtdUtilityParser() {
}
public static List<Node> getTextValuesWithAttributes(
final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
throws VtdException {

19
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -7,22 +7,19 @@ import java.time.format.DateTimeFormatter;
import java.time.format.DateTimeParseException;
import java.util.*;
import java.util.function.Function;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.jetbrains.annotations.NotNull;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import me.xuender.unidecode.Unidecode;
public class GraphCleaningFunctions extends CleaningFunctions {
@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(Objects::nonNull)
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.filter(
sp -> sp
sp -> {
final String title = sp
.getValue()
.toLowerCase()
.replaceAll(TITLE_FILTER_REGEX, "")
.length() > TITLE_FILTER_RESIDUAL_LENGTH)
.toLowerCase();
final String residual = Unidecode
.decode(title)
.replaceAll(TITLE_FILTER_REGEX, "");
return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
})
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
@ -283,7 +284,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
r
.getAuthor()
.stream()
.filter(a -> Objects.nonNull(a))
.filter(Objects::nonNull)
.filter(a -> StringUtils.isNotBlank(a.getFullname()))
.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
.collect(Collectors.toList()));

17
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -17,13 +17,16 @@ import eu.dnetlib.dhp.schema.oaf.*;
public class OafMapperUtils {
private OafMapperUtils() {
}
public static Oaf merge(final Oaf left, final Oaf right) {
if (ModelSupport.isSubClass(left, OafEntity.class)) {
return mergeEntities((OafEntity) left, (OafEntity) right);
} else if (ModelSupport.isSubClass(left, Relation.class)) {
((Relation) left).mergeFrom((Relation) right);
} else {
throw new RuntimeException("invalid Oaf type:" + left.getClass().getCanonicalName());
throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName());
}
return left;
}
@ -38,7 +41,7 @@ public class OafMapperUtils {
} else if (ModelSupport.isSubClass(left, Project.class)) {
left.mergeFrom(right);
} else {
throw new RuntimeException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
}
return left;
}
@ -62,7 +65,7 @@ public class OafMapperUtils {
public static List<KeyValue> listKeyValues(final String... s) {
if (s.length % 2 > 0) {
throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)");
throw new IllegalArgumentException("Invalid number of parameters (k,v,k,v,....)");
}
final List<KeyValue> list = new ArrayList<>();
@ -88,7 +91,7 @@ public class OafMapperUtils {
.stream(values)
.map(v -> field(v, info))
.filter(Objects::nonNull)
.filter(distinctByKey(f -> f.getValue()))
.filter(distinctByKey(Field::getValue))
.collect(Collectors.toList());
}
@ -97,7 +100,7 @@ public class OafMapperUtils {
.stream()
.map(v -> field(v, info))
.filter(Objects::nonNull)
.filter(distinctByKey(f -> f.getValue()))
.filter(distinctByKey(Field::getValue))
.collect(Collectors.toList());
}
@ -342,10 +345,10 @@ public class OafMapperUtils {
if (instanceList != null) {
final Optional<AccessRight> min = instanceList
.stream()
.map(i -> i.getAccessright())
.map(Instance::getAccessright)
.min(new AccessRightComparator<>());
final Qualifier rights = min.isPresent() ? qualifier(min.get()) : new Qualifier();
final Qualifier rights = min.map(OafMapperUtils::qualifier).orElseGet(Qualifier::new);
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);

32
dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
View File

@ -34,6 +34,9 @@ public class DHPUtils {
private static final Logger log = LoggerFactory.getLogger(DHPUtils.class);
private DHPUtils() {
}
public static Seq<String> toSeq(List<String> list) {
return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
}
@ -44,7 +47,7 @@ public class DHPUtils {
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
System.err.println("Error creating id");
log.error("Error creating id from {}", s);
return null;
}
}
@ -53,33 +56,6 @@ public class DHPUtils {
return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
}
public static String compressString(final String input) {
try (ByteArrayOutputStream out = new ByteArrayOutputStream();
Base64OutputStream b64os = new Base64OutputStream(out)) {
GZIPOutputStream gzip = new GZIPOutputStream(b64os);
gzip.write(input.getBytes(StandardCharsets.UTF_8));
gzip.close();
return out.toString();
} catch (Throwable e) {
return null;
}
}
public static String decompressString(final String input) {
byte[] byteArray = Base64.decodeBase64(input.getBytes());
int len;
try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray)));
ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) {
byte[] buffer = new byte[1024];
while ((len = gis.read(buffer)) != -1) {
bos.write(buffer, 0, len);
}
return bos.toString();
} catch (Exception e) {
return null;
}
}
public static String getJPathString(final String jsonPath, final String json) {
try {
Object o = JsonPath.read(json, jsonPath);

11
dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java
View File

@ -18,13 +18,16 @@ public class ISLookupClientFactory {
private static final int requestTimeout = 60000 * 10;
private static final int connectTimeout = 60000 * 10;
private ISLookupClientFactory() {
}
public static ISLookUpService getLookUpService(final String isLookupUrl) {
return getServiceStub(ISLookUpService.class, isLookupUrl);
}
@SuppressWarnings("unchecked")
private static <T> T getServiceStub(final Class<T> clazz, final String endpoint) {
log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint));
log.info("creating {} stub from {}", clazz.getName(), endpoint);
final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean();
jaxWsProxyFactory.setServiceClass(clazz);
jaxWsProxyFactory.setAddress(endpoint);
@ -38,12 +41,10 @@ public class ISLookupClientFactory {
log
.info(
String
.format(
"setting connectTimeout to %s, requestTimeout to %s for service %s",
"setting connectTimeout to {}, requestTimeout to {} for service {}",
connectTimeout,
requestTimeout,
clazz.getCanonicalName()));
clazz.getCanonicalName());
policy.setConnectionTimeout(connectTimeout);
policy.setReceiveTimeout(requestTimeout);

2
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java
View File

@ -10,7 +10,7 @@ import net.sf.saxon.trans.XPathException;
public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition {
public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
public static final String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
public abstract String getName();

5
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java
View File

@ -26,7 +26,7 @@ public class ExtractYear extends AbstractExtensionFunction {
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
if (arguments == null || arguments.length == 0) {
return new StringValue("");
}
final Item item = arguments[0].head();
@ -63,8 +63,7 @@ public class ExtractYear extends AbstractExtensionFunction {
for (String format : dateFormats) {
try {
c.setTime(new SimpleDateFormat(format).parse(s));
String year = String.valueOf(c.get(Calendar.YEAR));
return year;
return String.valueOf(c.get(Calendar.YEAR));
} catch (ParseException e) {
}
}

2
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java
View File

@ -30,7 +30,7 @@ public class NormalizeDate extends AbstractExtensionFunction {
@Override
public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
if (arguments == null | arguments.length == 0) {
if (arguments == null || arguments.length == 0) {
return new StringValue(BLANK);
}
String s = arguments[0].head().getStringValue();

5
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.utils.saxon;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import org.apache.commons.lang3.StringUtils;
import net.sf.saxon.expr.XPathContext;
@ -26,7 +28,8 @@ public class PickFirst extends AbstractExtensionFunction {
final String s1 = getValue(arguments[0]);
final String s2 = getValue(arguments[1]);
return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : "");
final String value = isNotBlank(s1) ? s1 : isNotBlank(s2) ? s2 : "";
return new StringValue(value);
}
private String getValue(final Sequence arg) throws XPathException {

3
dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java
View File

@ -12,6 +12,9 @@ import net.sf.saxon.TransformerFactoryImpl;
public class SaxonTransformerFactory {
private SaxonTransformerFactory() {
}
/**
* Creates the index record transformer from the given XSLT
*

4
dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java
View File

@ -7,10 +7,10 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
public class ArgumentApplicationParserTest {
class ArgumentApplicationParserTest {
@Test
public void testParseParameter() throws Exception {
void testParseParameter() throws Exception {
final String jsonConfiguration = IOUtils
.toString(
this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json"));

10
dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java
View File

@ -21,13 +21,13 @@ public class HdfsSupportTest {
class Remove {
@Test
public void shouldThrowARuntimeExceptionOnError() {
void shouldThrowARuntimeExceptionOnError() {
// when
assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
}
@Test
public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
// when
HdfsSupport.remove(tempDir.toString(), new Configuration());
@ -36,7 +36,7 @@ public class HdfsSupportTest {
}
@Test
public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
// given
Path file = Files.createTempFile(tempDir, "p", "s");
@ -52,13 +52,13 @@ public class HdfsSupportTest {
class ListFiles {
@Test
public void shouldThrowARuntimeExceptionOnError() {
void shouldThrowARuntimeExceptionOnError() {
// when
assertThrows(RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration()));
}
@Test
public void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
Path subDir1 = Files.createTempDirectory(tempDir, "list_me");
Path subDir2 = Files.createTempDirectory(tempDir, "list_me");

