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GNU AFFERO GENERAL PUBLIC LICENSE
Version 3, 19 November 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The GNU Affero General Public License is a free, copyleft license for
software and other kinds of works, specifically designed to ensure
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The licenses for most software and other practical works are designed
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When we speak of free software, we are referring to freedom, not
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An older license, called the Affero General Public License and
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0. Definitions.
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All rights granted under this License are granted for the term of
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and the Corresponding Source of the work is not available for anyone
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in a country, would infringe one or more identifiable patents in that
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arrangement, you convey, or propagate by procuring conveyance of, a
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A patent license is "discriminatory" if it does not include within
the scope of its coverage, prohibits the exercise of, or is
conditioned on the non-exercise of one or more of the rights that are
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in the business of distributing software, under which you make payment
to the third party based on the extent of your activity of conveying
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or that patent license was granted, prior to 28 March 2007.
Nothing in this License shall be construed as excluding or limiting
any implied license or other defenses to infringement that may
otherwise be available to you under applicable patent law.
12. No Surrender of Others' Freedom.
If conditions are imposed on you (whether by court order, agreement or
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covered work so as to satisfy simultaneously your obligations under this
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to collect a royalty for further conveying from those to whom you convey
the Program, the only way you could satisfy both those terms and this
License would be to refrain entirely from conveying the Program.
13. Remote Network Interaction; Use with the GNU General Public License.
Notwithstanding any other provision of this License, if you modify the
Program, your modified version must prominently offer all users
interacting with it remotely through a computer network (if your version
supports such interaction) an opportunity to receive the Corresponding
Source of your version by providing access to the Corresponding Source
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means of facilitating copying of software. This Corresponding Source
shall include the Corresponding Source for any work covered by version 3
of the GNU General Public License that is incorporated pursuant to the
following paragraph.
Notwithstanding any other provision of this License, you have
permission to link or combine any covered work with a work licensed
under version 3 of the GNU General Public License into a single
combined work, and to convey the resulting work. The terms of this
License will continue to apply to the part which is the covered work,
but the work with which it is combined will remain governed by version
3 of the GNU General Public License.
14. Revised Versions of this License.
The Free Software Foundation may publish revised and/or new versions of
the GNU Affero General Public License from time to time. Such new versions
will be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the
Program specifies that a certain numbered version of the GNU Affero General
Public License "or any later version" applies to it, you have the
option of following the terms and conditions either of that numbered
version or of any later version published by the Free Software
Foundation. If the Program does not specify a version number of the
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by the Free Software Foundation.
If the Program specifies that a proxy can decide which future
versions of the GNU Affero General Public License can be used, that proxy's
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to choose that version for the Program.
Later license versions may give you additional or different
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author or copyright holder as a result of your choosing to follow a
later version.
15. Disclaimer of Warranty.
THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
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IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
16. Limitation of Liability.
IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If your software can interact with users remotely through a computer
network, you should also make sure that it provides a way for users to
get its source. For example, if your program is a web application, its
interface could display a "Source" link that leads users to an archive
of the code. There are many ways you could offer source, and different
solutions will be better for different programs; see section 13 for the
specific requirements.
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU AGPL, see
<http://www.gnu.org/licenses/>.

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@ -12,6 +12,8 @@
<artifactId>dhp-build-assembly-resources</artifactId> <artifactId>dhp-build-assembly-resources</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<description>This module contains a set of scripts supporting the build lifecycle for the dnet-hadoop project</description>
<build> <build>
<plugins> <plugins>
<plugin> <plugin>

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@ -12,22 +12,29 @@
<artifactId>dhp-build-properties-maven-plugin</artifactId> <artifactId>dhp-build-properties-maven-plugin</artifactId>
<packaging>maven-plugin</packaging> <packaging>maven-plugin</packaging>
<description>This module is a maven plugin implementing custom properties substitutions in the build lifecycle</description>
<dependencies> <dependencies>
<dependency> <dependency>
<groupId>org.apache.maven</groupId> <groupId>org.apache.maven</groupId>
<artifactId>maven-plugin-api</artifactId> <artifactId>maven-plugin-api</artifactId>
<version>2.0</version> <version>3.6.3</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>org.apache.maven</groupId> <groupId>org.apache.maven</groupId>
<artifactId>maven-project</artifactId> <artifactId>maven-project</artifactId>
<version>2.0</version> <version>2.2.1</version>
</dependency> </dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-artifact</artifactId>
<version>2.2.1</version>
</dependency>
<dependency> <dependency>
<groupId>org.kuali.maven.plugins</groupId> <groupId>org.kuali.maven.plugins</groupId>
<artifactId>properties-maven-plugin</artifactId> <artifactId>properties-maven-plugin</artifactId>
<version>1.3.2</version> <version>${properties.maven.plugin.version}</version>
</dependency> </dependency>
<dependency> <dependency>
<groupId>com.google.code.findbugs</groupId> <groupId>com.google.code.findbugs</groupId>
@ -73,44 +80,10 @@
<artifactId>maven-javadoc-plugin</artifactId> <artifactId>maven-javadoc-plugin</artifactId>
<configuration> <configuration>
<detectLinks>true</detectLinks> <detectLinks>true</detectLinks>
<doclint>none</doclint>
</configuration> </configuration>
</plugin> </plugin>
</plugins> </plugins>
<pluginManagement>
<plugins>
<!--This plugin's configuration is used to store Eclipse m2e settings only. It has no influence on the Maven build itself.-->
<plugin>
<groupId>org.eclipse.m2e</groupId>
<artifactId>lifecycle-mapping</artifactId>
<version>1.0.0</version>
<configuration>
<lifecycleMappingMetadata>
<pluginExecutions>
<pluginExecution>
<pluginExecutionFilter>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-plugin-plugin
</artifactId>
<versionRange>
[3.2,)
</versionRange>
<goals>
<goal>descriptor</goal>
</goals>
</pluginExecutionFilter>
<action>
<ignore />
</action>
</pluginExecution>
</pluginExecutions>
</lifecycleMappingMetadata>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build> </build>
</project> </project>

View File

@ -1,3 +1,4 @@
package eu.dnetlib.maven.plugin.properties; package eu.dnetlib.maven.plugin.properties;
import java.io.File; import java.io.File;
@ -12,8 +13,8 @@ import org.apache.maven.plugin.MojoFailureException;
/** /**
* Generates oozie properties which were not provided from commandline. * Generates oozie properties which were not provided from commandline.
* @author mhorst
* *
* @author mhorst
* @goal generate-properties * @goal generate-properties
*/ */
public class GenerateOoziePropertiesMojo extends AbstractMojo { public class GenerateOoziePropertiesMojo extends AbstractMojo {
@ -21,26 +22,30 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir"; public static final String PROPERTY_NAME_WF_SOURCE_DIR = "workflow.source.dir";
public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName"; public static final String PROPERTY_NAME_SANDBOX_NAME = "sandboxName";
private final String[] limiters = {"dhp", "dnetlib", "eu"}; private final String[] limiters = {
"dhp", "dnetlib", "eu"
};
@Override @Override
public void execute() throws MojoExecutionException, MojoFailureException { public void execute() throws MojoExecutionException, MojoFailureException {
if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR) && if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
!System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) { && !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
String generatedSandboxName = generateSandboxName(System.getProperties().getProperty( String generatedSandboxName = generateSandboxName(
PROPERTY_NAME_WF_SOURCE_DIR));
if (generatedSandboxName!=null) {
System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME,
generatedSandboxName);
} else {
System.out.println("unable to generate sandbox name from path: " +
System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR)); System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
if (generatedSandboxName != null) {
System.getProperties().setProperty(PROPERTY_NAME_SANDBOX_NAME, generatedSandboxName);
} else {
System.out
.println(
"unable to generate sandbox name from path: "
+ System.getProperties().getProperty(PROPERTY_NAME_WF_SOURCE_DIR));
} }
} }
} }
/** /**
* Generates sandbox name from workflow source directory. * Generates sandbox name from workflow source directory.
*
* @param wfSourceDir * @param wfSourceDir
* @return generated sandbox name * @return generated sandbox name
*/ */
@ -53,8 +58,9 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
for (String token : tokens) { for (String token : tokens) {
for (String limiter : limiters) { for (String limiter : limiters) {
if (limiter.equals(token)) { if (limiter.equals(token)) {
return sandboxNameParts.size()>0? return sandboxNameParts.size() > 0
StringUtils.join(sandboxNameParts.toArray()):null; ? StringUtils.join(sandboxNameParts.toArray())
: null;
} }
} }
if (sandboxNameParts.size() > 0) { if (sandboxNameParts.size() > 0) {
@ -67,5 +73,4 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
return null; return null;
} }
} }
} }

View File

@ -1,17 +1,15 @@
/** /**
* Licensed under the Educational Community License, Version 2.0 (the "License"); you may not use
* this file except in compliance with the License. You may obtain a copy of the License at
* *
* Licensed under the Educational Community License, Version 2.0 (the "License"); * <p>http://www.opensource.org/licenses/ecl2.php
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
* *
* http://www.opensource.org/licenses/ecl2.php * <p>Unless required by applicable law or agreed to in writing, software distributed under the
* * License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either
* Unless required by applicable law or agreed to in writing, software * express or implied. See the License for the specific language governing permissions and
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License. * limitations under the License.
*/ */
package eu.dnetlib.maven.plugin.properties; package eu.dnetlib.maven.plugin.properties;
import java.io.File; import java.io.File;
@ -41,10 +39,9 @@ import org.springframework.core.io.ResourceLoader;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings; import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
/** /**
* Writes project properties for the keys listed in specified properties files. * Writes project properties for the keys listed in specified properties files. Based on:
* Based on: * http://site.kuali.org/maven/plugins/properties-maven-plugin/2.0.1/write-project-properties-mojo.html
* http://site.kuali.org/maven/plugins/properties-maven-plugin/1.3.2/write-project-properties-mojo.html *
* @author mhorst * @author mhorst
* @goal write-project-properties * @goal write-project-properties
*/ */
@ -56,9 +53,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
protected static final String PROPERTY_PREFIX_ENV = "env."; protected static final String PROPERTY_PREFIX_ENV = "env.";
private static final String ENCODING_UTF8 = "utf8"; private static final String ENCODING_UTF8 = "utf8";
/** /** @parameter property="properties.includePropertyKeysFromFiles" */
* @parameter property="properties.includePropertyKeysFromFiles"
*/
private String[] includePropertyKeysFromFiles; private String[] includePropertyKeysFromFiles;
/** /**
@ -123,11 +118,14 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
*/ */
private String include; private String include;
/* (non-Javadoc) /*
* (non-Javadoc)
* @see org.apache.maven.plugin.AbstractMojo#execute() * @see org.apache.maven.plugin.AbstractMojo#execute()
*/ */
@Override @Override
@SuppressFBWarnings({"NP_UNWRITTEN_FIELD","UWF_UNWRITTEN_FIELD"}) @SuppressFBWarnings({
"NP_UNWRITTEN_FIELD", "UWF_UNWRITTEN_FIELD"
})
public void execute() throws MojoExecutionException, MojoFailureException { public void execute() throws MojoExecutionException, MojoFailureException {
Properties properties = new Properties(); Properties properties = new Properties();
// Add project properties // Add project properties
@ -153,6 +151,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Provides environment variables. * Provides environment variables.
*
* @return environment variables * @return environment variables
*/ */
protected static Properties getEnvironmentVariables() { protected static Properties getEnvironmentVariables() {
@ -165,12 +164,14 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Removes properties which should not be written. * Removes properties which should not be written.
*
* @param properties * @param properties
* @param omitCSV * @param omitCSV
* @param includeCSV * @param includeCSV
* @throws MojoExecutionException * @throws MojoExecutionException
*/ */
protected void trim(Properties properties, String omitCSV, String includeCSV) throws MojoExecutionException { protected void trim(Properties properties, String omitCSV, String includeCSV)
throws MojoExecutionException {
List<String> omitKeys = getListFromCSV(omitCSV); List<String> omitKeys = getListFromCSV(omitCSV);
for (String key : omitKeys) { for (String key : omitKeys) {
properties.remove(key); properties.remove(key);
@ -201,6 +202,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Checks whether file exists. * Checks whether file exists.
*
* @param location * @param location
* @return true when exists, false otherwise. * @return true when exists, false otherwise.
*/ */
@ -219,6 +221,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Validates resource location. * Validates resource location.
*
* @param location * @param location
* @return true when valid, false otherwise * @return true when valid, false otherwise
* @throws MojoExecutionException * @throws MojoExecutionException
@ -238,6 +241,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Provides input stream. * Provides input stream.
*
* @param location * @param location
* @return input stream * @return input stream
* @throws IOException * @throws IOException
@ -254,6 +258,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Creates properties for given location. * Creates properties for given location.
*
* @param location * @param location
* @return properties for given location * @return properties for given location
* @throws MojoExecutionException * @throws MojoExecutionException
@ -278,6 +283,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Provides escape characters. * Provides escape characters.
*
* @param escapeChars * @param escapeChars
* @return escape characters * @return escape characters
*/ */
@ -293,6 +299,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Provides real token. * Provides real token.
*
* @param token * @param token
* @return real token * @return real token
*/ */
@ -310,6 +317,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Returns content. * Returns content.
*
* @param comment * @param comment
* @param properties * @param properties
* @param escapeTokens * @param escapeTokens
@ -332,13 +340,15 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Writes properties to given file. * Writes properties to given file.
*
* @param file * @param file
* @param comment * @param comment
* @param properties * @param properties
* @param escapeTokens * @param escapeTokens
* @throws MojoExecutionException * @throws MojoExecutionException
*/ */
protected void writeProperties(File file, String comment, Properties properties, List<String> escapeTokens) protected void writeProperties(
File file, String comment, Properties properties, List<String> escapeTokens)
throws MojoExecutionException { throws MojoExecutionException {
try { try {
String content = getContent(comment, properties, escapeTokens); String content = getContent(comment, properties, escapeTokens);
@ -350,6 +360,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Escapes characters. * Escapes characters.
*
* @param s * @param s
* @param escapeChars * @param escapeChars
* @return * @return
@ -364,6 +375,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Provides replacement token. * Provides replacement token.
*
* @param escapeChar * @param escapeChar
* @return replacement token * @return replacement token
*/ */
@ -381,6 +393,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Returns list from csv. * Returns list from csv.
*
* @param csv * @param csv
* @return list of values generated from CSV * @return list of values generated from CSV
*/ */
@ -422,15 +435,13 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
/** /**
* Sets property files for which keys properties should be included. * Sets property files for which keys properties should be included.
*
* @param includePropertyKeysFromFiles * @param includePropertyKeysFromFiles
*/ */
public void setIncludePropertyKeysFromFiles( public void setIncludePropertyKeysFromFiles(String[] includePropertyKeysFromFiles) {
String[] includePropertyKeysFromFiles) {
if (includePropertyKeysFromFiles != null) { if (includePropertyKeysFromFiles != null) {
this.includePropertyKeysFromFiles = Arrays.copyOf( this.includePropertyKeysFromFiles = Arrays
includePropertyKeysFromFiles, .copyOf(includePropertyKeysFromFiles, includePropertyKeysFromFiles.length);
includePropertyKeysFromFiles.length);
} }
} }
} }