6
dhp-common/src/test/java/eu/dnetlib/dhp/common/PacePersonTest.java
View File

@ -5,10 +5,10 @@ import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Test;
public class PacePersonTest {
class PacePersonTest {
@Test
public void pacePersonTest1() {
void pacePersonTest1() {
PacePerson p = new PacePerson("Artini, Michele", false);
assertEquals("Artini", p.getSurnameString());
@ -17,7 +17,7 @@ public class PacePersonTest {
}
@Test
public void pacePersonTest2() {
void pacePersonTest2() {
PacePerson p = new PacePerson("Michele G. Artini", false);
assertEquals("Artini, Michele G.", p.getNormalisedFullname());
assertEquals("Michele G", p.getNameString());

6
dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java
View File

@ -18,7 +18,8 @@ public class SparkSessionSupportTest {
class RunWithSparkSession {
@Test
public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
@SuppressWarnings("unchecked")
void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
throws Exception {
// given
SparkSession spark = mock(SparkSession.class);
@ -37,7 +38,8 @@ public class SparkSessionSupportTest {
}
@Test
public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
@SuppressWarnings("unchecked")
void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
throws Exception {
// given
SparkSession spark = mock(SparkSession.class);

10
dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java
View File

@ -12,7 +12,7 @@ import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
@Disabled
public class ZenodoAPIClientTest {
class ZenodoAPIClientTest {
private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions";
private final String ACCESS_TOKEN = "";
@ -22,7 +22,7 @@ public class ZenodoAPIClientTest {
private final String depositionId = "674915";
@Test
public void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
Assertions.assertEquals(200, client.uploadOpenDeposition(depositionId));
@ -44,7 +44,7 @@ public class ZenodoAPIClientTest {
}
@Test
public void testNewDeposition() throws IOException {
void testNewDeposition() throws IOException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
@ -67,7 +67,7 @@ public class ZenodoAPIClientTest {
}
@Test
public void testNewVersionNewName() throws IOException, MissingConceptDoiException {
void testNewVersionNewName() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);
@ -87,7 +87,7 @@ public class ZenodoAPIClientTest {
}
@Test
public void testNewVersionOldName() throws IOException, MissingConceptDoiException {
void testNewVersionOldName() throws IOException, MissingConceptDoiException {
ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
ACCESS_TOKEN);

4
dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java
View File

@ -21,7 +21,7 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class AuthorMergerTest {
class AuthorMergerTest {
private String publicationsBasePath;
@ -43,7 +43,7 @@ public class AuthorMergerTest {
}
@Test
public void mergeTest() { // used in the dedup: threshold set to 0.95
void mergeTest() { // used in the dedup: threshold set to 0.95
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));

61
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
View File

@ -4,12 +4,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException;
import java.time.LocalDate;
import java.time.format.DateTimeFormatter;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
@ -19,15 +15,34 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Result;
import me.xuender.unidecode.Unidecode;
public class OafMapperUtilsTest {
class OafMapperUtilsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
public void testDateValidation() {
public void testUnidecode() {
assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ"));
assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛"));
assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼"));
assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい"));
assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի"));
assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики"));
assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ"));
assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης"));
assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية"));
assertEquals("abc def ghi", Unidecode.decode("abc def ghi"));
}
@Test
void testDateValidation() {
assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z ").isPresent());
assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent());
@ -132,44 +147,46 @@ public class OafMapperUtilsTest {
}
@Test
public void testDate() {
System.out.println(GraphCleaningFunctions.cleanDate("23-FEB-1998"));
void testDate() {
final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
assertNotNull(date);
System.out.println(date);
}
@Test
public void testMergePubs() throws IOException {
void testMergePubs() throws IOException {
Publication p1 = read("publication_1.json", Publication.class);
Publication p2 = read("publication_2.json", Publication.class);
Dataset d1 = read("dataset_1.json", Dataset.class);
Dataset d2 = read("dataset_2.json", Dataset.class);
assertEquals(p1.getCollectedfrom().size(), 1);
assertEquals(p1.getCollectedfrom().get(0).getKey(), ModelConstants.CROSSREF_ID);
assertEquals(d2.getCollectedfrom().size(), 1);
assertEquals(1, p1.getCollectedfrom().size());
assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
assertEquals(1, d2.getCollectedfrom().size());
assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertTrue(
assertEquals(
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
OafMapperUtils
.mergeResults(p1, d2)
.getResulttype()
.getClassid()
.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID));
.getClassid());
assertEquals(p2.getCollectedfrom().size(), 1);
assertEquals(1, p2.getCollectedfrom().size());
assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertEquals(d1.getCollectedfrom().size(), 1);
assertEquals(1, d1.getCollectedfrom().size());
assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertTrue(
assertEquals(
ModelConstants.DATASET_RESULTTYPE_CLASSID,
OafMapperUtils
.mergeResults(p2, d1)
.getResulttype()
.getClassid()
.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID));
.getClassid());
}
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
return collectedfrom.stream().map(c -> c.getKey()).collect(Collectors.toCollection(HashSet::new));
return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}
protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {

4
dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java
View File

@ -3,10 +3,10 @@ package eu.dnetlib.scholexplorer.relation;
import org.junit.jupiter.api.Test;
public class RelationMapperTest {
class RelationMapperTest {
@Test
public void testLoadRels() throws Exception {
void testLoadRels() throws Exception {
RelationMapper relationMapper = RelationMapper.load();
relationMapper.keySet().forEach(System.out::println);

29
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
View File

@ -3,40 +3,37 @@ package eu.dnetlib.dhp.actionmanager;
import java.io.Serializable;
import java.io.StringReader;
import java.util.*;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.Optional;
import java.util.Set;
import java.util.stream.Collectors;
import org.apache.commons.lang3.tuple.Triple;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import org.jetbrains.annotations.NotNull;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.actionmanager.rmi.ActionManagerException;
import eu.dnetlib.actionmanager.set.ActionManagerSet;
import eu.dnetlib.actionmanager.set.ActionManagerSet.ImpactTypes;
import eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJob;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
public class ISClient implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final Logger log = LoggerFactory.getLogger(ISClient.class);
private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
private final ISLookUpService isLookup;
private final transient ISLookUpService isLookup;
public ISClient(String isLookupUrl) {
isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
@ -63,7 +60,7 @@ public class ISClient implements Serializable {
.map(
sets -> sets
.stream()
.map(set -> parseSetInfo(set))
.map(ISClient::parseSetInfo)
.filter(t -> ids.contains(t.getLeft()))
.map(t -> buildDirectory(basePath, t))
.collect(Collectors.toList()))
@ -73,15 +70,17 @@ public class ISClient implements Serializable {
}
}
private Triple<String, String, String> parseSetInfo(String set) {
private static Triple<String, String, String> parseSetInfo(String set) {
try {
Document doc = new SAXReader().read(new StringReader(set));
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
Document doc = reader.read(new StringReader(set));
return Triple
.of(
doc.valueOf("//SET/@id"),
doc.valueOf("//SET/@directory"),
doc.valueOf("//SET/@latest"));
} catch (DocumentException e) {
} catch (DocumentException | SAXException e) {
throw new IllegalStateException(e);
}
}
@ -99,7 +98,7 @@ public class ISClient implements Serializable {
final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
+ propertyName
+ "']/@value/string()";
log.debug("quering for service property: " + q);
log.debug("quering for service property: {}", q);
try {
final List<String> value = isLookup.quickSearchProfile(q);
return Iterables.getOnlyElement(value);

1
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java
View File

@ -62,6 +62,7 @@ public class MergeAndGet {
x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
}
@SuppressWarnings("unchecked")
private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {

4
dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
View File

@ -74,7 +74,9 @@ public class PromoteActionPayloadForGraphTableJob {
.orElse(true);
logger.info("shouldGroupById: {}", shouldGroupById);
@SuppressWarnings("unchecked")
Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
@SuppressWarnings("unchecked")
Class<? extends Oaf> actionPayloadClazz = (Class<? extends Oaf>) Class.forName(actionPayloadClassName);
throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz);
@ -152,7 +154,7 @@ public class PromoteActionPayloadForGraphTableJob {
return spark
.read()
.parquet(path)
.map((MapFunction<Row, String>) value -> extractPayload(value), Encoders.STRING())
.map((MapFunction<Row, String>) PromoteActionPayloadForGraphTableJob::extractPayload, Encoders.STRING())
.map(
(MapFunction<String, A>) value -> decodePayload(actionPayloadClazz, value),
Encoders.bean(actionPayloadClazz));

2
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java
View File

@ -80,7 +80,7 @@ public class PartitionActionSetsByPayloadTypeJobTest {
private ISClient isClient;
@Test
public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
// given
Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
Path outputDir = workingDir.resolve("output");

32
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java
View File

@ -20,7 +20,7 @@ public class MergeAndGetTest {
class MergeFromAndGetStrategy {
@Test
public void shouldThrowForOafAndOaf() {
void shouldThrowForOafAndOaf() {
// given
Oaf a = mock(Oaf.class);
Oaf b = mock(Oaf.class);
@ -33,7 +33,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForOafAndRelation() {
void shouldThrowForOafAndRelation() {
// given
Oaf a = mock(Oaf.class);
Relation b = mock(Relation.class);
@ -46,7 +46,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForOafAndOafEntity() {
void shouldThrowForOafAndOafEntity() {
// given
Oaf a = mock(Oaf.class);
OafEntity b = mock(OafEntity.class);
@ -59,7 +59,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForRelationAndOaf() {
void shouldThrowForRelationAndOaf() {
// given
Relation a = mock(Relation.class);
Oaf b = mock(Oaf.class);
@ -72,7 +72,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForRelationAndOafEntity() {
void shouldThrowForRelationAndOafEntity() {
// given
Relation a = mock(Relation.class);
OafEntity b = mock(OafEntity.class);
@ -85,7 +85,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldBehaveProperlyForRelationAndRelation() {
void shouldBehaveProperlyForRelationAndRelation() {
// given
Relation a = mock(Relation.class);
Relation b = mock(Relation.class);
@ -101,7 +101,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForOafEntityAndOaf() {
void shouldThrowForOafEntityAndOaf() {
// given
OafEntity a = mock(OafEntity.class);
Oaf b = mock(Oaf.class);
@ -114,7 +114,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForOafEntityAndRelation() {
void shouldThrowForOafEntityAndRelation() {
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
@ -127,7 +127,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
// given
class OafEntitySub1 extends OafEntity {
}
@ -145,7 +145,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldBehaveProperlyForOafEntityAndOafEntity() {
void shouldBehaveProperlyForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
OafEntity b = mock(OafEntity.class);
@ -165,7 +165,7 @@ public class MergeAndGetTest {
class SelectNewerAndGetStrategy {
@Test
public void shouldThrowForOafEntityAndRelation() {
void shouldThrowForOafEntityAndRelation() {
// given
OafEntity a = mock(OafEntity.class);
Relation b = mock(Relation.class);
@ -178,7 +178,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForRelationAndOafEntity() {
void shouldThrowForRelationAndOafEntity() {
// given
Relation a = mock(Relation.class);
OafEntity b = mock(OafEntity.class);
@ -191,7 +191,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowForOafEntityAndResult() {
void shouldThrowForOafEntityAndResult() {
// given
OafEntity a = mock(OafEntity.class);
Result b = mock(Result.class);
@ -204,7 +204,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
// given
// real types must be used because subclass-superclass resolution does not work for
// mocks
@ -221,7 +221,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldShouldReturnLeftForOafEntityAndOafEntity() {
void shouldShouldReturnLeftForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
when(a.getLastupdatetimestamp()).thenReturn(1L);
@ -238,7 +238,7 @@ public class MergeAndGetTest {
}
@Test
public void shouldShouldReturnRightForOafEntityAndOafEntity() {
void shouldShouldReturnRightForOafEntityAndOafEntity() {
// given
OafEntity a = mock(OafEntity.class);
when(a.getLastupdatetimestamp()).thenReturn(2L);

4
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java
View File

@ -77,7 +77,7 @@ public class PromoteActionPayloadForGraphTableJobTest {
class Main {
@Test
public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
// given
Class<Relation> rowClazz = Relation.class;
Class<OafEntity> actionPayloadClazz = OafEntity.class;
@ -116,7 +116,7 @@ public class PromoteActionPayloadForGraphTableJobTest {
@ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}")
@MethodSource("eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams")
public void shouldPromoteActionPayloadForGraphTable(
void shouldPromoteActionPayloadForGraphTable(
MergeAndGet.Strategy strategy,
Class<? extends Oaf> rowClazz,
Class<? extends Oaf> actionPayloadClazz)

8
dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java
View File

@ -44,7 +44,7 @@ public class PromoteActionPayloadFunctionsTest {
class JoinTableWithActionPayloadAndMerge {
@Test
public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
// given
class OafImpl extends Oaf {
}
@ -58,7 +58,7 @@ public class PromoteActionPayloadFunctionsTest {
}
@Test
public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
// given
String id0 = "id0";
String id1 = "id1";
@ -138,7 +138,7 @@ public class PromoteActionPayloadFunctionsTest {
}
@Test
public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
// given
String id0 = "id0";
String id1 = "id1";
@ -218,7 +218,7 @@ public class PromoteActionPayloadFunctionsTest {
class GroupTableByIdAndMerge {
@Test
public void shouldRunProperly() {
void shouldRunProperly() {
// given
String id1 = "id1";
String id2 = "id2";

8
dhp-workflows/dhp-aggregation/pom.xml
View File

@ -84,14 +84,6 @@
<artifactId>json</artifactId>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-csv</artifactId>
<version>1.8</version>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
<dependency>
<groupId>org.apache.poi</groupId>

8
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager.bipfinder;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.Serializable;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
@ -28,15 +29,16 @@ import eu.dnetlib.dhp.schema.oaf.Result;
public class CollectAndSave implements Serializable {
private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static <I extends Result> void main(String[] args) throws Exception {
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
Objects
.requireNonNull(
CollectAndSave.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json")));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java
View File

@ -87,7 +87,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
String bipScorePath, Class<I> inputClazz) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
.textFile(bipScorePath)
@ -101,8 +101,6 @@ public class SparkAtomicActionScoreJob implements Serializable {
return bs;
}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
System.out.println(bipScores.count());
Dataset<I> results = readPath(spark, inputPath, inputClazz);
results.createOrReplaceTempView("result");
@ -124,7 +122,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
ret.setId(value._2().getId());
return ret;
}, Encoders.bean(BipScore.class))
.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
.groupByKey((MapFunction<BipScore, String>) BipScore::getId, Encoders.STRING())
.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
Result ret = new Result();
ret.setDataInfo(getDataInfo());

48
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala
View File

@ -1,20 +1,22 @@
package eu.dnetlib.dhp.actionmanager.datacite
import org.apache.commons.io.IOUtils
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
import org.apache.http.entity.StringEntity
import org.apache.http.impl.client.HttpClients
import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
import java.io.IOException
abstract class AbstractRestClient extends Iterator[String]{
abstract class AbstractRestClient extends Iterator[String] {
var buffer: List[String] = List()
var current_index:Int = 0
var current_index: Int = 0
var scroll_value: Option[String] = None
var complete:Boolean = false
var complete: Boolean = false
def extractInfo(input: String): Unit
@ -22,13 +24,13 @@ abstract class AbstractRestClient extends Iterator[String]{
protected def getBufferData(): Unit
def doHTTPGETRequest(url:String): String = {
def doHTTPGETRequest(url: String): String = {
val httpGet = new HttpGet(url)
doHTTPRequest(httpGet)
}
def doHTTPPOSTRequest(url:String, json:String): String = {
def doHTTPPOSTRequest(url: String, json: String): String = {
val httpPost = new HttpPost(url)
if (json != null) {
val entity = new StringEntity(json)
@ -45,7 +47,7 @@ abstract class AbstractRestClient extends Iterator[String]{
override def next(): String = {
val next_item:String = buffer(current_index)
val next_item: String = buffer(current_index)
current_index = current_index + 1
if (current_index == buffer.size)
getBufferData()
@ -53,15 +55,18 @@ abstract class AbstractRestClient extends Iterator[String]{
}
private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
val client = HttpClients.createDefault
var tries = 4
private def doHTTPRequest[A <: HttpUriRequest](r: A): String = {
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
while (tries > 0) {
println(s"requesting ${r.getURI}")
try {
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
@ -69,18 +74,19 @@ abstract class AbstractRestClient extends Iterator[String]{
}
else
return IOUtils.toString(response.getEntity.getContent)
}
""
} catch {
case e: Throwable =>
throw new RuntimeException("Error on executing request ", e)
} finally try client.close()
catch {
case e: IOException =>
throw new RuntimeException("Unable to close client ", e)
println(s"Error on requesting ${r.getURI}")
e.printStackTrace()
tries -= 1
}
}
""
} finally {
if (client != null)
client.close()
}
}
getBufferData()
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala
View File

@ -367,7 +367,7 @@ object DataciteToOAFTransformation {
result.setDateofcollection(ISO8601FORMAT.format(d))
result.setDateoftransformation(ISO8601FORMAT.format(ts))
result.setDateoftransformation(ISO8601FORMAT.format(d))
result.setDataInfo(dataInfo)
val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala
View File

@ -140,7 +140,7 @@ object ImportDatacite {
private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = {
var from:Long = timestamp * 1000
val delta:Long = 50000000L
val delta:Long = 100000000L
var client: DataciteAPIImporter = null
val now :Long =System.currentTimeMillis()
var i = 0