View File

@ -1,19 +1,17 @@
package eu.dnetlib.maven.plugin.properties;
import org.junit.jupiter.api.BeforeEach; package eu.dnetlib.maven.plugin.properties;
import org.junit.jupiter.api.Test;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_SANDBOX_NAME; import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_SANDBOX_NAME;
import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_WF_SOURCE_DIR; import static eu.dnetlib.maven.plugin.properties.GenerateOoziePropertiesMojo.PROPERTY_NAME_WF_SOURCE_DIR;
import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.*;
/** import org.junit.jupiter.api.BeforeEach;
* @author mhorst, claudio.atzori import org.junit.jupiter.api.Test;
*
*/ /** @author mhorst, claudio.atzori */
public class GenerateOoziePropertiesMojoTest { public class GenerateOoziePropertiesMojoTest {
private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo(); private final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
@BeforeEach @BeforeEach
public void clearSystemProperties() { public void clearSystemProperties() {
@ -96,5 +94,4 @@ public class GenerateOoziePropertiesMojoTest {
// assert // assert
assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME)); assertEquals("wf/transformers", System.getProperty(PROPERTY_NAME_SANDBOX_NAME));
} }
} }

View File

@ -1,5 +1,14 @@
package eu.dnetlib.maven.plugin.properties; package eu.dnetlib.maven.plugin.properties;
import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.lenient;
import java.io.*;
import java.util.Properties;
import org.apache.maven.plugin.MojoExecutionException; import org.apache.maven.plugin.MojoExecutionException;
import org.apache.maven.project.MavenProject; import org.apache.maven.project.MavenProject;
import org.junit.jupiter.api.*; import org.junit.jupiter.api.*;
@ -9,18 +18,7 @@ import org.mockito.Mock;
import org.mockito.MockitoAnnotations; import org.mockito.MockitoAnnotations;
import org.mockito.junit.jupiter.MockitoExtension; import org.mockito.junit.jupiter.MockitoExtension;
import java.io.*; /** @author mhorst, claudio.atzori */
import java.util.Properties;
import static eu.dnetlib.maven.plugin.properties.WritePredefinedProjectProperties.PROPERTY_PREFIX_ENV;
import static org.junit.jupiter.api.Assertions.*;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.lenient;
/**
* @author mhorst, claudio.atzori
*
*/
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
public class WritePredefinedProjectPropertiesTest { public class WritePredefinedProjectPropertiesTest {
@ -150,7 +148,9 @@ public class WritePredefinedProjectPropertiesTest {
includedProperties.setProperty(includedKey, "irrelevantValue"); includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileWriter(includedPropertiesFile), null); includedProperties.store(new FileWriter(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()}); mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute // execute
mojo.execute(); mojo.execute();
@ -164,7 +164,8 @@ public class WritePredefinedProjectPropertiesTest {
} }
@Test @Test
public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder) throws Exception { public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
throws Exception {
// given // given
String key = "projectPropertyKey"; String key = "projectPropertyKey";
String value = "projectPropertyValue"; String value = "projectPropertyValue";
@ -175,7 +176,11 @@ public class WritePredefinedProjectPropertiesTest {
projectProperties.setProperty(includedKey, includedValue); projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties(); doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setIncludePropertyKeysFromFiles(new String[] {"/eu/dnetlib/maven/plugin/properties/included.properties"}); mojo
.setIncludePropertyKeysFromFiles(
new String[] {
"/eu/dnetlib/maven/plugin/properties/included.properties"
});
// execute // execute
mojo.execute(); mojo.execute();
@ -200,14 +205,17 @@ public class WritePredefinedProjectPropertiesTest {
projectProperties.setProperty(includedKey, includedValue); projectProperties.setProperty(includedKey, includedValue);
doReturn(projectProperties).when(mavenProject).getProperties(); doReturn(projectProperties).when(mavenProject).getProperties();
mojo.setIncludePropertyKeysFromFiles(new String[] {""}); mojo.setIncludePropertyKeysFromFiles(new String[] {
""
});
// execute // execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
} }
@Test @Test
public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder) throws Exception { public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
throws Exception {
// given // given
String key = "projectPropertyKey"; String key = "projectPropertyKey";
String value = "projectPropertyValue"; String value = "projectPropertyValue";
@ -223,7 +231,9 @@ public class WritePredefinedProjectPropertiesTest {
includedProperties.setProperty(includedKey, "irrelevantValue"); includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null); includedProperties.storeToXML(new FileOutputStream(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()}); mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute // execute
mojo.execute(); mojo.execute();
@ -237,7 +247,8 @@ public class WritePredefinedProjectPropertiesTest {
} }
@Test @Test
public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder) throws Exception { public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
throws Exception {
// given // given
String key = "projectPropertyKey"; String key = "projectPropertyKey";
String value = "projectPropertyValue"; String value = "projectPropertyValue";
@ -253,7 +264,9 @@ public class WritePredefinedProjectPropertiesTest {
includedProperties.setProperty(includedKey, "irrelevantValue"); includedProperties.setProperty(includedKey, "irrelevantValue");
includedProperties.store(new FileOutputStream(includedPropertiesFile), null); includedProperties.store(new FileOutputStream(includedPropertiesFile), null);
mojo.setIncludePropertyKeysFromFiles(new String[] {includedPropertiesFile.getAbsolutePath()}); mojo.setIncludePropertyKeysFromFiles(new String[] {
includedPropertiesFile.getAbsolutePath()
});
// execute // execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
@ -263,7 +276,9 @@ public class WritePredefinedProjectPropertiesTest {
public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception { public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
// given // given
mojo.setQuiet(true); mojo.setQuiet(true);
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"}); mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
});
// execute // execute
mojo.execute(); mojo.execute();
@ -277,7 +292,9 @@ public class WritePredefinedProjectPropertiesTest {
@Test @Test
public void testExecuteIncludingPropertyKeysFromInvalidFile() { public void testExecuteIncludingPropertyKeysFromInvalidFile() {
// given // given
mojo.setIncludePropertyKeysFromFiles(new String[] {"invalid location"}); mojo.setIncludePropertyKeysFromFiles(new String[] {
"invalid location"
});
// execute // execute
Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute()); Assertions.assertThrows(MojoExecutionException.class, () -> mojo.execute());
@ -320,7 +337,8 @@ public class WritePredefinedProjectPropertiesTest {
} }
@Test @Test
public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder) throws Exception { public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
throws Exception {
// given // given
String key = "systemPropertyKey "; String key = "systemPropertyKey ";
String value = "systemPropertyValue"; String value = "systemPropertyValue";
@ -347,7 +365,8 @@ public class WritePredefinedProjectPropertiesTest {
return new File(testFolder, "test.properties"); return new File(testFolder, "test.properties");
} }
private Properties getStoredProperties(File testFolder) throws FileNotFoundException, IOException { private Properties getStoredProperties(File testFolder)
throws IOException {
Properties properties = new Properties(); Properties properties = new Properties();
properties.load(new FileInputStream(getPropertiesFileLocation(testFolder))); properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
return properties; return properties;

View File

@ -0,0 +1,50 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-code-style</artifactId>
<version>1.1.7-SNAPSHOT</version>
<packaging>jar</packaging>
<description>This module contains resources supporting common code style conventions</description>
<distributionManagement>
<snapshotRepository>
<id>dnet45-snapshots</id>
<name>DNet45 Snapshots</name>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-snapshots</url>
<layout>default</layout>
</snapshotRepository>
<repository>
<id>dnet45-releases</id>
<url>http://maven.research-infrastructures.eu/nexus/content/repositories/dnet45-releases</url>
</repository>
</distributionManagement>
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-project-info-reports-plugin</artifactId>
<version>3.0.0</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
</plugin>
</plugins>
</pluginManagement>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
</project>

View File

@ -0,0 +1,252 @@
<?xml version="1.0" encoding="UTF-8"?>
<profiles version="10">
<profile kind="CodeFormatterProfile" name="Android" version="10">
<setting id="org.eclipse.jdt.core.formatter.align_type_members_on_columns" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_assignment" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_compact_if" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
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View File

@ -0,0 +1,727 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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</profiles>

View File

@ -0,0 +1,337 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation.count_dependent" value="16|-1|16"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_type" value="1585"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_cast" value="do not insert"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_local_variable.count_dependent" value="1585|-1|1585"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_anonymous_type_declaration" value="insert"/>
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<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_field.count_dependent" value="1585|-1|1585"/>
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<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_constructor_declaration_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_closing_angle_bracket_in_type_parameters" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_labeled_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_at_end_of_file_if_missing" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration.count_dependent" value="16|5|80"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_while" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_type" value="insert"/>
<setting id="org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode" value="enabled"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_try" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.put_empty_statement_on_new_line" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_label" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_parameter" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_while_in_do_statement" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant.count_dependent" value="16|-1|16"/>
<setting id="org.eclipse.jdt.core.formatter.comment.line_length" value="100"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_package" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_between_import_groups" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_enum_constant_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.number_of_blank_lines_at_beginning_of_method_body" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_annotation_type_member_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.wrap_before_binary_operator" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations" value="2"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_synchronized" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_block" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.join_lines_in_comments" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_field_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_compact_if" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_for_inits" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_default" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_and_in_type_parameter" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_constructor_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_imports" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_field" value="1585"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_angle_bracket_in_type_parameters" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_bracket_in_array_allocation_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_anonymous_type_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_colon_in_conditional" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer.count_dependent" value="16|5|80"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_postfix_operator" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_source_code" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_synchronized" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_allocation_expression" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_constructor_declaration_throws" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_brace_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.compiler.codegen.targetPlatform" value="1.7"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_resources_in_try" value="80"/>
<setting id="org.eclipse.jdt.core.formatter.use_tabs_only_for_leading_indentations" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.comment.format_block_comments" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_enum_constant" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="0"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_block" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_parenthesized_expression" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_catch" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_multiple_local_declarations" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration.count_dependent" value="16|4|48"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_switch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_for_increments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_method.count_dependent" value="1585|-1|1585"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_invocation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_assert" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration" value="end_of_line"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_array_initializer" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_braces_in_array_initializer" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression.count_dependent" value="16|-1|16"/>
<setting id="org.eclipse.jdt.core.formatter.wrap_non_simple_member_annotation" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_annotations_on_local_variable" value="1585"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_method_declaration" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_for" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call.count_dependent" value="16|5|80"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_catch" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_parameterized_type_reference" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_field_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_closing_paren_in_annotation" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_generic_type_arguments.count_dependent" value="16|-1|16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_parameterized_type_reference" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression.count_dependent" value="16|5|80"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_method_invocation_arguments" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration.count_dependent" value="16|5|80"/>
<setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_multiple_local_declarations" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header" value="true"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_after_semicolon_in_for" value="insert"/>
<setting id="org.eclipse.jdt.core.formatter.never_indent_line_comments_on_first_column" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_semicolon_in_try_resources" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.alignment_for_for_statement" value="16"/>
<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_angle_bracket_in_type_arguments" value="do not insert"/>
<setting id="org.eclipse.jdt.core.formatter.never_indent_block_comments_on_first_column" value="false"/>
<setting id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line" value="false"/>
</profile>
</profiles>

View File

@ -8,7 +8,11 @@
</parent> </parent>
<artifactId>dhp-build</artifactId> <artifactId>dhp-build</artifactId>
<packaging>pom</packaging> <packaging>pom</packaging>
<description>This module is a container for the build tools used in dnet-hadoop</description>
<modules> <modules>
<module>dhp-code-style</module>
<module>dhp-build-assembly-resources</module> <module>dhp-build-assembly-resources</module>
<module>dhp-build-properties-maven-plugin</module> <module>dhp-build-properties-maven-plugin</module>
</modules> </modules>

View File

@ -12,6 +12,8 @@
<artifactId>dhp-common</artifactId> <artifactId>dhp-common</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
<dependencies> <dependencies>
<dependency> <dependency>

View File

@ -1,9 +1,9 @@
package eu.dnetlib.collector.worker.model; package eu.dnetlib.collector.worker.model;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
public class ApiDescriptor { public class ApiDescriptor {
private String id; private String id;
@ -45,5 +45,4 @@ public class ApiDescriptor {
public void setProtocol(final String protocol) { public void setProtocol(final String protocol) {
this.protocol = protocol; this.protocol = protocol;
} }
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.data.mdstore.manager.common.model; package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable; import java.io.Serializable;
@ -12,9 +13,7 @@ import javax.persistence.Table;
@Table(name = "mdstores") @Table(name = "mdstores")
public class MDStore implements Serializable { public class MDStore implements Serializable {
/** /** */
*
*/
private static final long serialVersionUID = 3160530489149700055L; private static final long serialVersionUID = 3160530489149700055L;
@Id @Id
@ -95,11 +94,13 @@ public class MDStore implements Serializable {
this.apiId = apiId; this.apiId = apiId;
} }
public static MDStore newInstance(final String format, final String layout, final String interpretation) { public static MDStore newInstance(
final String format, final String layout, final String interpretation) {
return newInstance(format, layout, interpretation, null, null, null); return newInstance(format, layout, interpretation, null, null, null);
} }
public static MDStore newInstance(final String format, public static MDStore newInstance(
final String format,
final String layout, final String layout,
final String interpretation, final String interpretation,
final String dsName, final String dsName,
@ -115,5 +116,4 @@ public class MDStore implements Serializable {
md.setApiId(apiId); md.setApiId(apiId);
return md; return md;
} }
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.data.mdstore.manager.common.model; package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable; import java.io.Serializable;
@ -11,9 +12,7 @@ import javax.persistence.Table;
@Table(name = "mdstore_current_versions") @Table(name = "mdstore_current_versions")
public class MDStoreCurrentVersion implements Serializable { public class MDStoreCurrentVersion implements Serializable {
/** /** */
*
*/
private static final long serialVersionUID = -4757725888593745773L; private static final long serialVersionUID = -4757725888593745773L;
@Id @Id