53
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala Normal file
View File

@ -0,0 +1,53 @@
package eu.dnetlib.dhp.actionmanager.datacite
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
import org.apache.hadoop.conf.Configuration
import org.apache.hadoop.fs.LocalFileSystem
import org.apache.hadoop.hdfs.DistributedFileSystem
import org.apache.spark.SparkConf
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
import org.apache.spark.sql.functions.max
import org.slf4j.{Logger, LoggerFactory}
import java.text.SimpleDateFormat
import java.util.{Date, Locale}
import scala.io.Source
object SparkDownloadUpdateDatacite {
val log: Logger = LoggerFactory.getLogger(getClass)
def main(args: Array[String]): Unit = {
val conf = new SparkConf
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString)
parser.parseArgument(args)
val master = parser.get("master")
val sourcePath = parser.get("sourcePath")
val workingPath = parser.get("workingPath")
val hdfsuri = parser.get("namenode")
log.info(s"namenode is $hdfsuri")
val spark: SparkSession = SparkSession.builder().config(conf)
.appName(getClass.getSimpleName)
.master(master)
.getOrCreate()
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result]
import spark.implicits._
val maxDate:String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0)
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
val string_to_date =ISO8601FORMAT.parse(maxDate)
val ts = string_to_date.getTime
}
}

15
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java
View File

@ -20,7 +20,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import scala.Tuple2;
@ -171,26 +171,23 @@ public class PrepareProgramme {
}
private static CSVProgramme groupProgrammeByCode(CSVProgramme a, CSVProgramme b) {
if (!a.getLanguage().equals("en")) {
if (b.getLanguage().equalsIgnoreCase("en")) {
if (!a.getLanguage().equals("en") && b.getLanguage().equalsIgnoreCase("en")) {
a.setTitle(b.getTitle());
a.setLanguage(b.getLanguage());
}
}
if (StringUtils.isEmpty(a.getShortTitle())) {
if (!StringUtils.isEmpty(b.getShortTitle())) {
if (StringUtils.isEmpty(a.getShortTitle()) && !StringUtils.isEmpty(b.getShortTitle())) {
a.setShortTitle(b.getShortTitle());
}
}
return a;
}
@SuppressWarnings("unchecked")
private static List<CSVProgramme> prepareClassification(JavaRDD<CSVProgramme> h2020Programmes) {
Object[] codedescription = h2020Programmes
.map(
value -> new Tuple2<>(value.getCode(),
new Tuple2<String, String>(value.getTitle(), value.getShortTitle())))
new Tuple2<>(value.getTitle(), value.getShortTitle())))
.collect()
.toArray();
@ -216,7 +213,7 @@ public class PrepareProgramme {
String[] tmp = ent.split("\\.");
if (tmp.length <= 2) {
if (StringUtils.isEmpty(entry._2()._2())) {
map.put(entry._1(), new Tuple2<String, String>(entry._2()._1(), entry._2()._1()));
map.put(entry._1(), new Tuple2<>(entry._2()._1(), entry._2()._1()));
} else {
map.put(entry._1(), entry._2());
}

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java
View File

@ -18,7 +18,7 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import scala.Tuple2;
@ -29,7 +29,7 @@ import scala.Tuple2;
*/
public class PrepareProjects {
private static final Logger log = LoggerFactory.getLogger(PrepareProgramme.class);
private static final Logger log = LoggerFactory.getLogger(PrepareProjects.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {

21
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java
View File

@ -31,15 +31,16 @@ import eu.dnetlib.dhp.common.DbClient;
*/
public class ReadProjectsFromDB implements Closeable {
private final DbClient dbClient;
private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class);
private static final String query = "SELECT code " +
"from projects where id like 'corda__h2020%' ";
private final DbClient dbClient;
private final Configuration conf;
private final BufferedWriter writer;
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private final static String query = "SELECT code " +
"from projects where id like 'corda__h2020%' ";
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
@ -65,9 +66,9 @@ public class ReadProjectsFromDB implements Closeable {
}
}
public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) throws Exception {
public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) {
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r));
final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(this::writeProject);
dbClient.processResults(sql, consumer);
}
@ -94,20 +95,20 @@ public class ReadProjectsFromDB implements Closeable {
public ReadProjectsFromDB(
final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
throws Exception {
throws IOException {
this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, false);
}
fsDataOutputStream = fileSystem.create(hdfsWritePath);
FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
this.writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8));
}
@Override

28
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java
View File

@ -4,7 +4,6 @@ package eu.dnetlib.dhp.actionmanager.project;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.util.Arrays;
import java.util.HashMap;
import java.util.Objects;
import java.util.Optional;
@ -22,15 +21,16 @@ import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme;
import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject;
import eu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.H2020Classification;
import eu.dnetlib.dhp.schema.oaf.H2020Programme;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.utils.DHPUtils;
import scala.Tuple2;
@ -47,13 +47,10 @@ import scala.Tuple2;
*
* To produce one single entry for each project code a step of groupoing is needed: each project can be associated to more
* than one programme.
*
*
*/
public class SparkAtomicActionJob {
private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final HashMap<String, String> programmeMap = new HashMap<>();
public static void main(String[] args) throws Exception {
@ -137,7 +134,6 @@ public class SparkAtomicActionJob {
h2020classification.setClassification(csvProgramme.getClassification());
h2020classification.setH2020Programme(pm);
setLevelsandProgramme(h2020classification, csvProgramme.getClassification_short());
// setProgramme(h2020classification, ocsvProgramme.get().getClassification());
pp.setH2020classification(Arrays.asList(h2020classification));
return pp;
@ -152,20 +148,16 @@ public class SparkAtomicActionJob {
.map((MapFunction<Tuple2<Project, EXCELTopic>, Project>) p -> {
Optional<EXCELTopic> op = Optional.ofNullable(p._2());
Project rp = p._1();
if (op.isPresent()) {
rp.setH2020topicdescription(op.get().getTitle());
}
op.ifPresent(excelTopic -> rp.setH2020topicdescription(excelTopic.getTitle()));
return rp;
}, Encoders.bean(Project.class))
.filter(Objects::nonNull)
.groupByKey(
(MapFunction<Project, String>) p -> p.getId(),
(MapFunction<Project, String>) OafEntity::getId,
Encoders.STRING())
.mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> {
Project first = it.next();
it.forEachRemaining(p -> {
first.mergeFrom(p);
});
it.forEachRemaining(first::mergeFrom);
return first;
}, Encoders.bean(Project.class))
.toJavaRDD()
@ -189,12 +181,6 @@ public class SparkAtomicActionJob {
h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]);
}
// private static void setProgramme(H2020Classification h2020Classification, String classification) {
// String[] tmp = classification.split(" \\| ");
//
// h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]);
// }
public static <R> Dataset<R> readPath(
SparkSession spark, String inputPath, Class<R> clazz) {
return spark

40
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVParser.java
View File

@ -1,40 +0,0 @@
package eu.dnetlib.dhp.actionmanager.project.utils;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang.reflect.FieldUtils;
/**
* Reads a generic csv and maps it into classes that mirror its schema
*/
public class CSVParser {
public <R> List<R> parse(String csvFile, String classForName)
throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException {
final CSVFormat format = CSVFormat.EXCEL
.withHeader()
.withDelimiter(';')
.withQuote('"')
.withTrim();
List<R> ret = new ArrayList<>();
final org.apache.commons.csv.CSVParser parser = org.apache.commons.csv.CSVParser.parse(csvFile, format);
final Set<String> headers = parser.getHeaderMap().keySet();
Class<?> clazz = Class.forName(classForName);
for (CSVRecord csvRecord : parser.getRecords()) {
final Object cc = clazz.newInstance();
for (String header : headers) {
FieldUtils.writeField(cc, header, csvRecord.get(header), true);
}
ret.add((R) cc);
}
return ret;
}
}

200
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProject.java
View File

@ -1,200 +0,0 @@
package eu.dnetlib.dhp.actionmanager.project.utils;
import java.io.Serializable;
/**
* the mmodel for the projects csv file
*/
public class CSVProject implements Serializable {
private String rcn;
private String id;
private String acronym;
private String status;
private String programme;
private String topics;
private String frameworkProgramme;
private String title;
private String startDate;
private String endDate;
private String projectUrl;
private String objective;
private String totalCost;
private String ecMaxContribution;
private String call;
private String fundingScheme;
private String coordinator;
private String coordinatorCountry;
private String participants;
private String participantCountries;
private String subjects;
public String getRcn() {
return rcn;
}
public void setRcn(String rcn) {
this.rcn = rcn;
}
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getAcronym() {
return acronym;
}
public void setAcronym(String acronym) {
this.acronym = acronym;
}
public String getStatus() {
return status;
}
public void setStatus(String status) {
this.status = status;
}
public String getProgramme() {
return programme;
}
public void setProgramme(String programme) {
this.programme = programme;
}
public String getTopics() {
return topics;
}
public void setTopics(String topics) {
this.topics = topics;
}
public String getFrameworkProgramme() {
return frameworkProgramme;
}
public void setFrameworkProgramme(String frameworkProgramme) {
this.frameworkProgramme = frameworkProgramme;
}
public String getTitle() {
return title;
}
public void setTitle(String title) {
this.title = title;
}
public String getStartDate() {
return startDate;
}
public void setStartDate(String startDate) {
this.startDate = startDate;
}
public String getEndDate() {
return endDate;
}
public void setEndDate(String endDate) {
this.endDate = endDate;
}
public String getProjectUrl() {
return projectUrl;
}
public void setProjectUrl(String projectUrl) {
this.projectUrl = projectUrl;
}
public String getObjective() {
return objective;
}
public void setObjective(String objective) {
this.objective = objective;
}
public String getTotalCost() {
return totalCost;
}
public void setTotalCost(String totalCost) {
this.totalCost = totalCost;
}
public String getEcMaxContribution() {
return ecMaxContribution;
}
public void setEcMaxContribution(String ecMaxContribution) {
this.ecMaxContribution = ecMaxContribution;
}
public String getCall() {
return call;
}
public void setCall(String call) {
this.call = call;
}
public String getFundingScheme() {
return fundingScheme;
}
public void setFundingScheme(String fundingScheme) {
this.fundingScheme = fundingScheme;
}
public String getCoordinator() {
return coordinator;
}
public void setCoordinator(String coordinator) {
this.coordinator = coordinator;
}
public String getCoordinatorCountry() {
return coordinatorCountry;
}
public void setCoordinatorCountry(String coordinatorCountry) {
this.coordinatorCountry = coordinatorCountry;
}
public String getParticipants() {
return participants;
}
public void setParticipants(String participants) {
this.participants = participants;
}
public String getParticipantCountries() {
return participantCountries;
}
public void setParticipantCountries(String participantCountries) {
this.participantCountries = participantCountries;
}
public String getSubjects() {
return subjects;
}
public void setSubjects(String subjects) {
this.subjects = subjects;
}
}

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java
View File

@ -17,6 +17,8 @@ import org.apache.poi.ss.usermodel.Row;
import org.apache.poi.xssf.usermodel.XSSFSheet;
import org.apache.poi.xssf.usermodel.XSSFWorkbook;
import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
/**
* Reads a generic excel file and maps it into classes that mirror its schema
*/
@ -26,13 +28,12 @@ public class EXCELParser {
throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException,
InvalidFormatException {
OPCPackage pkg = OPCPackage.open(file);
XSSFWorkbook wb = new XSSFWorkbook(pkg);
try (OPCPackage pkg = OPCPackage.open(file); XSSFWorkbook wb = new XSSFWorkbook(pkg)) {
XSSFSheet sheet = wb.getSheet(sheetName);
if (sheetName == null) {
throw new RuntimeException("Sheet name " + sheetName + " not present in current file");
if (sheet == null) {
throw new IllegalArgumentException("Sheet name " + sheetName + " not present in current file");
}
List<R> ret = new ArrayList<>();
@ -73,5 +74,6 @@ public class EXCELParser {
return ret;
}
}
}

79
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java
View File

@ -1,34 +1,21 @@
package eu.dnetlib.dhp.actionmanager.project.utils;
import java.io.BufferedWriter;
import java.io.Closeable;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.StandardCharsets;
import java.io.*;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.HttpConnector2;
import eu.dnetlib.dhp.common.collection.GetCSV;
import eu.dnetlib.dhp.common.collection.HttpConnector2;
/**
* Applies the parsing of a csv file and writes the Serialization of it in hdfs
*/
public class ReadCSV implements Closeable {
private static final Log log = LogFactory.getLog(ReadCSV.class);
private final Configuration conf;
private final BufferedWriter writer;
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private final String csvFile;
public class ReadCSV {
public static void main(final String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@ -44,56 +31,22 @@ public class ReadCSV implements Closeable {
final String hdfsPath = parser.get("hdfsPath");
final String hdfsNameNode = parser.get("hdfsNameNode");
final String classForName = parser.get("classForName");
Optional<String> delimiter = Optional.ofNullable(parser.get("delimiter"));
char del = ';';
if (delimiter.isPresent())
del = delimiter.get().charAt(0);
try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL)) {
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
log.info("Getting CSV file...");
readCSV.execute(classForName);
FileSystem fileSystem = FileSystem.get(conf);
BufferedReader reader = new BufferedReader(
new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL)));
}
}
GetCSV.getCsv(fileSystem, reader, hdfsPath, classForName, del);
public void execute(final String classForName) throws Exception {
CSVParser csvParser = new CSVParser();
csvParser
.parse(csvFile, classForName)
.stream()
.forEach(p -> write(p));
reader.close();
}
@Override
public void close() throws IOException {
writer.close();
}
public ReadCSV(
final String hdfsPath,
final String hdfsNameNode,
final String fileURL)
throws Exception {
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
HttpConnector2 httpConnector = new HttpConnector2();
FileSystem fileSystem = FileSystem.get(this.conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, false);
}
fsDataOutputStream = fileSystem.create(hdfsWritePath);
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
this.csvFile = httpConnector.getInputSource(fileURL);
}
protected void write(final Object p) {
try {
writer.write(OBJECT_MAPPER.writeValueAsString(p));
writer.newLine();
} catch (final Exception e) {
throw new RuntimeException(e);
}
}
}

34
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java
View File

@ -11,18 +11,20 @@ import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.collection.HttpConnector2;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpConnector2;
/**
* Applies the parsing of an excel file and writes the Serialization of it in hdfs
*/
public class ReadExcel implements Closeable {
private static final Log log = LogFactory.getLog(ReadCSV.class);
private final Configuration conf;
private static final Log log = LogFactory.getLog(ReadExcel.class);
private final BufferedWriter writer;
private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private final InputStream excelFile;
@ -31,7 +33,7 @@ public class ReadExcel implements Closeable {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
ReadCSV.class
ReadExcel.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/project/parameters.json")));
@ -51,13 +53,15 @@ public class ReadExcel implements Closeable {
}
}
public void execute(final String classForName, final String sheetName) throws Exception {
public void execute(final String classForName, final String sheetName)
throws IOException, ClassNotFoundException, InvalidFormatException, IllegalAccessException,
InstantiationException {
EXCELParser excelParser = new EXCELParser();
excelParser
.parse(excelFile, classForName, sheetName)
.stream()
.forEach(p -> write(p));
.forEach(this::write);
}
@Override
@ -68,20 +72,20 @@ public class ReadExcel implements Closeable {
public ReadExcel(
final String hdfsPath,
final String hdfsNameNode,
final String fileURL)
throws Exception {
this.conf = new Configuration();
this.conf.set("fs.defaultFS", hdfsNameNode);
final String fileURL) throws CollectorException, IOException {
final Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
HttpConnector2 httpConnector = new HttpConnector2();
FileSystem fileSystem = FileSystem.get(this.conf);
FileSystem fileSystem = FileSystem.get(conf);
Path hdfsWritePath = new Path(hdfsPath);
FSDataOutputStream fsDataOutputStream = null;
if (fileSystem.exists(hdfsWritePath)) {
fileSystem.delete(hdfsWritePath, false);
}
fsDataOutputStream = fileSystem.create(hdfsWritePath);
FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
this.writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8));
this.excelFile = httpConnector.getInputSourceAsStream(fileURL);
}

25
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProgramme.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/model/CSVProgramme.java
View File

@ -1,20 +1,32 @@
package eu.dnetlib.dhp.actionmanager.project.utils;
package eu.dnetlib.dhp.actionmanager.project.utils.model;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByName;
import com.opencsv.bean.CsvIgnore;
/**
* The model for the programme csv file
*/
public class CSVProgramme implements Serializable {
private String rcn;
@CsvBindByName(column = "code")
private String code;
@CsvBindByName(column = "title")
private String title;
@CsvBindByName(column = "shortTitle")
private String shortTitle;
@CsvBindByName(column = "language")
private String language;
@CsvIgnore
private String classification;
@CsvIgnore
private String classification_short;
public String getClassification_short() {
@ -33,14 +45,6 @@ public class CSVProgramme implements Serializable {
this.classification = classification;
}
public String getRcn() {
return rcn;
}
public void setRcn(String rcn) {
this.rcn = rcn;
}
public String getCode() {
return code;
}
@ -73,5 +77,4 @@ public class CSVProgramme implements Serializable {
this.language = language;
}
//
}

46
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/model/CSVProject.java Normal file
View File