View File

@ -1,3 +1,4 @@
package eu.dnetlib.data.mdstore.manager.common.model; package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable; import java.io.Serializable;
@ -14,9 +15,7 @@ import javax.persistence.TemporalType;
@Table(name = "mdstore_versions") @Table(name = "mdstore_versions")
public class MDStoreVersion implements Serializable { public class MDStoreVersion implements Serializable {
/** /** */
*
*/
private static final long serialVersionUID = -4763494442274298339L; private static final long serialVersionUID = -4763494442274298339L;
@Id @Id
@ -97,5 +96,4 @@ public class MDStoreVersion implements Serializable {
public void setSize(final long size) { public void setSize(final long size) {
this.size = size; this.size = size;
} }
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.data.mdstore.manager.common.model; package eu.dnetlib.data.mdstore.manager.common.model;
import java.io.Serializable; import java.io.Serializable;
@ -14,9 +15,7 @@ import javax.persistence.TemporalType;
@Table(name = "mdstores_with_info") @Table(name = "mdstores_with_info")
public class MDStoreWithInfo implements Serializable { public class MDStoreWithInfo implements Serializable {
/** /** */
*
*/
private static final long serialVersionUID = -8445784770687571492L; private static final long serialVersionUID = -8445784770687571492L;
@Id @Id
@ -141,5 +140,4 @@ public class MDStoreWithInfo implements Serializable {
public void setNumberOfVersions(final long numberOfVersions) { public void setNumberOfVersions(final long numberOfVersions) {
this.numberOfVersions = numberOfVersions; this.numberOfVersions = numberOfVersions;
} }
} }

View File

@ -1,9 +1,5 @@
package eu.dnetlib.dhp.application;
import com.fasterxml.jackson.databind.ObjectMapper; package eu.dnetlib.dhp.application;
import org.apache.commons.cli.*;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import java.io.ByteArrayInputStream; import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream; import java.io.ByteArrayOutputStream;
@ -12,7 +8,12 @@ import java.io.StringWriter;
import java.util.*; import java.util.*;
import java.util.zip.GZIPInputStream; import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream; import java.util.zip.GZIPOutputStream;
import java.util.zip.Inflater;
import org.apache.commons.cli.*;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class ArgumentApplicationParser implements Serializable { public class ArgumentApplicationParser implements Serializable {
@ -33,7 +34,10 @@ public class ArgumentApplicationParser implements Serializable {
private void createOptionMap(final OptionsParameter[] configuration) { private void createOptionMap(final OptionsParameter[] configuration) {
Arrays.stream(configuration).map(conf -> { Arrays
.stream(configuration)
.map(
conf -> {
final Option o = new Option(conf.getParamName(), true, conf.getParamDescription()); final Option o = new Option(conf.getParamName(), true, conf.getParamDescription());
o.setLongOpt(conf.getParamLongName()); o.setLongOpt(conf.getParamLongName());
o.setRequired(conf.isParamRequired()); o.setRequired(conf.isParamRequired());
@ -41,15 +45,14 @@ public class ArgumentApplicationParser implements Serializable {
compressedValues.add(conf.getParamLongName()); compressedValues.add(conf.getParamLongName());
} }
return o; return o;
}).forEach(options::addOption); })
.forEach(options::addOption);
// HelpFormatter formatter = new HelpFormatter(); // HelpFormatter formatter = new HelpFormatter();
// formatter.printHelp("myapp", null, options, null, true); // formatter.printHelp("myapp", null, options, null, true);
} }
public static String decompressValue(final String abstractCompressed) { public static String decompressValue(final String abstractCompressed) {
try { try {
byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes()); byte[] byteArray = Base64.decodeBase64(abstractCompressed.getBytes());
@ -74,7 +77,15 @@ public class ArgumentApplicationParser implements Serializable {
public void parseArgument(final String[] args) throws Exception { public void parseArgument(final String[] args) throws Exception {
CommandLineParser parser = new BasicParser(); CommandLineParser parser = new BasicParser();
CommandLine cmd = parser.parse(options, args); CommandLine cmd = parser.parse(options, args);
Arrays.stream(cmd.getOptions()).forEach(it -> objectMap.put(it.getLongOpt(), compressedValues.contains(it.getLongOpt())? decompressValue(it.getValue()): it.getValue())); Arrays
.stream(cmd.getOptions())
.forEach(
it -> objectMap
.put(
it.getLongOpt(),
compressedValues.contains(it.getLongOpt())
? decompressValue(it.getValue())
: it.getValue()));
} }
public String get(final String key) { public String get(final String key) {

View File

@ -1,5 +1,5 @@
package eu.dnetlib.dhp.application;
package eu.dnetlib.dhp.application;
public class OptionsParameter { public class OptionsParameter {

View File

@ -1,11 +1,10 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import java.io.Serializable; import java.io.Serializable;
import java.util.function.Supplier; import java.util.function.Supplier;
/** /** Provides serializable and throwing extensions to standard functional interfaces. */
* Provides serializable and throwing extensions to standard functional interfaces.
*/
public class FunctionalInterfaceSupport { public class FunctionalInterfaceSupport {
private FunctionalInterfaceSupport() { private FunctionalInterfaceSupport() {
@ -52,5 +51,4 @@ public class FunctionalInterfaceSupport {
public interface ThrowingRunnable<E extends Exception> { public interface ThrowingRunnable<E extends Exception> {
void run() throws E; void run() throws E;
} }
} }

View File

@ -1,5 +1,12 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
import java.util.Arrays;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileStatus; import org.apache.hadoop.fs.FileStatus;
import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.FileSystem;
@ -7,21 +14,29 @@ import org.apache.hadoop.fs.Path;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.util.Arrays; /** HDFS utility methods. */
import java.util.List;
import java.util.stream.Collectors;
import static eu.dnetlib.dhp.common.ThrowingSupport.rethrowAsRuntimeException;
/**
* HDFS utility methods.
*/
public class HdfsSupport { public class HdfsSupport {
private static final Logger logger = LoggerFactory.getLogger(HdfsSupport.class); private static final Logger logger = LoggerFactory.getLogger(HdfsSupport.class);
private HdfsSupport() { private HdfsSupport() {
} }
/**
* Checks a path (file or dir) exists on HDFS.
*
* @param path Path to be checked
* @param configuration Configuration of hadoop env
*/
public static boolean exists(String path, Configuration configuration) {
logger.info("Removing path: {}", path);
return rethrowAsRuntimeException(
() -> {
Path f = new Path(path);
FileSystem fileSystem = FileSystem.get(configuration);
return fileSystem.exists(f);
});
}
/** /**
* Removes a path (file or dir) from HDFS. * Removes a path (file or dir) from HDFS.
* *
@ -30,7 +45,8 @@ public class HdfsSupport {
*/ */
public static void remove(String path, Configuration configuration) { public static void remove(String path, Configuration configuration) {
logger.info("Removing path: {}", path); logger.info("Removing path: {}", path);
rethrowAsRuntimeException(() -> { rethrowAsRuntimeException(
() -> {
Path f = new Path(path); Path f = new Path(path);
FileSystem fileSystem = FileSystem.get(configuration); FileSystem fileSystem = FileSystem.get(configuration);
if (fileSystem.exists(f)) { if (fileSystem.exists(f)) {
@ -48,7 +64,8 @@ public class HdfsSupport {
*/ */
public static List<String> listFiles(String path, Configuration configuration) { public static List<String> listFiles(String path, Configuration configuration) {
logger.info("Listing files in path: {}", path); logger.info("Listing files in path: {}", path);
return rethrowAsRuntimeException(() -> Arrays return rethrowAsRuntimeException(
() -> Arrays
.stream(FileSystem.get(configuration).listStatus(new Path(path))) .stream(FileSystem.get(configuration).listStatus(new Path(path)))
.filter(FileStatus::isDirectory) .filter(FileStatus::isDirectory)
.map(x -> x.getPath().toString()) .map(x -> x.getPath().toString())

View File

@ -1,15 +1,15 @@
package eu.dnetlib.dhp.common;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer; package eu.dnetlib.dhp.common;
import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession;
import java.util.Objects; import java.util.Objects;
import java.util.function.Function; import java.util.function.Function;
/** import org.apache.spark.SparkConf;
* SparkSession utility methods. import org.apache.spark.sql.SparkSession;
*/
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
/** SparkSession utility methods. */
public class SparkSessionSupport { public class SparkSessionSupport {
private SparkSessionSupport() { private SparkSessionSupport() {
@ -23,36 +23,40 @@ public class SparkSessionSupport {
* @param isSparkSessionManaged When true will stop SparkSession * @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession * @param fn Consumer to be applied to constructed SparkSession
*/ */
public static void runWithSparkSession(SparkConf conf, public static void runWithSparkSession(
Boolean isSparkSessionManaged, SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
ThrowingConsumer<SparkSession, Exception> fn) { runWithSparkSession(
runWithSparkSession(c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn); c -> SparkSession.builder().config(c).getOrCreate(), conf, isSparkSessionManaged, fn);
} }
/** /**
* Runs a given function using SparkSession created with hive support and using default builder and supplied SparkConf. * Runs a given function using SparkSession created with hive support and using default builder and supplied
* Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally. * SparkConf. Stops SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally.
* *
* @param conf SparkConf instance * @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession * @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession * @param fn Consumer to be applied to constructed SparkSession
*/ */
public static void runWithSparkHiveSession(SparkConf conf, public static void runWithSparkHiveSession(
Boolean isSparkSessionManaged, SparkConf conf, Boolean isSparkSessionManaged, ThrowingConsumer<SparkSession, Exception> fn) {
ThrowingConsumer<SparkSession, Exception> fn) { runWithSparkSession(
runWithSparkSession(c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(), conf, isSparkSessionManaged, fn); c -> SparkSession.builder().config(c).enableHiveSupport().getOrCreate(),
conf,
isSparkSessionManaged,
fn);
} }
/** /**
* Runs a given function using SparkSession created using supplied builder and supplied SparkConf. Stops SparkSession * Runs a given function using SparkSession created using supplied builder and supplied SparkConf. Stops
* when SparkSession is managed. Allows to reuse SparkSession created externally. * SparkSession when SparkSession is managed. Allows to reuse SparkSession created externally.
* *
* @param sparkSessionBuilder Builder of SparkSession * @param sparkSessionBuilder Builder of SparkSession
* @param conf SparkConf instance * @param conf SparkConf instance
* @param isSparkSessionManaged When true will stop SparkSession * @param isSparkSessionManaged When true will stop SparkSession
* @param fn Consumer to be applied to constructed SparkSession * @param fn Consumer to be applied to constructed SparkSession
*/ */
public static void runWithSparkSession(Function<SparkConf, SparkSession> sparkSessionBuilder, public static void runWithSparkSession(
Function<SparkConf, SparkSession> sparkSessionBuilder,
SparkConf conf, SparkConf conf,
Boolean isSparkSessionManaged, Boolean isSparkSessionManaged,
ThrowingConsumer<SparkSession, Exception> fn) { ThrowingConsumer<SparkSession, Exception> fn) {

View File

@ -1,11 +1,10 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingRunnable; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingRunnable;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingSupplier; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingSupplier;
/** /** Exception handling utility methods. */
* Exception handling utility methods.
*/
public class ThrowingSupport { public class ThrowingSupport {
private ThrowingSupport() { private ThrowingSupport() {
@ -32,7 +31,8 @@ public class ThrowingSupport {
* @param msg Message to be set for rethrown exception * @param msg Message to be set for rethrown exception
* @param <E> Type of exception thrown * @param <E> Type of exception thrown
*/ */
public static <E extends Exception> void rethrowAsRuntimeException(ThrowingRunnable<E> fn, String msg) { public static <E extends Exception> void rethrowAsRuntimeException(
ThrowingRunnable<E> fn, String msg) {
try { try {
fn.run(); fn.run();
} catch (Exception e) { } catch (Exception e) {
@ -65,12 +65,12 @@ public class ThrowingSupport {
* @param <E> Type of exception thrown * @param <E> Type of exception thrown
* @return Result of supplier execution * @return Result of supplier execution
*/ */
public static <T, E extends Exception> T rethrowAsRuntimeException(ThrowingSupplier<T, E> fn, String msg) { public static <T, E extends Exception> T rethrowAsRuntimeException(
ThrowingSupplier<T, E> fn, String msg) {
try { try {
return fn.get(); return fn.get();
} catch (Exception e) { } catch (Exception e) {
throw new RuntimeException(msg, e); throw new RuntimeException(msg, e);
} }
} }
} }

View File

@ -1,59 +1,46 @@
package eu.dnetlib.dhp.model.mdstore;
import eu.dnetlib.dhp.utils.DHPUtils; package eu.dnetlib.dhp.model.mdstore;
import java.io.Serializable; import java.io.Serializable;
import eu.dnetlib.dhp.utils.DHPUtils;
/** /** This class models a record inside the new Metadata store collection on HDFS * */
* This class models a record inside the new Metadata store collection on HDFS *
*
*/
public class MetadataRecord implements Serializable { public class MetadataRecord implements Serializable {
/** /** The D-Net Identifier associated to the record */
* The D-Net Identifier associated to the record
*/
private String id; private String id;
/** /** The original Identifier of the record */
* The original Identifier of the record
*/
private String originalId; private String originalId;
/** The encoding of the record, should be JSON or XML */
/**
* The encoding of the record, should be JSON or XML
*/
private String encoding; private String encoding;
/** /**
* The information about the provenance of the record see @{@link Provenance} * The information about the provenance of the record see @{@link Provenance} for the model of this information
* for the model of this information
*/ */
private Provenance provenance; private Provenance provenance;
/** /** The content of the metadata */
* The content of the metadata
*/
private String body; private String body;
/** /** the date when the record has been stored */
* the date when the record has been stored
*/
private long dateOfCollection; private long dateOfCollection;
/** /** the date when the record has been stored */
* the date when the record has been stored
*/
private long dateOfTransformation; private long dateOfTransformation;
public MetadataRecord() { public MetadataRecord() {
this.dateOfCollection = System.currentTimeMillis(); this.dateOfCollection = System.currentTimeMillis();
} }
public MetadataRecord(String originalId, String encoding, Provenance provenance, String body, long dateOfCollection) { public MetadataRecord(
String originalId,
String encoding,
Provenance provenance,
String body,
long dateOfCollection) {
this.originalId = originalId; this.originalId = originalId;
this.encoding = encoding; this.encoding = encoding;
@ -71,7 +58,6 @@ public class MetadataRecord implements Serializable {
this.id = id; this.id = id;
} }
public String getOriginalId() { public String getOriginalId() {
return originalId; return originalId;
} }
@ -96,7 +82,6 @@ public class MetadataRecord implements Serializable {
this.provenance = provenance; this.provenance = provenance;
} }
public String getBody() { public String getBody() {
return body; return body;
} }
@ -127,7 +112,6 @@ public class MetadataRecord implements Serializable {
return false; return false;
} }
return ((MetadataRecord) o).getId().equalsIgnoreCase(id); return ((MetadataRecord) o).getId().equalsIgnoreCase(id);
} }
@Override @Override