@ -0,0 +1,46 @@
package eu.dnetlib.dhp.actionmanager.project.utils.model;
import java.io.Serializable;
import com.opencsv.bean.CsvBindByName;
/**
* the mmodel for the projects csv file
*/
public class CSVProject implements Serializable {
@CsvBindByName(column = "id")
private String id;
@CsvBindByName(column = "programme")
private String programme;
@CsvBindByName(column = "topics")
private String topics;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public String getProgramme() {
return programme;
}
public void setProgramme(String programme) {
this.programme = programme;
}
public String getTopics() {
return topics;
}
public void setTopics(String topics) {
this.topics = topics;
}
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELTopic.java → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/model/EXCELTopic.java
View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.actionmanager.project.utils;
package eu.dnetlib.dhp.actionmanager.project.utils.model;
import java.io.Serializable;

7
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
View File

@ -9,6 +9,7 @@ import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Arrays;
@ -74,7 +75,7 @@ public class GenerateRorActionSetJob {
final String jsonConfiguration = IOUtils
.toString(
SparkAtomicActionJob.class
GenerateRorActionSetJob.class
.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@ -108,7 +109,7 @@ public class GenerateRorActionSetJob {
private static void processRorOrganizations(final SparkSession spark,
final String inputPath,
final String outputPath) throws Exception {
final String outputPath) throws IOException {
readInputPath(spark, inputPath)
.map(
@ -203,7 +204,7 @@ public class GenerateRorActionSetJob {
private static Dataset<RorOrganization> readInputPath(
final SparkSession spark,
final String path) throws Exception {
final String path) throws IOException {
try (final FileSystem fileSystem = FileSystem.get(new Configuration());
final InputStream is = fileSystem.open(new Path(path))) {

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Address.java
View File

@ -7,6 +7,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public class Address implements Serializable {
private static final long serialVersionUID = 2444635485253443195L;
@JsonProperty("lat")
private Float lat;
@ -37,8 +39,6 @@ public class Address implements Serializable {
@JsonProperty("line")
private String line;
private final static long serialVersionUID = 2444635485253443195L;
public Float getLat() {
return lat;
}

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Country.java
View File

@ -7,14 +7,14 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public class Country implements Serializable {
private static final long serialVersionUID = 4357848706229493627L;
@JsonProperty("country_code")
private String countryCode;
@JsonProperty("country_name")
private String countryName;
private final static long serialVersionUID = 4357848706229493627L;
public String getCountryCode() {
return countryCode;
}

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/ExternalIdType.java
View File

@ -13,7 +13,7 @@ public class ExternalIdType implements Serializable {
private String preferred;
private final static long serialVersionUID = 2616688352998387611L;
private static final long serialVersionUID = 2616688352998387611L;
public ExternalIdType() {
}

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/ExternalIdTypeDeserializer.java
View File

@ -15,8 +15,7 @@ import com.fasterxml.jackson.databind.JsonNode;
public class ExternalIdTypeDeserializer extends JsonDeserializer<ExternalIdType> {
@Override
public ExternalIdType deserialize(final JsonParser p, final DeserializationContext ctxt)
throws IOException, JsonProcessingException {
public ExternalIdType deserialize(final JsonParser p, final DeserializationContext ctxt) throws IOException {
final ObjectCodec oc = p.getCodec();
final JsonNode node = oc.readTree(p);

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/GeonamesAdmin.java
View File

@ -19,7 +19,7 @@ public class GeonamesAdmin implements Serializable {
@JsonProperty("code")
private String code;
private final static long serialVersionUID = 7294958526269195673L;
private static final long serialVersionUID = 7294958526269195673L;
public String getAsciiName() {
return asciiName;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/GeonamesCity.java
View File

@ -31,7 +31,7 @@ public class GeonamesCity implements Serializable {
@JsonProperty("license")
private License license;
private final static long serialVersionUID = -8389480201526252955L;
private static final long serialVersionUID = -8389480201526252955L;
public NameAndCode getNutsLevel2() {
return nutsLevel2;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Label.java
View File

@ -13,7 +13,7 @@ public class Label implements Serializable {
@JsonProperty("label")
private String label;
private final static long serialVersionUID = -6576156103297850809L;
private static final long serialVersionUID = -6576156103297850809L;
public String getIso639() {
return iso639;

2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/License.java
View File

@ -13,7 +13,7 @@ public class License implements Serializable {
@JsonProperty("license")
private String license;
private final static long serialVersionUID = -194308261058176439L;
private static final long serialVersionUID = -194308261058176439L;
public String getAttribution() {
return attribution;

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/NameAndCode.java
View File

@ -7,14 +7,14 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public class NameAndCode implements Serializable {
private static final long serialVersionUID = 5459836979206140843L;
@JsonProperty("name")
private String name;
@JsonProperty("code")
private String code;
private final static long serialVersionUID = 5459836979206140843L;
public String getName() {
return name;
}

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Relationship.java
View File

@ -7,6 +7,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public class Relationship implements Serializable {
private static final long serialVersionUID = 7847399503395576960L;
@JsonProperty("type")
private String type;
@ -16,8 +18,6 @@ public class Relationship implements Serializable {
@JsonProperty("label")
private String label;
private final static long serialVersionUID = 7847399503395576960L;
public String getType() {
return type;
}

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/RorOrganization.java
View File

@ -11,6 +11,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
public class RorOrganization implements Serializable {
private static final long serialVersionUID = -2658312087616043225L;
@JsonProperty("ip_addresses")
private List<String> ipAddresses = new ArrayList<>();
@ -59,8 +61,6 @@ public class RorOrganization implements Serializable {
@JsonProperty("status")
private String status;
private final static long serialVersionUID = -2658312087616043225L;
public List<String> getIpAddresses() {
return ipAddresses;
}

69
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala Normal file
View File

@ -0,0 +1,69 @@
package eu.dnetlib.dhp.actionmanager.scholix
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import org.apache.spark.SparkConf
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkCreateActionset {
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
val workingDirFolder = parser.get("workingDirFolder")
log.info(s"workingDirFolder -> $workingDirFolder")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
import spark.implicits._
val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
log.info("extract source and target Identifier involved in relations")
log.info("save relation filtered")
relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
log.info("saving entities")
val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
entities
.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
.map(p => p._1._2)
.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
}
}

86
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala Normal file
View File

@ -0,0 +1,86 @@
package eu.dnetlib.dhp.actionmanager.scholix
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
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.sql.{Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}
import scala.io.Source
object SparkSaveActionSet {
def toActionSet(item: Oaf): (String, String) = {
val mapper = new ObjectMapper()
item match {
case dataset: OafDataset =>
val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
a.setClazz(classOf[OafDataset])
a.setPayload(dataset)
(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
case publication: Publication =>
val a: AtomicAction[Publication] = new AtomicAction[Publication]
a.setClazz(classOf[Publication])
a.setPayload(publication)
(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
case software: Software =>
val a: AtomicAction[Software] = new AtomicAction[Software]
a.setClazz(classOf[Software])
a.setPayload(software)
(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
case orp: OtherResearchProduct =>
val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
a.setClazz(classOf[OtherResearchProduct])
a.setPayload(orp)
(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
case relation: Relation =>
val a: AtomicAction[Relation] = new AtomicAction[Relation]
a.setClazz(classOf[Relation])
a.setPayload(relation)
(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
case _ =>
null
}
}
def main(args: Array[String]): Unit = {
val log: Logger = LoggerFactory.getLogger(getClass)
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
parser.parseArgument(args)
val spark: SparkSession =
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(parser.get("master")).getOrCreate()
val sourcePath = parser.get("sourcePath")
log.info(s"sourcePath -> $sourcePath")
val targetPath = parser.get("targetPath")
log.info(s"targetPath -> $targetPath")
implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
spark.read.load(sourcePath).as[Oaf]
.map(o => toActionSet(o))
.filter(o => o != null)
.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
}
}

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/ReportingJob.java
View File

@ -6,6 +6,8 @@ import java.util.concurrent.Executors;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.TimeUnit;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
public abstract class ReportingJob {
/**
@ -22,7 +24,7 @@ public abstract class ReportingJob {
protected final AggregatorReport report;
public ReportingJob(AggregatorReport report) {
protected ReportingJob(AggregatorReport report) {
this.report = report;
}

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/mdstore/MDStoreActionNode.java
View File

@ -25,7 +25,7 @@ public class MDStoreActionNode {
NEW_VERSION, ROLLBACK, COMMIT, READ_LOCK, READ_UNLOCK
}
public static String NEW_VERSION_URI = "%s/mdstore/%s/newVersion";
public static final String NEW_VERSION_URI = "%s/mdstore/%s/newVersion";
public static final String COMMIT_VERSION_URL = "%s/version/%s/commit/%s";
public static final String ROLLBACK_VERSION_URL = "%s/version/%s/abort";
@ -70,7 +70,7 @@ public class MDStoreActionNode {
if (StringUtils.isBlank(hdfsuri)) {
throw new IllegalArgumentException("missing or empty argument namenode");
}
final String mdStoreVersion_params = argumentParser.get("mdStoreVersion");
final String mdStoreVersion_params = argumentParser.get(MDSTOREVERSIONPARAM);
final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
if (StringUtils.isBlank(mdStoreVersion.getId())) {
@ -94,7 +94,7 @@ public class MDStoreActionNode {
break;
}
case ROLLBACK: {
final String mdStoreVersion_params = argumentParser.get("mdStoreVersion");
final String mdStoreVersion_params = argumentParser.get(MDSTOREVERSIONPARAM);
final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
if (StringUtils.isBlank(mdStoreVersion.getId())) {

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
View File

@ -16,7 +16,6 @@ import org.apache.hadoop.io.compress.DeflateCodec;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
import eu.dnetlib.dhp.aggregation.common.ReportingJob;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
@ -24,6 +23,9 @@ import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion;
public class CollectorWorker extends ReportingJob {
@ -116,7 +118,7 @@ public class CollectorWorker extends ReportingJob {
final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
.ofNullable(api.getParams().get("other_plugin_type"))
.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
.get();
.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
switch (plugin) {
case mdstore_mongodb_dump:

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorkerApplication.java
View File

@ -13,8 +13,10 @@ import org.apache.hadoop.fs.FileSystem;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.message.MessageSender;
import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion;

1
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java
View File

@ -207,6 +207,7 @@ public class GenerateNativeStoreSparkJob {
totalItems.add(1);
try {
SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
Document document = reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
Node node = document.selectSingleNode(xpath);
final String originalIdentifier = node.getText();

4
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
View File

@ -3,9 +3,9 @@ package eu.dnetlib.dhp.collection.plugin;
import java.util.stream.Stream;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
public interface CollectorPlugin {

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MDStoreCollectorPlugin.java
View File

@ -11,15 +11,13 @@ import org.bson.Document;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.mongodb.MongoClient;
import com.mongodb.MongoClientURI;
import com.mongodb.client.MongoCollection;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.MdstoreClient;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
public class MDStoreCollectorPlugin implements CollectorPlugin {

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MongoDbDumpCollectorPlugin.java
View File

@ -12,10 +12,10 @@ import java.util.zip.GZIPInputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.utils.DHPUtils;
public class MongoDbDumpCollectorPlugin implements CollectorPlugin {
@ -23,7 +23,7 @@ public class MongoDbDumpCollectorPlugin implements CollectorPlugin {
public static final String PATH_PARAM = "path";
public static final String BODY_JSONPATH = "$.body";
public FileSystem fileSystem;
private final FileSystem fileSystem;
public MongoDbDumpCollectorPlugin(FileSystem fileSystem) {
this.fileSystem = fileSystem;

10
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java
View File

@ -13,11 +13,11 @@ import com.google.common.base.Splitter;
import com.google.common.collect.Iterators;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
public class OaiCollectorPlugin implements CollectorPlugin {
@ -66,11 +66,11 @@ public class OaiCollectorPlugin implements CollectorPlugin {
}
if (fromDate != null && !fromDate.matches(DATE_REGEX) && !fromDate.matches(UTC_DATETIME_REGEX)) {
throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate);
throw new CollectorException("Invalid date (YYYY-MM-DD or YYYY-MM-DDT00:00:00Z): " + fromDate);
}
if (untilDate != null && !untilDate.matches(DATE_REGEX) && !untilDate.matches(UTC_DATETIME_REGEX)) {
throw new CollectorException("Invalid date (YYYY-MM-DD): " + untilDate);
throw new CollectorException("Invalid date (YYYY-MM-DD or YYYY-MM-DDT00:00:00Z): " + untilDate);
}
final Iterator<Iterator<String>> iters = sets

30
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java
View File

@ -2,7 +2,6 @@
package eu.dnetlib.dhp.collection.plugin.oai;
import java.io.IOException;
import java.io.StringReader;
import java.io.StringWriter;
import java.io.UnsupportedEncodingException;
import java.net.URLEncoder;
@ -16,21 +15,21 @@ import org.dom4j.DocumentException;
import org.dom4j.DocumentHelper;
import org.dom4j.Node;
import org.dom4j.io.OutputFormat;
import org.dom4j.io.SAXReader;
import org.dom4j.io.XMLWriter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpConnector2;
import eu.dnetlib.dhp.collection.XmlCleaner;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpConnector2;
public class OaiIterator implements Iterator<String> {
private static final Logger log = LoggerFactory.getLogger(OaiIterator.class);
private final static String REPORT_PREFIX = "oai:";
private static final String REPORT_PREFIX = "oai:";
public static final String UTF_8 = "UTF-8";
private final Queue<String> queue = new PriorityBlockingQueue<>();
@ -68,7 +67,7 @@ public class OaiIterator implements Iterator<String> {
try {
this.token = firstPage();
} catch (final CollectorException e) {
throw new RuntimeException(e);
throw new IllegalStateException(e);
}
}
}
@ -90,7 +89,7 @@ public class OaiIterator implements Iterator<String> {
try {
token = otherPages(token);
} catch (final CollectorException e) {
throw new RuntimeException(e);
throw new IllegalStateException(e);
}
}
return res;
@ -99,23 +98,24 @@ public class OaiIterator implements Iterator<String> {
@Override
public void remove() {
throw new UnsupportedOperationException();
}
private String firstPage() throws CollectorException {
try {
String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8");
String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, UTF_8);
if (set != null && !set.isEmpty()) {
url += "&set=" + URLEncoder.encode(set, "UTF-8");
url += "&set=" + URLEncoder.encode(set, UTF_8);
}
if (fromDate != null && (fromDate.matches(OaiCollectorPlugin.DATE_REGEX)
|| fromDate.matches(OaiCollectorPlugin.UTC_DATETIME_REGEX))) {
url += "&from=" + URLEncoder.encode(fromDate, "UTF-8");
url += "&from=" + URLEncoder.encode(fromDate, UTF_8);
}
if (untilDate != null && (untilDate.matches(OaiCollectorPlugin.DATE_REGEX)
|| untilDate.matches(OaiCollectorPlugin.UTC_DATETIME_REGEX))) {
url += "&until=" + URLEncoder.encode(untilDate, "UTF-8");
url += "&until=" + URLEncoder.encode(untilDate, UTF_8);
}
log.info("Start harvesting using url: " + url);
log.info("Start harvesting using url: {}", url);
return downloadPage(url);
} catch (final UnsupportedEncodingException e) {
@ -143,7 +143,7 @@ public class OaiIterator implements Iterator<String> {
return downloadPage(
baseUrl
+ "?verb=ListRecords&resumptionToken="
+ URLEncoder.encode(resumptionToken, "UTF-8"));
+ URLEncoder.encode(resumptionToken, UTF_8));
} catch (final UnsupportedEncodingException e) {
report.put(e.getClass().getName(), e.getMessage());
throw new CollectorException(e);
@ -161,7 +161,7 @@ public class OaiIterator implements Iterator<String> {
report.put(e.getClass().getName(), e.getMessage());
final String cleaned = XmlCleaner.cleanAllEntities(xml);
try {
doc = DocumentHelper.parseText(xml);
doc = DocumentHelper.parseText(cleaned);
} catch (final DocumentException e1) {
final String resumptionToken = extractResumptionToken(xml);
if (resumptionToken == null) {

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIteratorFactory.java
View File

@ -3,9 +3,9 @@ package eu.dnetlib.dhp.collection.plugin.oai;
import java.util.Iterator;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.HttpConnector2;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
import eu.dnetlib.dhp.common.collection.HttpConnector2;
public class OaiIteratorFactory {

6
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPlugin.java
View File

@ -9,11 +9,11 @@ import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
import eu.dnetlib.dhp.collection.ApiDescriptor;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
/**
* TODO: delegate HTTP requests to the common HttpConnector2 implementation.