View File

@ -1,27 +1,23 @@
package eu.dnetlib.dhp.model.mdstore; package eu.dnetlib.dhp.model.mdstore;
import java.io.Serializable; import java.io.Serializable;
/** /**
* @author Sandro La Bruzzo * @author Sandro La Bruzzo
* * <p>
* Provenace class models the provenance of the record in the metadataStore * Provenace class models the provenance of the record in the metadataStore It contains the identifier and the
* It contains the identifier and the name of the datasource that gives the * name of the datasource that gives the record
* record
*
*/ */
public class Provenance implements Serializable { public class Provenance implements Serializable {
private String datasourceId; private String datasourceId;
private String datasourceName; private String datasourceName;
private String nsPrefix; private String nsPrefix;
public Provenance() { public Provenance() {
} }
public Provenance(String datasourceId, String datasourceName, String nsPrefix) { public Provenance(String datasourceId, String datasourceName, String nsPrefix) {

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.parser.utility; package eu.dnetlib.dhp.parser.utility;
public class VtdException extends Exception { public class VtdException extends Exception {

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.parser.utility; package eu.dnetlib.dhp.parser.utility;
import java.util.ArrayList; import java.util.ArrayList;
@ -5,16 +6,14 @@ import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import com.ximpleware.AutoPilot; import com.ximpleware.AutoPilot;
import com.ximpleware.VTDNav; import com.ximpleware.VTDNav;
/** /** Created by sandro on 9/29/16. */
* Created by sandro on 9/29/16.
*/
public class VtdUtilityParser { public class VtdUtilityParser {
public static List<Node> getTextValuesWithAttributes(final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes) public static List<Node> getTextValuesWithAttributes(
final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
throws VtdException { throws VtdException {
final List<Node> results = new ArrayList<>(); final List<Node> results = new ArrayList<>();
try { try {
@ -39,7 +38,9 @@ public class VtdUtilityParser {
final Map<String, String> currentAttributes = new HashMap<>(); final Map<String, String> currentAttributes = new HashMap<>();
if (attributes != null) { if (attributes != null) {
attributes.forEach(attributeKey -> { attributes
.forEach(
attributeKey -> {
try { try {
int attr = vn.getAttrVal(attributeKey); int attr = vn.getAttrVal(attributeKey);
if (attr > -1) { if (attr > -1) {
@ -53,13 +54,15 @@ public class VtdUtilityParser {
return currentAttributes; return currentAttributes;
} }
public static List<String> getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath) throws VtdException { public static List<String> getTextValue(final AutoPilot ap, final VTDNav vn, final String xpath)
throws VtdException {
List<String> results = new ArrayList<>(); List<String> results = new ArrayList<>();
try { try {
ap.selectXPath(xpath); ap.selectXPath(xpath);
while (ap.evalXPath() != -1) { while (ap.evalXPath() != -1) {
int t = vn.getText(); int t = vn.getText();
if (t > -1) results.add(vn.toNormalizedString(t)); if (t > -1)
results.add(vn.toNormalizedString(t));
} }
return results; return results;
} catch (Exception e) { } catch (Exception e) {
@ -67,7 +70,8 @@ public class VtdUtilityParser {
} }
} }
public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath) throws VtdException { public static String getSingleValue(final AutoPilot ap, final VTDNav nav, final String xpath)
throws VtdException {
try { try {
ap.selectXPath(xpath); ap.selectXPath(xpath);
while (ap.evalXPath() != -1) { while (ap.evalXPath() != -1) {
@ -103,5 +107,4 @@ public class VtdUtilityParser {
this.attributes = attributes; this.attributes = attributes;
} }
} }
} }

View File

@ -1,11 +1,5 @@
package eu.dnetlib.dhp.utils;
import com.jayway.jsonpath.JsonPath; package eu.dnetlib.dhp.utils;
import net.minidev.json.JSONArray;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import java.io.ByteArrayInputStream; import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream; import java.io.ByteArrayOutputStream;
@ -14,12 +8,20 @@ import java.security.MessageDigest;
import java.util.zip.GZIPInputStream; import java.util.zip.GZIPInputStream;
import java.util.zip.GZIPOutputStream; import java.util.zip.GZIPOutputStream;
import org.apache.commons.codec.binary.Base64;
import org.apache.commons.codec.binary.Base64OutputStream;
import org.apache.commons.codec.binary.Hex;
import com.jayway.jsonpath.JsonPath;
import net.minidev.json.JSONArray;
public class DHPUtils { public class DHPUtils {
public static String md5(final String s) { public static String md5(final String s) {
try { try {
final MessageDigest md = MessageDigest.getInstance("MD5"); final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes("UTF-8")); md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest())); return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) { } catch (final Exception e) {
System.err.println("Error creating id"); System.err.println("Error creating id");
@ -32,7 +34,8 @@ public class DHPUtils {
} }
public static String compressString(final String input) { public static String compressString(final String input) {
try ( ByteArrayOutputStream out = new ByteArrayOutputStream(); Base64OutputStream b64os = new Base64OutputStream(out)) { try (ByteArrayOutputStream out = new ByteArrayOutputStream();
Base64OutputStream b64os = new Base64OutputStream(out)) {
GZIPOutputStream gzip = new GZIPOutputStream(b64os); GZIPOutputStream gzip = new GZIPOutputStream(b64os);
gzip.write(input.getBytes(StandardCharsets.UTF_8)); gzip.write(input.getBytes(StandardCharsets.UTF_8));
gzip.close(); gzip.close();
@ -42,11 +45,11 @@ public class DHPUtils {
} }
} }
public static String decompressString(final String input) { public static String decompressString(final String input) {
byte[] byteArray = Base64.decodeBase64(input.getBytes()); byte[] byteArray = Base64.decodeBase64(input.getBytes());
int len; int len;
try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray))); ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) { try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray)));
ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) {
byte[] buffer = new byte[1024]; byte[] buffer = new byte[1024];
while ((len = gis.read(buffer)) != -1) { while ((len = gis.read(buffer)) != -1) {
bos.write(buffer, 0, len); bos.write(buffer, 0, len);
@ -55,7 +58,6 @@ public class DHPUtils {
} catch (Exception e) { } catch (Exception e) {
return null; return null;
} }
} }
public static String getJPathString(final String jsonPath, final String json) { public static String getJPathString(final String jsonPath, final String json) {
@ -70,5 +72,4 @@ public class DHPUtils {
return ""; return "";
} }
} }
} }

View File

@ -1,10 +1,12 @@
package eu.dnetlib.dhp.utils; package eu.dnetlib.dhp.utils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import org.apache.commons.logging.Log; import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory; import org.apache.commons.logging.LogFactory;
import org.apache.cxf.jaxws.JaxWsProxyFactoryBean; import org.apache.cxf.jaxws.JaxWsProxyFactoryBean;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class ISLookupClientFactory { public class ISLookupClientFactory {
private static final Log log = LogFactory.getLog(ISLookupClientFactory.class); private static final Log log = LogFactory.getLog(ISLookupClientFactory.class);

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.utils.saxon; package eu.dnetlib.dhp.utils.saxon;
import net.sf.saxon.expr.XPathContext; import net.sf.saxon.expr.XPathContext;
@ -12,6 +13,7 @@ public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinit
public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension"; public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
public abstract String getName(); public abstract String getName();
public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException; public abstract Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException;
@Override @Override
@ -28,5 +30,4 @@ public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinit
} }
}; };
} }
} }

View File

@ -1,5 +1,11 @@
package eu.dnetlib.dhp.utils.saxon; package eu.dnetlib.dhp.utils.saxon;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.GregorianCalendar;
import net.sf.saxon.expr.XPathContext; import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Item; import net.sf.saxon.om.Item;
import net.sf.saxon.om.Sequence; import net.sf.saxon.om.Sequence;
@ -7,14 +13,11 @@ import net.sf.saxon.trans.XPathException;
import net.sf.saxon.value.SequenceType; import net.sf.saxon.value.SequenceType;
import net.sf.saxon.value.StringValue; import net.sf.saxon.value.StringValue;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Calendar;
import java.util.GregorianCalendar;
public class ExtractYear extends AbstractExtensionFunction { public class ExtractYear extends AbstractExtensionFunction {
private static final String[] dateFormats = { "yyyy-MM-dd", "yyyy/MM/dd" }; private static final String[] dateFormats = {
"yyyy-MM-dd", "yyyy/MM/dd"
};
@Override @Override
public String getName() { public String getName() {
@ -45,7 +48,9 @@ public class ExtractYear extends AbstractExtensionFunction {
@Override @Override
public SequenceType[] getArgumentTypes() { public SequenceType[] getArgumentTypes() {
return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; return new SequenceType[] {
SequenceType.OPTIONAL_ITEM
};
} }
@Override @Override
@ -60,7 +65,8 @@ public class ExtractYear extends AbstractExtensionFunction {
c.setTime(new SimpleDateFormat(format).parse(s)); c.setTime(new SimpleDateFormat(format).parse(s));
String year = String.valueOf(c.get(Calendar.YEAR)); String year = String.valueOf(c.get(Calendar.YEAR));
return year; return year;
} catch (ParseException e) {} } catch (ParseException e) {
}
} }
return ""; return "";
} }

View File

@ -1,20 +1,23 @@
package eu.dnetlib.dhp.utils.saxon; package eu.dnetlib.dhp.utils.saxon;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
import net.sf.saxon.expr.XPathContext; import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Sequence; import net.sf.saxon.om.Sequence;
import net.sf.saxon.trans.XPathException; import net.sf.saxon.trans.XPathException;
import net.sf.saxon.value.SequenceType; import net.sf.saxon.value.SequenceType;
import net.sf.saxon.value.StringValue; import net.sf.saxon.value.StringValue;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.Date;
public class NormalizeDate extends AbstractExtensionFunction { public class NormalizeDate extends AbstractExtensionFunction {
private static final String[] normalizeDateFormats = { "yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy" }; private static final String[] normalizeDateFormats = {
"yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy"
};
private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'"); private static final String normalizeOutFormat = "yyyy-MM-dd'T'hh:mm:ss'Z'";
@Override @Override
public String getName() { public String getName() {
@ -42,7 +45,9 @@ public class NormalizeDate extends AbstractExtensionFunction {
@Override @Override
public SequenceType[] getArgumentTypes() { public SequenceType[] getArgumentTypes() {
return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; return new SequenceType[] {
SequenceType.OPTIONAL_ITEM
};
} }
@Override @Override
@ -58,9 +63,9 @@ public class NormalizeDate extends AbstractExtensionFunction {
Date parse = new SimpleDateFormat(format).parse(date); Date parse = new SimpleDateFormat(format).parse(date);
String res = new SimpleDateFormat(normalizeOutFormat).format(parse); String res = new SimpleDateFormat(normalizeOutFormat).format(parse);
return res; return res;
} catch (ParseException e) {} } catch (ParseException e) {
}
} }
return ""; return "";
} }
} }

View File

@ -1,12 +1,14 @@
package eu.dnetlib.dhp.utils.saxon; package eu.dnetlib.dhp.utils.saxon;
import org.apache.commons.lang3.StringUtils;
import net.sf.saxon.expr.XPathContext; import net.sf.saxon.expr.XPathContext;
import net.sf.saxon.om.Item; import net.sf.saxon.om.Item;
import net.sf.saxon.om.Sequence; import net.sf.saxon.om.Sequence;
import net.sf.saxon.trans.XPathException; import net.sf.saxon.trans.XPathException;
import net.sf.saxon.value.SequenceType; import net.sf.saxon.value.SequenceType;
import net.sf.saxon.value.StringValue; import net.sf.saxon.value.StringValue;
import org.apache.commons.lang3.StringUtils;
public class PickFirst extends AbstractExtensionFunction { public class PickFirst extends AbstractExtensionFunction {
@ -49,12 +51,13 @@ public class PickFirst extends AbstractExtensionFunction {
@Override @Override
public SequenceType[] getArgumentTypes() { public SequenceType[] getArgumentTypes() {
return new SequenceType[] { SequenceType.OPTIONAL_ITEM }; return new SequenceType[] {
SequenceType.OPTIONAL_ITEM
};
} }
@Override @Override
public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) { public SequenceType getResultType(SequenceType[] suppliedArgumentTypes) {
return SequenceType.SINGLE_STRING; return SequenceType.SINGLE_STRING;
} }
} }

View File

@ -1,17 +1,20 @@
package eu.dnetlib.dhp.utils.saxon; package eu.dnetlib.dhp.utils.saxon;
import net.sf.saxon.Configuration; import java.io.StringReader;
import net.sf.saxon.TransformerFactoryImpl;
import javax.xml.transform.Transformer; import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException; import javax.xml.transform.TransformerException;
import javax.xml.transform.stream.StreamSource; import javax.xml.transform.stream.StreamSource;
import java.io.StringReader;
import net.sf.saxon.Configuration;
import net.sf.saxon.TransformerFactoryImpl;
public class SaxonTransformerFactory { public class SaxonTransformerFactory {
/** /**
* Creates the index record transformer from the given XSLT * Creates the index record transformer from the given XSLT
*
* @param xslt * @param xslt
* @return * @return
* @throws TransformerException * @throws TransformerException
@ -26,5 +29,4 @@ public class SaxonTransformerFactory {
return factory.newTransformer(new StreamSource(new StringReader(xslt))); return factory.newTransformer(new StreamSource(new StringReader(xslt)));
} }
} }