27
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
View File

@ -30,9 +30,9 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import org.xml.sax.InputSource;
import eu.dnetlib.dhp.collection.CollectorException;
import eu.dnetlib.dhp.collection.HttpClientParams;
import eu.dnetlib.dhp.collection.JsonUtils;
import eu.dnetlib.dhp.common.collection.CollectorException;
import eu.dnetlib.dhp.common.collection.HttpClientParams;
/**
* log.info(...) equal to log.trace(...) in the application-logs
@ -131,7 +131,8 @@ public class RestIterator implements Iterator<String> {
private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
throws TransformerConfigurationException, XPathExpressionException {
transformer = TransformerFactory.newInstance().newTransformer();
final TransformerFactory factory = TransformerFactory.newInstance();
transformer = factory.newTransformer();
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
xpath = XPathFactory.newInstance().newXPath();
@ -142,7 +143,7 @@ public class RestIterator implements Iterator<String> {
private void initQueue() {
query = baseUrl + "?" + queryParams + querySize + queryFormat;
log.info("REST calls starting with " + query);
log.info("REST calls starting with {}", query);
}
private void disconnect() {
@ -174,7 +175,7 @@ public class RestIterator implements Iterator<String> {
try {
query = downloadPage(query);
} catch (CollectorException e) {
log.debug("CollectorPlugin.next()-Exception: " + e);
log.debug("CollectorPlugin.next()-Exception: {}", e);
throw new RuntimeException(e);
}
}
@ -198,7 +199,7 @@ public class RestIterator implements Iterator<String> {
// check if cursor=* is initial set otherwise add it to the queryParam URL
if (resumptionType.equalsIgnoreCase("deep-cursor")) {
log.debug("check resumptionType deep-cursor and check cursor=*?" + query);
log.debug("check resumptionType deep-cursor and check cursor=*?{}", query);
if (!query.contains("&cursor=")) {
query += "&cursor=*";
}
@ -208,16 +209,16 @@ public class RestIterator implements Iterator<String> {
log.info("requestig URL [{}]", query);
URL qUrl = new URL(query);
log.debug("authMethod :" + authMethod);
log.debug("authMethod: {}", authMethod);
if ("bearer".equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: " + resultXml);
log.trace("authMethod before inputStream: {}", resultXml);
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + authToken);
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
conn.setRequestMethod("GET");
theHttpInputStream = conn.getInputStream();
} else if (BASIC.equalsIgnoreCase(this.authMethod)) {
log.trace("authMethod before inputStream: " + resultXml);
log.trace("authMethod before inputStream: {}", resultXml);
HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + authToken);
conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
@ -237,13 +238,13 @@ public class RestIterator implements Iterator<String> {
if (!(emptyXml).equalsIgnoreCase(resultXml)) {
resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
log.debug("nodeList.length: " + nodeList.getLength());
log.debug("nodeList.length: {}", nodeList.getLength());
for (int i = 0; i < nodeList.getLength(); i++) {
StringWriter sw = new StringWriter();
transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
String toEnqueue = sw.toString();
if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || emptyXml.equalsIgnoreCase(toEnqueue)) {
log.warn("The following record resulted in empty item for the feeding queue: " + resultXml);
log.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
} else {
recordQueue.add(sw.toString());
}
@ -274,9 +275,9 @@ public class RestIterator implements Iterator<String> {
String[] resumptionKeyValue = arrayUrlArgStr.split("=");
if (isInteger(resumptionKeyValue[1])) {
urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
log.debug("discover OldResumptionSize from Url (int): " + urlOldResumptionSize);
log.debug("discover OldResumptionSize from Url (int): {}", urlOldResumptionSize);
} else {
log.debug("discover OldResumptionSize from Url (str): " + resumptionKeyValue[1]);
log.debug("discover OldResumptionSize from Url (str): {}", resumptionKeyValue[1]);
}
}
}

65
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala → dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
View File

@ -1,14 +1,12 @@
package eu.dnetlib.dhp.sx.graph.bio
package eu.dnetlib.dhp.sx.bio
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf._
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.{compact, parse, render}
import scala.collection.JavaConverters._
import collection.JavaConverters._
object BioDBToOAF {
case class EBILinkItem(id: Long, links: String) {}
@ -17,23 +15,23 @@ object BioDBToOAF {
case class UniprotDate(date: String, date_info: String) {}
case class ScholixResolved(pid:String, pidType:String, typology:String, tilte:List[String], datasource:List[String], date:List[String], authors:List[String]){}
case class ScholixResolved(pid: String, pidType: String, typology: String, tilte: List[String], datasource: List[String], date: List[String], authors: List[String]) {}
val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
val SUBJ_CLASS = "Keywords"
val DATE_RELATION_KEY = "RelationDate"
val resolvedURL:Map[String,String] = Map(
"genbank"-> "https://www.ncbi.nlm.nih.gov/nuccore/",
val resolvedURL: Map[String, String] = Map(
"genbank" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/",
"ena" -> "https://www.ebi.ac.uk/ena/browser/view/",
"clinicaltrials.gov"-> "https://clinicaltrials.gov/ct2/show/",
"onim"-> "https://omim.org/entry/",
"refseq"-> "https://www.ncbi.nlm.nih.gov/nuccore/",
"geo"-> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
"clinicaltrials.gov" -> "https://clinicaltrials.gov/ct2/show/",
"onim" -> "https://omim.org/entry/",
"refseq" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
"geo" -> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
)
@ -45,7 +43,7 @@ object BioDBToOAF {
val ElsevierCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier")
val springerNatureCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature")
val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::83e60e09c222f206c725385f53d7e567c", "EMBL-EBIs Protein Data Bank in Europe (PDBe)")
val pubmedCollectedFrom:KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
val pubmedCollectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
UNIPROTCollectedFrom.setDataInfo(DATA_INFO)
PDBCollectedFrom.setDataInfo(DATA_INFO)
@ -58,9 +56,9 @@ object BioDBToOAF {
Map(
"uniprot" -> UNIPROTCollectedFrom,
"pdb"-> PDBCollectedFrom,
"elsevier" ->ElsevierCollectedFrom,
"ebi" ->EBICollectedFrom,
"pdb" -> PDBCollectedFrom,
"elsevier" -> ElsevierCollectedFrom,
"ebi" -> EBICollectedFrom,
"Springer Nature" -> springerNatureCollectedFrom,
"NCBI Nucleotide" -> ncbiCollectedFrom,
"European Nucleotide Archive" -> enaCollectedFrom,
@ -68,7 +66,7 @@ object BioDBToOAF {
)
}
def crossrefLinksToOaf(input:String):Oaf = {
def crossrefLinksToOaf(input: String): Oaf = {
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json = parse(input)
val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase
@ -77,16 +75,16 @@ object BioDBToOAF {
val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase
val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
val relation_semantic= (json \ "RelationshipType" \ "Name").extract[String]
val relation_semantic = (json \ "RelationshipType" \ "Name").extract[String]
val date = GraphCleaningFunctions.cleanDate((json \ "LinkedPublicationDate").extract[String])
createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type),collectedFromMap("elsevier"),"relationship", relation_semantic, date)
createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type), collectedFromMap("elsevier"), "relationship", relation_semantic, date)
}
def scholixResolvedToOAF(input:ScholixResolved):Oaf = {
def scholixResolvedToOAF(input: ScholixResolved): Oaf = {
val d = new Dataset
@ -127,14 +125,14 @@ object BioDBToOAF {
d.setInstance(List(i).asJava)
if (input.authors != null && input.authors.nonEmpty) {
val authors = input.authors.map(a =>{
val authors = input.authors.map(a => {
val authorOAF = new Author
authorOAF.setFullname(a)
authorOAF
})
d.setAuthor(authors.asJava)
}
if (input.date!= null && input.date.nonEmpty) {
if (input.date != null && input.date.nonEmpty) {
val dt = input.date.head
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
@ -190,7 +188,7 @@ object BioDBToOAF {
OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
).asJava)
}
var i_date:Option[UniprotDate] = None
var i_date: Option[UniprotDate] = None
if (dates.nonEmpty) {
i_date = dates.find(d => d.date_info.contains("entry version"))
@ -199,7 +197,7 @@ object BioDBToOAF {
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
}
val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version"))
.map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
.map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
if (relevant_dates != null && relevant_dates.nonEmpty)
d.setRelevantdate(relevant_dates.asJava)
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
@ -218,12 +216,12 @@ object BioDBToOAF {
if (references_pmid != null && references_pmid.nonEmpty) {
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null)
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
rel.getCollectedfrom
List(d, rel)
}
else if (references_doi != null && references_doi.nonEmpty) {
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null)
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
List(d, rel)
}
else
@ -231,19 +229,18 @@ object BioDBToOAF {
}
def generate_unresolved_id(pid:String, pidType:String) :String = {
def generate_unresolved_id(pid: String, pidType: String): String = {
s"unresolved::$pid::$pidType"
}
def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String, date:String):Relation = {
def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType: String, relClass: String, date: String): Relation = {
val rel = new Relation
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
rel.setDataInfo(DATA_INFO)
rel.setRelType("resultResult")
rel.setRelType(ModelConstants.RESULT_RESULT)
rel.setSubRelType(subRelType)
rel.setRelClass(relClass)
@ -251,7 +248,7 @@ object BioDBToOAF {
rel.setTarget(s"unresolved::$pid::$pidType")
val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
rel.setProperties(List(dateProps).asJava)
@ -262,8 +259,8 @@ object BioDBToOAF {
}
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = {
createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date)
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date: String): Relation = {
createRelation(pid, pidType, sourceId, collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
}
@ -392,6 +389,6 @@ object BioDBToOAF {
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", GraphCleaningFunctions.cleanDate(input.date)))
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date)))
}
}

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