View File

@ -1,11 +1,12 @@
package eu.dnetlib.message;
import com.fasterxml.jackson.core.JsonProcessingException; package eu.dnetlib.message;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.IOException; import java.io.IOException;
import java.util.Map; import java.util.Map;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class Message { public class Message {
private String workflowId; private String workflowId;
@ -16,19 +17,12 @@ public class Message {
private Map<String, String> body; private Map<String, String> body;
public static Message fromJson(final String json) throws IOException { public static Message fromJson(final String json) throws IOException {
final ObjectMapper jsonMapper = new ObjectMapper(); final ObjectMapper jsonMapper = new ObjectMapper();
return jsonMapper.readValue(json, Message.class); return jsonMapper.readValue(json, Message.class);
} }
public Message() { public Message() {
} }
public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) { public Message(String workflowId, String jobName, MessageType type, Map<String, String> body) {

View File

@ -1,19 +1,19 @@
package eu.dnetlib.message; package eu.dnetlib.message;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
import com.rabbitmq.client.AMQP; import com.rabbitmq.client.AMQP;
import com.rabbitmq.client.Channel; import com.rabbitmq.client.Channel;
import com.rabbitmq.client.DefaultConsumer; import com.rabbitmq.client.DefaultConsumer;
import com.rabbitmq.client.Envelope; import com.rabbitmq.client.Envelope;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.concurrent.LinkedBlockingQueue;
public class MessageConsumer extends DefaultConsumer { public class MessageConsumer extends DefaultConsumer {
final LinkedBlockingQueue<Message> queueMessages; final LinkedBlockingQueue<Message> queueMessages;
/** /**
* Constructs a new instance and records its association to the passed-in channel. * Constructs a new instance and records its association to the passed-in channel.
* *
@ -25,9 +25,10 @@ public class MessageConsumer extends DefaultConsumer {
this.queueMessages = queueMessages; this.queueMessages = queueMessages;
} }
@Override @Override
public void handleDelivery(String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body) throws IOException { public void handleDelivery(
String consumerTag, Envelope envelope, AMQP.BasicProperties properties, byte[] body)
throws IOException {
final String json = new String(body, StandardCharsets.UTF_8); final String json = new String(body, StandardCharsets.UTF_8);
Message message = Message.fromJson(json); Message message = Message.fromJson(json);
try { try {

View File

@ -1,9 +1,5 @@
package eu.dnetlib.message;
import com.rabbitmq.client.Channel; package eu.dnetlib.message;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
import sun.rmi.runtime.Log;
import java.io.IOException; import java.io.IOException;
import java.util.HashMap; import java.util.HashMap;
@ -11,6 +7,10 @@ import java.util.Map;
import java.util.concurrent.LinkedBlockingQueue; import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.TimeoutException; import java.util.concurrent.TimeoutException;
import com.rabbitmq.client.Channel;
import com.rabbitmq.client.Connection;
import com.rabbitmq.client.ConnectionFactory;
public class MessageManager { public class MessageManager {
private final String messageHost; private final String messageHost;
@ -21,23 +21,32 @@ public class MessageManager {
private Connection connection; private Connection connection;
private Map<String , Channel> channels = new HashMap<>(); private final Map<String, Channel> channels = new HashMap<>();
private boolean durable; private boolean durable;
private boolean autodelete; private boolean autodelete;
final private LinkedBlockingQueue<Message> queueMessages; private final LinkedBlockingQueue<Message> queueMessages;
public MessageManager(String messageHost, String username, String password, final LinkedBlockingQueue<Message> queueMessages) { public MessageManager(
String messageHost,
String username,
String password,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages; this.queueMessages = queueMessages;
this.messageHost = messageHost; this.messageHost = messageHost;
this.username = username; this.username = username;
this.password = password; this.password = password;
} }
public MessageManager(
public MessageManager(String messageHost, String username, String password, boolean durable, boolean autodelete, final LinkedBlockingQueue<Message> queueMessages) { String messageHost,
String username,
String password,
boolean durable,
boolean autodelete,
final LinkedBlockingQueue<Message> queueMessages) {
this.queueMessages = queueMessages; this.queueMessages = queueMessages;
this.messageHost = messageHost; this.messageHost = messageHost;
this.username = username; this.username = username;
@ -55,7 +64,12 @@ public class MessageManager {
return factory.newConnection(); return factory.newConnection();
} }
private Channel createChannel(final Connection connection, final String queueName, final boolean durable, final boolean autodelete ) throws Exception { private Channel createChannel(
final Connection connection,
final String queueName,
final boolean durable,
final boolean autodelete)
throws Exception {
Map<String, Object> args = new HashMap<>(); Map<String, Object> args = new HashMap<>();
args.put("x-message-ttl", 10000); args.put("x-message-ttl", 10000);
Channel channel = connection.createChannel(); Channel channel = connection.createChannel();
@ -63,7 +77,8 @@ public class MessageManager {
return channel; return channel;
} }
private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete) throws Exception { private Channel getOrCreateChannel(final String queueName, boolean durable, boolean autodelete)
throws Exception {
if (channels.containsKey(queueName)) { if (channels.containsKey(queueName)) {
return channels.get(queueName); return channels.get(queueName);
} }
@ -75,10 +90,11 @@ public class MessageManager {
return channels.get(queueName); return channels.get(queueName);
} }
public void close() throws IOException { public void close() throws IOException {
channels.values().forEach(ch-> { channels
.values()
.forEach(
ch -> {
try { try {
ch.close(); ch.close();
} catch (Exception e) { } catch (Exception e) {
@ -99,7 +115,9 @@ public class MessageManager {
} }
} }
public boolean sendMessage(final Message message, String queueName, boolean durable_var, boolean autodelete_var) throws Exception { public boolean sendMessage(
final Message message, String queueName, boolean durable_var, boolean autodelete_var)
throws Exception {
try { try {
Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var); Channel channel = getOrCreateChannel(queueName, durable_var, autodelete_var);
channel.basicPublish("", queueName, null, message.toString().getBytes()); channel.basicPublish("", queueName, null, message.toString().getBytes());
@ -109,7 +127,8 @@ public class MessageManager {
} }
} }
public void startConsumingMessage(final String queueName, final boolean durable, final boolean autodelete) throws Exception{ public void startConsumingMessage(
final String queueName, final boolean durable, final boolean autodelete) throws Exception {
Channel channel = createChannel(createConnection(), queueName, durable, autodelete); Channel channel = createChannel(createConnection(), queueName, durable, autodelete);
channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages)); channel.basicConsume(queueName, false, new MessageConsumer(channel, queueMessages));

View File

@ -1,8 +1,6 @@
package eu.dnetlib.message; package eu.dnetlib.message;
public enum MessageType { public enum MessageType {
ONGOING, REPORT
ONGOING,
REPORT
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.scholexplorer.relation; package eu.dnetlib.scholexplorer.relation;
import java.io.Serializable; import java.io.Serializable;

View File

@ -1,11 +1,13 @@
package eu.dnetlib.scholexplorer.relation;
import com.fasterxml.jackson.databind.ObjectMapper; package eu.dnetlib.scholexplorer.relation;
import org.apache.commons.io.IOUtils;
import java.io.Serializable; import java.io.Serializable;
import java.util.HashMap; import java.util.HashMap;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class RelationMapper extends HashMap<String, RelInfo> implements Serializable { public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
public static RelationMapper load() throws Exception { public static RelationMapper load() throws Exception {
@ -15,5 +17,4 @@ public class RelationMapper extends HashMap<String,RelInfo > implements Serializ
ObjectMapper mapper = new ObjectMapper(); ObjectMapper mapper = new ObjectMapper();
return mapper.readValue(json, RelationMapper.class); return mapper.readValue(json, RelationMapper.class);
} }
} }

View File

@ -1,29 +1,46 @@
package eu.dnetlib.dhp.application;
import org.apache.commons.io.IOUtils; package eu.dnetlib.dhp.application;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertEquals; import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull; import static org.junit.jupiter.api.Assertions.assertNotNull;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
public class ArgumentApplicationParserTest { public class ArgumentApplicationParserTest {
@Test @Test
public void testParseParameter() throws Exception { public void testParseParameter() throws Exception {
final String jsonConfiguration = IOUtils.toString(this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json")); final String jsonConfiguration = IOUtils
.toString(
this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json"));
assertNotNull(jsonConfiguration); assertNotNull(jsonConfiguration);
ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(new String[]{"-p", "value0", parser
"-a", "value1", .parseArgument(
"-n", "value2", new String[] {
"-u", "value3", "-p",
"-ru", "value4", "value0",
"-rp", "value5", "-a",
"-rh", "value6", "value1",
"-ro", "value7", "-n",
"-rr", "value8", "value2",
"-w", "value9", "-u",
"-cc", ArgumentApplicationParser.compressArgument(jsonConfiguration) "value3",
"-ru",
"value4",
"-rp",
"value5",
"-rh",
"value6",
"-ro",
"value7",
"-rr",
"value8",
"-w",
"value9",
"-cc",
ArgumentApplicationParser.compressArgument(jsonConfiguration)
}); });
assertNotNull(parser.get("hdfsPath")); assertNotNull(parser.get("hdfsPath"));
assertNotNull(parser.get("apidescriptor")); assertNotNull(parser.get("apidescriptor"));
@ -47,10 +64,4 @@ public class ArgumentApplicationParserTest {
assertEquals("value9", parser.get("workflowId")); assertEquals("value9", parser.get("workflowId"));
assertEquals(jsonConfiguration, parser.get("ccCoco")); assertEquals(jsonConfiguration, parser.get("ccCoco"));
} }
} }

View File

@ -1,9 +1,7 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import org.apache.hadoop.conf.Configuration; import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
import java.io.IOException; import java.io.IOException;
import java.nio.file.Files; import java.nio.file.Files;
@ -12,7 +10,10 @@ import java.util.Arrays;
import java.util.List; import java.util.List;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import static org.junit.jupiter.api.Assertions.*; import org.apache.hadoop.conf.Configuration;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.io.TempDir;
public class HdfsSupportTest { public class HdfsSupportTest {
@ -22,8 +23,7 @@ public class HdfsSupportTest {
@Test @Test
public void shouldThrowARuntimeExceptionOnError() { public void shouldThrowARuntimeExceptionOnError() {
// when // when
assertThrows(RuntimeException.class, () -> assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
HdfsSupport.remove(null, new Configuration()));
} }
@Test @Test
@ -54,8 +54,7 @@ public class HdfsSupportTest {
@Test @Test
public void shouldThrowARuntimeExceptionOnError() { public void shouldThrowARuntimeExceptionOnError() {
// when // when
assertThrows(RuntimeException.class, () -> assertThrows(RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration()));
HdfsSupport.listFiles(null, new Configuration()));
} }
@Test @Test
@ -68,8 +67,11 @@ public class HdfsSupportTest {
// then // then
assertEquals(2, paths.size()); assertEquals(2, paths.size());
List<String> expecteds = Arrays.stream(new String[]{subDir1.toString(), subDir2.toString()}) List<String> expecteds = Arrays.stream(new String[] {
.sorted().collect(Collectors.toList()); subDir1.toString(), subDir2.toString()
})
.sorted()
.collect(Collectors.toList());
List<String> actuals = paths.stream().sorted().collect(Collectors.toList()); List<String> actuals = paths.stream().sorted().collect(Collectors.toList());
assertTrue(actuals.get(0).contains(expecteds.get(0))); assertTrue(actuals.get(0).contains(expecteds.get(0)));
assertTrue(actuals.get(1).contains(expecteds.get(1))); assertTrue(actuals.get(1).contains(expecteds.get(1)));

View File

@ -1,14 +1,16 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer; import static org.mockito.Mockito.*;
import java.util.function.Function;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.sql.SparkSession; import org.apache.spark.sql.SparkSession;
import org.junit.jupiter.api.Nested; import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
import java.util.function.Function; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.ThrowingConsumer;
import static org.mockito.Mockito.*;
public class SparkSessionSupportTest { public class SparkSessionSupportTest {
@ -16,7 +18,8 @@ public class SparkSessionSupportTest {
class RunWithSparkSession { class RunWithSparkSession {
@Test @Test
public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged() throws Exception { public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
throws Exception {
// given // given
SparkSession spark = mock(SparkSession.class); SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class); SparkConf conf = mock(SparkConf.class);
@ -34,7 +37,8 @@ public class SparkSessionSupportTest {
} }
@Test @Test
public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged() throws Exception { public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
throws Exception {
// given // given
SparkSession spark = mock(SparkSession.class); SparkSession spark = mock(SparkSession.class);
SparkConf conf = mock(SparkConf.class); SparkConf conf = mock(SparkConf.class);

View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.model.mdstore; package eu.dnetlib.dhp.model.mdstore;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertTrue; import static org.junit.jupiter.api.Assertions.assertTrue;
import org.junit.jupiter.api.Test;
public class MetadataRecordTest { public class MetadataRecordTest {
@Test @Test

View File

@ -1,12 +1,13 @@
package eu.dnetlib.message; package eu.dnetlib.message;
import org.junit.jupiter.api.Test; import static org.junit.jupiter.api.Assertions.*;
import java.io.IOException; import java.io.IOException;
import java.util.HashMap; import java.util.HashMap;
import java.util.Map; import java.util.Map;
import static org.junit.jupiter.api.Assertions.*; import org.junit.jupiter.api.Test;
public class MessageTest { public class MessageTest {
@ -46,10 +47,5 @@ public class MessageTest {
m.setBody(body); m.setBody(body);
assertEquals(expectedJson, m.toString()); assertEquals(expectedJson, m.toString());
} }
} }

View File

@ -1,8 +1,8 @@
package eu.dnetlib.scholexplorer.relation; package eu.dnetlib.scholexplorer.relation;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
public class RelationMapperTest { public class RelationMapperTest {
@Test @Test
@ -10,6 +10,5 @@ public class RelationMapperTest {
RelationMapper relationMapper = RelationMapper.load(); RelationMapper relationMapper = RelationMapper.load();
relationMapper.keySet().forEach(System.out::println); relationMapper.keySet().forEach(System.out::println);
} }
} }

View File

@ -12,7 +12,7 @@
<artifactId>dhp-schemas</artifactId> <artifactId>dhp-schemas</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<description>This module contains common schema classes meant to be used across the dnet-hadoop submodules</description>
<dependencies> <dependencies>

View File

@ -1,10 +1,12 @@
package eu.dnetlib.dhp.schema.action; package eu.dnetlib.dhp.schema.action;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.io.Serializable; import java.io.Serializable;
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
import eu.dnetlib.dhp.schema.oaf.Oaf;
@JsonDeserialize(using = AtomicActionDeserializer.class) @JsonDeserialize(using = AtomicActionDeserializer.class)
public class AtomicAction<T extends Oaf> implements Serializable { public class AtomicAction<T extends Oaf> implements Serializable {

View File

@ -1,19 +1,22 @@
package eu.dnetlib.dhp.schema.action; package eu.dnetlib.dhp.schema.action;
import java.io.IOException;
import com.fasterxml.jackson.core.JsonParser; import com.fasterxml.jackson.core.JsonParser;
import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationContext; import com.fasterxml.jackson.databind.DeserializationContext;
import com.fasterxml.jackson.databind.JsonDeserializer; import com.fasterxml.jackson.databind.JsonDeserializer;
import com.fasterxml.jackson.databind.JsonNode; import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import java.io.IOException; import eu.dnetlib.dhp.schema.oaf.Oaf;
public class AtomicActionDeserializer extends JsonDeserializer { public class AtomicActionDeserializer extends JsonDeserializer {
@Override @Override
public Object deserialize(JsonParser jp, DeserializationContext ctxt) throws IOException, JsonProcessingException { public Object deserialize(JsonParser jp, DeserializationContext ctxt)
throws IOException {
JsonNode node = jp.getCodec().readTree(jp); JsonNode node = jp.getCodec().readTree(jp);
String classTag = node.get("clazz").asText(); String classTag = node.get("clazz").asText();
JsonNode payload = node.get("payload"); JsonNode payload = node.get("payload");

View File

@ -1,16 +1,15 @@
package eu.dnetlib.dhp.schema.common; package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
/** /** Actual entity types in the Graph */
* Actual entity types in the Graph
*/
public enum EntityType { public enum EntityType {
publication, dataset, otherresearchproduct, software, datasource, organization, project; publication, dataset, otherresearchproduct, software, datasource, organization, project;
/** /**
* Resolves the EntityType, given the relative class name * Resolves the EntityType, given the relative class name
*
* @param clazz the given class name * @param clazz the given class name
* @param <T> actual OafEntity subclass * @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class * @return the EntityType associated to the given class
@ -19,5 +18,4 @@ public enum EntityType {
return EntityType.valueOf(clazz.getSimpleName().toLowerCase()); return EntityType.valueOf(clazz.getSimpleName().toLowerCase());
} }
} }

View File

@ -1,9 +1,7 @@
package eu.dnetlib.dhp.schema.common; package eu.dnetlib.dhp.schema.common;
/** /** Main entity types in the Graph */
* Main entity types in the Graph
*/
public enum MainEntityType { public enum MainEntityType {
result, datasource, organization, project result, datasource, organization, project
} }

View File

@ -0,0 +1,41 @@
package eu.dnetlib.dhp.schema.common;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
public class ModelConstants {
public static final String DNET_RESULT_TYPOLOGIES = "dnet:result_typologies";
public static final String DATASET_RESULTTYPE_CLASSID = "dataset";
public static final String PUBLICATION_RESULTTYPE_CLASSID = "publication";
public static final String SOFTWARE_RESULTTYPE_CLASSID = "software";
public static final String ORP_RESULTTYPE_CLASSID = "other";
public static Qualifier PUBLICATION_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier DATASET_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier SOFTWARE_DEFAULT_RESULTTYPE = new Qualifier();
public static Qualifier ORP_DEFAULT_RESULTTYPE = new Qualifier();
static {
PUBLICATION_DEFAULT_RESULTTYPE.setClassid(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setClassname(PUBLICATION_RESULTTYPE_CLASSID);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
PUBLICATION_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setClassid(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setClassname(DATASET_RESULTTYPE_CLASSID);
DATASET_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
DATASET_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setClassid(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setClassname(SOFTWARE_RESULTTYPE_CLASSID);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
SOFTWARE_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setClassid(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setClassname(ORP_RESULTTYPE_CLASSID);
ORP_DEFAULT_RESULTTYPE.setSchemeid(DNET_RESULT_TYPOLOGIES);
ORP_DEFAULT_RESULTTYPE.setSchemename(DNET_RESULT_TYPOLOGIES);
}
}

View File

@ -1,19 +1,19 @@
package eu.dnetlib.dhp.schema.common; package eu.dnetlib.dhp.schema.common;
import java.util.Map;
import java.util.Optional;
import java.util.function.Function;
import com.google.common.collect.Maps; import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.*; import eu.dnetlib.dhp.schema.oaf.*;
import java.util.Map; /** Oaf model utility methods. */
/**
* Oaf model utility methods.
*/
public class ModelSupport { public class ModelSupport {
/** /** Defines the mapping between the actual entity type and the main entity type */
* Defines the mapping between the actual entity type and the main entity type private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
*/
private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
static { static {
entityMapping.put(EntityType.publication, MainEntityType.result); entityMapping.put(EntityType.publication, MainEntityType.result);
@ -28,7 +28,7 @@ public class ModelSupport {
/** /**
* Defines the mapping between the actual entity types and the relative classes implementing them * Defines the mapping between the actual entity types and the relative classes implementing them
*/ */
public final static Map<EntityType, Class> entityTypes = Maps.newHashMap(); public static final Map<EntityType, Class> entityTypes = Maps.newHashMap();
static { static {
entityTypes.put(EntityType.datasource, Datasource.class); entityTypes.put(EntityType.datasource, Datasource.class);
@ -40,7 +40,7 @@ public class ModelSupport {
entityTypes.put(EntityType.publication, Publication.class); entityTypes.put(EntityType.publication, Publication.class);
} }
public final static Map<String, Class> oafTypes = Maps.newHashMap(); public static final Map<String, Class> oafTypes = Maps.newHashMap();
static { static {
oafTypes.put("datasource", Datasource.class); oafTypes.put("datasource", Datasource.class);
@ -67,7 +67,8 @@ public class ModelSupport {
* @param <Y> Superclass type * @param <Y> Superclass type
* @return True if X is a subclass of Y * @return True if X is a subclass of Y
*/ */
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(X subClazzObject, Y superClazzObject) { public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Y superClazzObject) {
return isSubClass(subClazzObject.getClass(), superClazzObject.getClass()); return isSubClass(subClazzObject.getClass(), superClazzObject.getClass());
} }
@ -80,7 +81,8 @@ public class ModelSupport {
* @param <Y> Superclass type * @param <Y> Superclass type
* @return True if X is a subclass of Y * @return True if X is a subclass of Y
*/ */
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(X subClazzObject, Class<Y> superClazz) { public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
X subClazzObject, Class<Y> superClazz) {
return isSubClass(subClazzObject.getClass(), superClazz); return isSubClass(subClazzObject.getClass(), superClazz);
} }
@ -93,7 +95,8 @@ public class ModelSupport {
* @param <Y> Superclass type * @param <Y> Superclass type
* @return True if X is a subclass of Y * @return True if X is a subclass of Y
*/ */
public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(Class<X> subClazz, Class<Y> superClazz) { public static <X extends Oaf, Y extends Oaf> Boolean isSubClass(
Class<X> subClazz, Class<Y> superClazz) {
return superClazz.isAssignableFrom(subClazz); return superClazz.isAssignableFrom(subClazz);
} }
@ -143,9 +146,60 @@ public class ModelSupport {
} }
public static String getScheme(final String sourceType, final String targetType) { public static String getScheme(final String sourceType, final String targetType) {
return String.format(schemeTemplate, return String
.format(
schemeTemplate,
entityMapping.get(EntityType.valueOf(sourceType)).name(), entityMapping.get(EntityType.valueOf(sourceType)).name(),
entityMapping.get(EntityType.valueOf(targetType)).name()); entityMapping.get(EntityType.valueOf(targetType)).name());
} }
public static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional
.ofNullable(r.getSource())
.map(
source -> Optional
.ofNullable(r.getTarget())
.map(
target -> Optional
.ofNullable(r.getRelType())
.map(
relType -> Optional
.ofNullable(r.getSubRelType())
.map(
subRelType -> Optional
.ofNullable(r.getRelClass())
.map(
relClass -> String
.join(
source,
target,
relType,
subRelType,
relClass))
.orElse(
String
.join(
source,
target,
relType,
subRelType)))
.orElse(String.join(source, target, relType)))
.orElse(String.join(source, target)))
.orElse(source))
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
}
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -68,15 +69,17 @@ public class Author implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
Author author = (Author) o; Author author = (Author) o;
return Objects.equals(fullname, author.fullname) && return Objects.equals(fullname, author.fullname)
Objects.equals(name, author.name) && && Objects.equals(name, author.name)
Objects.equals(surname, author.surname) && && Objects.equals(surname, author.surname)
Objects.equals(rank, author.rank) && && Objects.equals(rank, author.rank)
Objects.equals(pid, author.pid) && && Objects.equals(pid, author.pid)
Objects.equals(affiliation, author.affiliation); && Objects.equals(affiliation, author.affiliation);
} }
@Override @Override

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.util.Objects; import java.util.Objects;
@ -16,9 +17,12 @@ public class Country extends Qualifier {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (!super.equals(o)) return false; if (o == null || getClass() != o.getClass())
return false;
if (!super.equals(o))
return false;
Country country = (Country) o; Country country = (Country) o;
return Objects.equals(dataInfo, country.dataInfo); return Objects.equals(dataInfo, country.dataInfo);
} }

View File

@ -1,7 +1,7 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List;
import java.util.Objects; import java.util.Objects;
public class DataInfo implements Serializable { public class DataInfo implements Serializable {
@ -13,7 +13,6 @@ public class DataInfo implements Serializable {
private String inferenceprovenance; private String inferenceprovenance;
private Qualifier provenanceaction; private Qualifier provenanceaction;
public Boolean getInvisible() { public Boolean getInvisible() {
return invisible; return invisible;
} }
@ -64,19 +63,23 @@ public class DataInfo implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
DataInfo dataInfo = (DataInfo) o; DataInfo dataInfo = (DataInfo) o;
return Objects.equals(invisible, dataInfo.invisible) && return Objects.equals(invisible, dataInfo.invisible)
Objects.equals(inferred, dataInfo.inferred) && && Objects.equals(inferred, dataInfo.inferred)
Objects.equals(deletedbyinference, dataInfo.deletedbyinference) && && Objects.equals(deletedbyinference, dataInfo.deletedbyinference)
Objects.equals(trust, dataInfo.trust) && && Objects.equals(trust, dataInfo.trust)
Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance) && && Objects.equals(inferenceprovenance, dataInfo.inferenceprovenance)
Objects.equals(provenanceaction, dataInfo.provenanceaction); && Objects.equals(provenanceaction, dataInfo.provenanceaction);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction); return Objects
.hash(
invisible, inferred, deletedbyinference, trust, inferenceprovenance, provenanceaction);
} }
} }

View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Dataset extends Result implements Serializable { public class Dataset extends Result implements Serializable {
@ -20,6 +22,10 @@ public class Dataset extends Result implements Serializable {
private List<GeoLocation> geolocation; private List<GeoLocation> geolocation;
public Dataset() {
setResulttype(ModelConstants.DATASET_DEFAULT_RESULTTYPE);
}
public Field<String> getStoragedate() { public Field<String> getStoragedate() {
return storagedate; return storagedate;
} }
@ -94,32 +100,16 @@ public class Dataset extends Result implements Serializable {
version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version; version = d.getVersion() != null && compareTrust(this, e) < 0 ? d.getVersion() : version;
lastmetadataupdate= d.getLastmetadataupdate() != null && compareTrust(this, e)<0? d.getLastmetadataupdate() :lastmetadataupdate; lastmetadataupdate = d.getLastmetadataupdate() != null && compareTrust(this, e) < 0
? d.getLastmetadataupdate()
: lastmetadataupdate;
metadataversionnumber= d.getMetadataversionnumber() != null && compareTrust(this, e)<0? d.getMetadataversionnumber() : metadataversionnumber; metadataversionnumber = d.getMetadataversionnumber() != null && compareTrust(this, e) < 0
? d.getMetadataversionnumber()
: metadataversionnumber;
geolocation = mergeLists(geolocation, d.getGeolocation()); geolocation = mergeLists(geolocation, d.getGeolocation());
mergeOAFDataInfo(d); mergeOAFDataInfo(d);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Dataset dataset = (Dataset) o;
return Objects.equals(storagedate, dataset.storagedate) &&
Objects.equals(device, dataset.device) &&
Objects.equals(size, dataset.size) &&
Objects.equals(version, dataset.version) &&
Objects.equals(lastmetadataupdate, dataset.lastmetadataupdate) &&
Objects.equals(metadataversionnumber, dataset.metadataversionnumber) &&
Objects.equals(geolocation, dataset.geolocation);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), storagedate, device, size, version, lastmetadataupdate, metadataversionnumber, geolocation);
}
} }

View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Datasource extends OafEntity implements Serializable { public class Datasource extends OafEntity implements Serializable {
@ -373,55 +373,95 @@ public class Datasource extends OafEntity implements Serializable {
Datasource d = (Datasource) e; Datasource d = (Datasource) e;
datasourcetype = d.getDatasourcetype() != null && compareTrust(this, e)<0? d.getDatasourcetype() : datasourcetype; datasourcetype = d.getDatasourcetype() != null && compareTrust(this, e) < 0
openairecompatibility = d.getOpenairecompatibility() != null && compareTrust(this, e)<0? d.getOpenairecompatibility() : openairecompatibility; ? d.getDatasourcetype()
officialname = d.getOfficialname() != null && compareTrust(this, e)<0? d.getOfficialname() : officialname; : datasourcetype;
openairecompatibility = d.getOpenairecompatibility() != null && compareTrust(this, e) < 0
? d.getOpenairecompatibility()
: openairecompatibility;
officialname = d.getOfficialname() != null && compareTrust(this, e) < 0
? d.getOfficialname()
: officialname;
englishname = d.getEnglishname() != null && compareTrust(this, e) < 0 ? d.getEnglishname() : officialname; englishname = d.getEnglishname() != null && compareTrust(this, e) < 0 ? d.getEnglishname() : officialname;
websiteurl = d.getWebsiteurl() != null && compareTrust(this, e) < 0 ? d.getWebsiteurl() : websiteurl; websiteurl = d.getWebsiteurl() != null && compareTrust(this, e) < 0 ? d.getWebsiteurl() : websiteurl;
logourl = d.getLogourl() != null && compareTrust(this, e) < 0 ? d.getLogourl() : getLogourl(); logourl = d.getLogourl() != null && compareTrust(this, e) < 0 ? d.getLogourl() : getLogourl();
contactemail = d.getContactemail() != null && compareTrust(this, e)<0? d.getContactemail() : contactemail; contactemail = d.getContactemail() != null && compareTrust(this, e) < 0
namespaceprefix = d.getNamespaceprefix() != null && compareTrust(this, e)<0? d.getNamespaceprefix() : namespaceprefix; ? d.getContactemail()
: contactemail;
namespaceprefix = d.getNamespaceprefix() != null && compareTrust(this, e) < 0
? d.getNamespaceprefix()
: namespaceprefix;
latitude = d.getLatitude() != null && compareTrust(this, e) < 0 ? d.getLatitude() : latitude; latitude = d.getLatitude() != null && compareTrust(this, e) < 0 ? d.getLatitude() : latitude;
longitude = d.getLongitude() != null && compareTrust(this, e) < 0 ? d.getLongitude() : longitude; longitude = d.getLongitude() != null && compareTrust(this, e) < 0 ? d.getLongitude() : longitude;
dateofvalidation = d.getDateofvalidation() != null && compareTrust(this, e)<0? d.getDateofvalidation() : dateofvalidation; dateofvalidation = d.getDateofvalidation() != null && compareTrust(this, e) < 0
? d.getDateofvalidation()
: dateofvalidation;
description = d.getDescription() != null && compareTrust(this, e) < 0 ? d.getDescription() : description; description = d.getDescription() != null && compareTrust(this, e) < 0 ? d.getDescription() : description;
subjects = mergeLists(subjects, d.getSubjects()); subjects = mergeLists(subjects, d.getSubjects());
// opendoar specific fields (od*) // opendoar specific fields (od*)
odnumberofitems = d.getOdnumberofitems() != null && compareTrust(this, e)<0? d.getOdnumberofitems() : odnumberofitems; odnumberofitems = d.getOdnumberofitems() != null && compareTrust(this, e) < 0
odnumberofitemsdate = d.getOdnumberofitemsdate() != null && compareTrust(this, e)<0? d.getOdnumberofitemsdate() : odnumberofitemsdate; ? d.getOdnumberofitems()
: odnumberofitems;
odnumberofitemsdate = d.getOdnumberofitemsdate() != null && compareTrust(this, e) < 0
? d.getOdnumberofitemsdate()
: odnumberofitemsdate;
odpolicies = d.getOdpolicies() != null && compareTrust(this, e) < 0 ? d.getOdpolicies() : odpolicies; odpolicies = d.getOdpolicies() != null && compareTrust(this, e) < 0 ? d.getOdpolicies() : odpolicies;
odlanguages = mergeLists(odlanguages, d.getOdlanguages()); odlanguages = mergeLists(odlanguages, d.getOdlanguages());
odcontenttypes = mergeLists(odcontenttypes, d.getOdcontenttypes()); odcontenttypes = mergeLists(odcontenttypes, d.getOdcontenttypes());
accessinfopackage = mergeLists(accessinfopackage, d.getAccessinfopackage()); accessinfopackage = mergeLists(accessinfopackage, d.getAccessinfopackage());
// re3data fields // re3data fields
releasestartdate = d.getReleasestartdate() != null && compareTrust(this, e)<0? d.getReleasestartdate() : releasestartdate; releasestartdate = d.getReleasestartdate() != null && compareTrust(this, e) < 0
releaseenddate = d.getReleaseenddate() != null && compareTrust(this, e)<0? d.getReleaseenddate() : releaseenddate; ? d.getReleasestartdate()
missionstatementurl = d.getMissionstatementurl() != null && compareTrust(this, e)<0? d.getMissionstatementurl() : missionstatementurl; : releasestartdate;
dataprovider = d.getDataprovider() != null && compareTrust(this, e)<0? d.getDataprovider() : dataprovider; releaseenddate = d.getReleaseenddate() != null && compareTrust(this, e) < 0
serviceprovider = d.getServiceprovider() != null && compareTrust(this, e)<0? d.getServiceprovider() : serviceprovider; ? d.getReleaseenddate()
: releaseenddate;
missionstatementurl = d.getMissionstatementurl() != null && compareTrust(this, e) < 0
? d.getMissionstatementurl()
: missionstatementurl;
dataprovider = d.getDataprovider() != null && compareTrust(this, e) < 0
? d.getDataprovider()
: dataprovider;
serviceprovider = d.getServiceprovider() != null && compareTrust(this, e) < 0
? d.getServiceprovider()
: serviceprovider;
// {open, restricted or closed} // {open, restricted or closed}
databaseaccesstype = d.getDatabaseaccesstype() != null && compareTrust(this, e)<0? d.getDatabaseaccesstype() : databaseaccesstype; databaseaccesstype = d.getDatabaseaccesstype() != null && compareTrust(this, e) < 0
? d.getDatabaseaccesstype()
: databaseaccesstype;
// {open, restricted or closed} // {open, restricted or closed}
datauploadtype = d.getDatauploadtype() != null && compareTrust(this, e)<0? d.getDatauploadtype() : datauploadtype; datauploadtype = d.getDatauploadtype() != null && compareTrust(this, e) < 0
? d.getDatauploadtype()
: datauploadtype;
// {feeRequired, registration, other} // {feeRequired, registration, other}
databaseaccessrestriction = d.getDatabaseaccessrestriction() != null && compareTrust(this, e)<0? d.getDatabaseaccessrestriction() : databaseaccessrestriction; databaseaccessrestriction = d.getDatabaseaccessrestriction() != null && compareTrust(this, e) < 0
? d.getDatabaseaccessrestriction()
: databaseaccessrestriction;
// {feeRequired, registration, other} // {feeRequired, registration, other}
datauploadrestriction = d.getDatauploadrestriction() != null && compareTrust(this, e)<0? d.getDatauploadrestriction() : datauploadrestriction; datauploadrestriction = d.getDatauploadrestriction() != null && compareTrust(this, e) < 0
? d.getDatauploadrestriction()
: datauploadrestriction;
versioning = d.getVersioning() != null && compareTrust(this, e) < 0 ? d.getVersioning() : versioning; versioning = d.getVersioning() != null && compareTrust(this, e) < 0 ? d.getVersioning() : versioning;
citationguidelineurl = d.getCitationguidelineurl() != null && compareTrust(this, e)<0? d.getCitationguidelineurl() : citationguidelineurl; citationguidelineurl = d.getCitationguidelineurl() != null && compareTrust(this, e) < 0
? d.getCitationguidelineurl()
: citationguidelineurl;
// {yes, no, unknown} // {yes, no, unknown}
qualitymanagementkind = d.getQualitymanagementkind() != null && compareTrust(this, e)<0? d.getQualitymanagementkind() : qualitymanagementkind; qualitymanagementkind = d.getQualitymanagementkind() != null && compareTrust(this, e) < 0
? d.getQualitymanagementkind()
: qualitymanagementkind;
pidsystems = d.getPidsystems() != null && compareTrust(this, e) < 0 ? d.getPidsystems() : pidsystems; pidsystems = d.getPidsystems() != null && compareTrust(this, e) < 0 ? d.getPidsystems() : pidsystems;
certificates = d.getCertificates() != null && compareTrust(this, e)<0? d.getCertificates() : certificates; certificates = d.getCertificates() != null && compareTrust(this, e) < 0
? d.getCertificates()
: certificates;
policies = mergeLists(policies, d.getPolicies()); policies = mergeLists(policies, d.getPolicies());
@ -429,52 +469,4 @@ public class Datasource extends OafEntity implements Serializable {
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Datasource that = (Datasource) o;
return Objects.equals(datasourcetype, that.datasourcetype) &&
Objects.equals(openairecompatibility, that.openairecompatibility) &&
Objects.equals(officialname, that.officialname) &&
Objects.equals(englishname, that.englishname) &&
Objects.equals(websiteurl, that.websiteurl) &&
Objects.equals(logourl, that.logourl) &&
Objects.equals(contactemail, that.contactemail) &&
Objects.equals(namespaceprefix, that.namespaceprefix) &&
Objects.equals(latitude, that.latitude) &&
Objects.equals(longitude, that.longitude) &&
Objects.equals(dateofvalidation, that.dateofvalidation) &&
Objects.equals(description, that.description) &&
Objects.equals(subjects, that.subjects) &&
Objects.equals(odnumberofitems, that.odnumberofitems) &&
Objects.equals(odnumberofitemsdate, that.odnumberofitemsdate) &&
Objects.equals(odpolicies, that.odpolicies) &&
Objects.equals(odlanguages, that.odlanguages) &&
Objects.equals(odcontenttypes, that.odcontenttypes) &&
Objects.equals(accessinfopackage, that.accessinfopackage) &&
Objects.equals(releasestartdate, that.releasestartdate) &&
Objects.equals(releaseenddate, that.releaseenddate) &&
Objects.equals(missionstatementurl, that.missionstatementurl) &&
Objects.equals(dataprovider, that.dataprovider) &&
Objects.equals(serviceprovider, that.serviceprovider) &&
Objects.equals(databaseaccesstype, that.databaseaccesstype) &&
Objects.equals(datauploadtype, that.datauploadtype) &&
Objects.equals(databaseaccessrestriction, that.databaseaccessrestriction) &&
Objects.equals(datauploadrestriction, that.datauploadrestriction) &&
Objects.equals(versioning, that.versioning) &&
Objects.equals(citationguidelineurl, that.citationguidelineurl) &&
Objects.equals(qualitymanagementkind, that.qualitymanagementkind) &&
Objects.equals(pidsystems, that.pidsystems) &&
Objects.equals(certificates, that.certificates) &&
Objects.equals(policies, that.policies) &&
Objects.equals(journal, that.journal);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), datasourcetype, openairecompatibility, officialname, englishname, websiteurl, logourl, contactemail, namespaceprefix, latitude, longitude, dateofvalidation, description, subjects, odnumberofitems, odnumberofitemsdate, odpolicies, odlanguages, odcontenttypes, accessinfopackage, releasestartdate, releaseenddate, missionstatementurl, dataprovider, serviceprovider, databaseaccesstype, datauploadtype, databaseaccessrestriction, datauploadrestriction, versioning, citationguidelineurl, qualitymanagementkind, pidsystems, certificates, policies, journal);
}
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -94,21 +95,25 @@ public class ExternalReference implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
ExternalReference that = (ExternalReference) o; ExternalReference that = (ExternalReference) o;
return Objects.equals(sitename, that.sitename) && return Objects.equals(sitename, that.sitename)
Objects.equals(label, that.label) && && Objects.equals(label, that.label)
Objects.equals(url, that.url) && && Objects.equals(url, that.url)
Objects.equals(description, that.description) && && Objects.equals(description, that.description)
Objects.equals(qualifier, that.qualifier) && && Objects.equals(qualifier, that.qualifier)
Objects.equals(refidentifier, that.refidentifier) && && Objects.equals(refidentifier, that.refidentifier)
Objects.equals(query, that.query) && && Objects.equals(query, that.query)
Objects.equals(dataInfo, that.dataInfo); && Objects.equals(dataInfo, that.dataInfo);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(sitename, label, url, description, qualifier, refidentifier, query, dataInfo); return Objects
.hash(
sitename, label, url, description, qualifier, refidentifier, query, dataInfo);
} }
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -57,14 +58,16 @@ public class ExtraInfo implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
ExtraInfo extraInfo = (ExtraInfo) o; ExtraInfo extraInfo = (ExtraInfo) o;
return Objects.equals(name, extraInfo.name) && return Objects.equals(name, extraInfo.name)
Objects.equals(typology, extraInfo.typology) && && Objects.equals(typology, extraInfo.typology)
Objects.equals(provenance, extraInfo.provenance) && && Objects.equals(provenance, extraInfo.provenance)
Objects.equals(trust, extraInfo.trust) && && Objects.equals(trust, extraInfo.trust)
Objects.equals(value, extraInfo.value); && Objects.equals(value, extraInfo.value);
} }
@Override @Override

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;

View File

@ -1,9 +1,11 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore; import java.io.Serializable;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import java.io.Serializable; import com.fasterxml.jackson.annotation.JsonIgnore;
public class GeoLocation implements Serializable { public class GeoLocation implements Serializable {
@ -39,13 +41,18 @@ public class GeoLocation implements Serializable {
@JsonIgnore @JsonIgnore
public boolean isBlank() { public boolean isBlank() {
return StringUtils.isBlank(point) && return StringUtils.isBlank(point) && StringUtils.isBlank(box) && StringUtils.isBlank(place);
StringUtils.isBlank(box) &&
StringUtils.isBlank(place);
} }
public String toComparableString() { public String toComparableString() {
return isBlank()?"":String.format("%s::%s%s", point != null ? point.toLowerCase() : "", box != null ? box.toLowerCase() : "", place != null ? place.toLowerCase() : ""); return isBlank()
? ""
: String
.format(
"%s::%s%s",
point != null ? point.toLowerCase() : "",
box != null ? box.toLowerCase() : "",
place != null ? place.toLowerCase() : "");
} }
@Override @Override
@ -64,7 +71,6 @@ public class GeoLocation implements Serializable {
GeoLocation other = (GeoLocation) obj; GeoLocation other = (GeoLocation) obj;
return toComparableString() return toComparableString().equals(other.toComparableString());
.equals(other.toComparableString());
} }
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -22,10 +23,12 @@ public class Instance implements Serializable {
private Field<String> dateofacceptance; private Field<String> dateofacceptance;
// ( article | book ) processing charges. Defined here to cope with possible wrongly typed results // ( article | book ) processing charges. Defined here to cope with possible wrongly typed
// results
private Field<String> processingchargeamount; private Field<String> processingchargeamount;
// currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly typed results // currency - alphabetic code describe in ISO-4217. Defined here to cope with possible wrongly
// typed results
private Field<String> processingchargecurrency; private Field<String> processingchargecurrency;
private Field<String> refereed; // peer-review status private Field<String> refereed; // peer-review status
@ -119,7 +122,9 @@ public class Instance implements Serializable {
} }
public String toComparableString() { public String toComparableString() {
return String.format("%s::%s::%s::%s", return String
.format(
"%s::%s::%s::%s",
hostedby != null && hostedby.getKey() != null ? hostedby.getKey().toLowerCase() : "", hostedby != null && hostedby.getKey() != null ? hostedby.getKey().toLowerCase() : "",
accessright != null && accessright.getClassid() != null ? accessright.getClassid() : "", accessright != null && accessright.getClassid() != null ? accessright.getClassid() : "",
instancetype != null && instancetype.getClassid() != null ? instancetype.getClassid() : "", instancetype != null && instancetype.getClassid() != null ? instancetype.getClassid() : "",
@ -142,7 +147,6 @@ public class Instance implements Serializable {
Instance other = (Instance) obj; Instance other = (Instance) obj;
return toComparableString() return toComparableString().equals(other.toComparableString());
.equals(other.toComparableString());
} }
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -127,25 +128,40 @@ public class Journal implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
Journal journal = (Journal) o; Journal journal = (Journal) o;
return Objects.equals(name, journal.name) && return Objects.equals(name, journal.name)
Objects.equals(issnPrinted, journal.issnPrinted) && && Objects.equals(issnPrinted, journal.issnPrinted)
Objects.equals(issnOnline, journal.issnOnline) && && Objects.equals(issnOnline, journal.issnOnline)
Objects.equals(issnLinking, journal.issnLinking) && && Objects.equals(issnLinking, journal.issnLinking)
Objects.equals(ep, journal.ep) && && Objects.equals(ep, journal.ep)
Objects.equals(iss, journal.iss) && && Objects.equals(iss, journal.iss)
Objects.equals(sp, journal.sp) && && Objects.equals(sp, journal.sp)
Objects.equals(vol, journal.vol) && && Objects.equals(vol, journal.vol)
Objects.equals(edition, journal.edition) && && Objects.equals(edition, journal.edition)
Objects.equals(conferenceplace, journal.conferenceplace) && && Objects.equals(conferenceplace, journal.conferenceplace)
Objects.equals(conferencedate, journal.conferencedate) && && Objects.equals(conferencedate, journal.conferencedate)
Objects.equals(dataInfo, journal.dataInfo); && Objects.equals(dataInfo, journal.dataInfo);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, conferenceplace, conferencedate, dataInfo); return Objects
.hash(
name,
issnPrinted,
issnOnline,
issnLinking,
ep,
iss,
sp,
vol,
edition,
conferenceplace,
conferencedate,
dataInfo);
} }
} }

View File

@ -1,9 +1,11 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore; import java.io.Serializable;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import java.io.Serializable; import com.fasterxml.jackson.annotation.JsonIgnore;
public class KeyValue implements Serializable { public class KeyValue implements Serializable {
@ -38,7 +40,12 @@ public class KeyValue implements Serializable {
} }
public String toComparableString() { public String toComparableString() {
return isBlank()?"":String.format("%s::%s", key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : ""); return isBlank()
? ""
: String
.format(
"%s::%s",
key != null ? key.toLowerCase() : "", value != null ? value.toLowerCase() : "");
} }
@JsonIgnore @JsonIgnore

View File

@ -0,0 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
public class Measure {
}

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -17,8 +18,10 @@ public class OAIProvenance implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
OAIProvenance that = (OAIProvenance) o; OAIProvenance that = (OAIProvenance) o;
return Objects.equals(originDescription, that.originDescription); return Objects.equals(originDescription, that.originDescription);
} }

View File

@ -1,14 +1,29 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List;
import java.util.Objects; import java.util.Objects;
public abstract class Oaf implements Serializable { public abstract class Oaf implements Serializable {
/**
* The list of datasource id/name pairs providing this relationship.
*/
protected List<KeyValue> collectedfrom;
private DataInfo dataInfo; private DataInfo dataInfo;
private Long lastupdatetimestamp; private Long lastupdatetimestamp;
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public DataInfo getDataInfo() { public DataInfo getDataInfo() {
return dataInfo; return dataInfo;
} }
@ -25,7 +40,6 @@ public abstract class Oaf implements Serializable {
this.lastupdatetimestamp = lastupdatetimestamp; this.lastupdatetimestamp = lastupdatetimestamp;
} }
public void mergeOAFDataInfo(Oaf e) { public void mergeOAFDataInfo(Oaf e) {
if (e.getDataInfo() != null && compareTrust(this, e) < 0) if (e.getDataInfo() != null && compareTrust(this, e) < 0)
dataInfo = e.getDataInfo(); dataInfo = e.getDataInfo();
@ -35,23 +49,21 @@ public abstract class Oaf implements Serializable {
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null) if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null)
return "0.0"; return "0.0";
return e.getDataInfo().getTrust(); return e.getDataInfo().getTrust();
} }
protected int compareTrust(Oaf a, Oaf b) { protected int compareTrust(Oaf a, Oaf b) {
return extractTrust(a).compareTo(extractTrust(b)); return extractTrust(a).compareTo(extractTrust(b));
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
Oaf oaf = (Oaf) o; Oaf oaf = (Oaf) o;
return Objects.equals(dataInfo, oaf.dataInfo) && return Objects.equals(dataInfo, oaf.dataInfo)
Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp); && Objects.equals(lastupdatetimestamp, oaf.lastupdatetimestamp);
} }
@Override @Override

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -10,8 +11,6 @@ public abstract class OafEntity extends Oaf implements Serializable {
private List<String> originalId; private List<String> originalId;
private List<KeyValue> collectedfrom;
private List<StructuredProperty> pid; private List<StructuredProperty> pid;
private String dateofcollection; private String dateofcollection;
@ -38,14 +37,6 @@ public abstract class OafEntity extends Oaf implements Serializable {
this.originalId = originalId; this.originalId = originalId;
} }
public List<KeyValue> getCollectedfrom() {
return collectedfrom;
}
public void setCollectedfrom(List<KeyValue> collectedfrom) {
this.collectedfrom = collectedfrom;
}
public List<StructuredProperty> getPid() { public List<StructuredProperty> getPid() {
return pid; return pid;
} }
@ -86,7 +77,6 @@ public abstract class OafEntity extends Oaf implements Serializable {
this.oaiprovenance = oaiprovenance; this.oaiprovenance = oaiprovenance;
} }
public void mergeFrom(OafEntity e) { public void mergeFrom(OafEntity e) {
if (e == null) if (e == null)
@ -108,32 +98,32 @@ public abstract class OafEntity extends Oaf implements Serializable {
if (e.getOaiprovenance() != null && compareTrust(this, e) < 0) if (e.getOaiprovenance() != null && compareTrust(this, e) < 0)
oaiprovenance = e.getOaiprovenance(); oaiprovenance = e.getOaiprovenance();
} }
protected <T> List<T> mergeLists(final List<T>... lists) { protected <T> List<T> mergeLists(final List<T>... lists) {
return Arrays.stream(lists).filter(Objects::nonNull).flatMap(List::stream).distinct().collect(Collectors.toList()); return Arrays
.stream(lists)
.filter(Objects::nonNull)
.flatMap(List::stream)
.distinct()
.collect(Collectors.toList());
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (!super.equals(o)) return false; if (o == null || getClass() != o.getClass())
return false;
if (!super.equals(o))
return false;
OafEntity oafEntity = (OafEntity) o; OafEntity oafEntity = (OafEntity) o;
return Objects.equals(id, oafEntity.id) && return Objects.equals(id, oafEntity.id);
Objects.equals(originalId, oafEntity.originalId) &&
Objects.equals(collectedfrom, oafEntity.collectedfrom) &&
Objects.equals(pid, oafEntity.pid) &&
Objects.equals(dateofcollection, oafEntity.dateofcollection) &&
Objects.equals(dateoftransformation, oafEntity.dateoftransformation) &&
Objects.equals(extraInfo, oafEntity.extraInfo) &&
Objects.equals(oaiprovenance, oafEntity.oaiprovenance);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(super.hashCode(), id, originalId, collectedfrom, pid, dateofcollection, dateoftransformation, extraInfo, oaiprovenance); return Objects.hash(super.hashCode(), id);
} }
} }

View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Organization extends OafEntity implements Serializable { public class Organization extends OafEntity implements Serializable {
@ -122,7 +122,8 @@ public class Organization extends OafEntity implements Serializable {
return ecinternationalorganizationeurinterests; return ecinternationalorganizationeurinterests;
} }
public void setEcinternationalorganizationeurinterests(Field<String> ecinternationalorganizationeurinterests) { public void setEcinternationalorganizationeurinterests(
Field<String> ecinternationalorganizationeurinterests) {
this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests; this.ecinternationalorganizationeurinterests = ecinternationalorganizationeurinterests;
} }
@ -166,7 +167,6 @@ public class Organization extends OafEntity implements Serializable {
this.country = country; this.country = country;
} }
@Override @Override
public void mergeFrom(OafEntity e) { public void mergeFrom(OafEntity e) {
super.mergeFrom(e); super.mergeFrom(e);
@ -176,51 +176,39 @@ public class Organization extends OafEntity implements Serializable {
} }
final Organization o = (Organization) e; final Organization o = (Organization) e;
legalshortname = o.getLegalshortname() != null && compareTrust(this, e)<0? o.getLegalshortname() : legalshortname; legalshortname = o.getLegalshortname() != null && compareTrust(this, e) < 0
? o.getLegalshortname()
: legalshortname;
legalname = o.getLegalname() != null && compareTrust(this, e) < 0 ? o.getLegalname() : legalname; legalname = o.getLegalname() != null && compareTrust(this, e) < 0 ? o.getLegalname() : legalname;
alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames); alternativeNames = mergeLists(o.getAlternativeNames(), alternativeNames);
websiteurl = o.getWebsiteurl() != null && compareTrust(this, e) < 0 ? o.getWebsiteurl() : websiteurl; websiteurl = o.getWebsiteurl() != null && compareTrust(this, e) < 0 ? o.getWebsiteurl() : websiteurl;
logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl; logourl = o.getLogourl() != null && compareTrust(this, e) < 0 ? o.getLogourl() : logourl;
eclegalbody = o.getEclegalbody() != null && compareTrust(this, e) < 0 ? o.getEclegalbody() : eclegalbody; eclegalbody = o.getEclegalbody() != null && compareTrust(this, e) < 0 ? o.getEclegalbody() : eclegalbody;
eclegalperson = o.getEclegalperson() != null && compareTrust(this, e)<0? o.getEclegalperson() : eclegalperson; eclegalperson = o.getEclegalperson() != null && compareTrust(this, e) < 0
? o.getEclegalperson()
: eclegalperson;
ecnonprofit = o.getEcnonprofit() != null && compareTrust(this, e) < 0 ? o.getEcnonprofit() : ecnonprofit; ecnonprofit = o.getEcnonprofit() != null && compareTrust(this, e) < 0 ? o.getEcnonprofit() : ecnonprofit;
ecresearchorganization = o.getEcresearchorganization() != null && compareTrust(this, e)<0? o.getEcresearchorganization() : ecresearchorganization; ecresearchorganization = o.getEcresearchorganization() != null && compareTrust(this, e) < 0
echighereducation = o.getEchighereducation() != null && compareTrust(this, e)<0? o.getEchighereducation() : echighereducation; ? o.getEcresearchorganization()
ecinternationalorganizationeurinterests = o.getEcinternationalorganizationeurinterests() != null && compareTrust(this, e)<0? o.getEcinternationalorganizationeurinterests() : ecinternationalorganizationeurinterests; : ecresearchorganization;
ecinternationalorganization = o.getEcinternationalorganization() != null && compareTrust(this, e)<0? o.getEcinternationalorganization() : ecinternationalorganization; echighereducation = o.getEchighereducation() != null && compareTrust(this, e) < 0
ecenterprise = o.getEcenterprise() != null && compareTrust(this, e)<0? o.getEcenterprise() :ecenterprise; ? o.getEchighereducation()
ecsmevalidated = o.getEcsmevalidated() != null && compareTrust(this, e)<0? o.getEcsmevalidated() :ecsmevalidated; : echighereducation;
ecinternationalorganizationeurinterests = o.getEcinternationalorganizationeurinterests() != null
&& compareTrust(this, e) < 0
? o.getEcinternationalorganizationeurinterests()
: ecinternationalorganizationeurinterests;
ecinternationalorganization = o.getEcinternationalorganization() != null && compareTrust(this, e) < 0
? o.getEcinternationalorganization()
: ecinternationalorganization;
ecenterprise = o.getEcenterprise() != null && compareTrust(this, e) < 0
? o.getEcenterprise()
: ecenterprise;
ecsmevalidated = o.getEcsmevalidated() != null && compareTrust(this, e) < 0
? o.getEcsmevalidated()
: ecsmevalidated;
ecnutscode = o.getEcnutscode() != null && compareTrust(this, e) < 0 ? o.getEcnutscode() : ecnutscode; ecnutscode = o.getEcnutscode() != null && compareTrust(this, e) < 0 ? o.getEcnutscode() : ecnutscode;
country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country; country = o.getCountry() != null && compareTrust(this, e) < 0 ? o.getCountry() : country;
mergeOAFDataInfo(o); mergeOAFDataInfo(o);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Organization that = (Organization) o;
return Objects.equals(legalshortname, that.legalshortname) &&
Objects.equals(legalname, that.legalname) &&
Objects.equals(alternativeNames, that.alternativeNames) &&
Objects.equals(websiteurl, that.websiteurl) &&
Objects.equals(logourl, that.logourl) &&
Objects.equals(eclegalbody, that.eclegalbody) &&
Objects.equals(eclegalperson, that.eclegalperson) &&
Objects.equals(ecnonprofit, that.ecnonprofit) &&
Objects.equals(ecresearchorganization, that.ecresearchorganization) &&
Objects.equals(echighereducation, that.echighereducation) &&
Objects.equals(ecinternationalorganizationeurinterests, that.ecinternationalorganizationeurinterests) &&
Objects.equals(ecinternationalorganization, that.ecinternationalorganization) &&
Objects.equals(ecenterprise, that.ecenterprise) &&
Objects.equals(ecsmevalidated, that.ecsmevalidated) &&
Objects.equals(ecnutscode, that.ecnutscode) &&
Objects.equals(country, that.country);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), legalshortname, legalname, alternativeNames, websiteurl, logourl, eclegalbody, eclegalperson, ecnonprofit, ecresearchorganization, echighereducation, ecinternationalorganizationeurinterests, ecinternationalorganization, ecenterprise, ecsmevalidated, ecnutscode, country);
}
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -67,15 +68,17 @@ public class OriginDescription implements Serializable {
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
OriginDescription that = (OriginDescription) o; OriginDescription that = (OriginDescription) o;
return Objects.equals(harvestDate, that.harvestDate) && return Objects.equals(harvestDate, that.harvestDate)
Objects.equals(altered, that.altered) && && Objects.equals(altered, that.altered)
Objects.equals(baseURL, that.baseURL) && && Objects.equals(baseURL, that.baseURL)
Objects.equals(identifier, that.identifier) && && Objects.equals(identifier, that.identifier)
Objects.equals(datestamp, that.datestamp) && && Objects.equals(datestamp, that.datestamp)
Objects.equals(metadataNamespace, that.metadataNamespace); && Objects.equals(metadataNamespace, that.metadataNamespace);
} }
@Override @Override

View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class OtherResearchProduct extends Result implements Serializable { public class OtherResearchProduct extends Result implements Serializable {
@ -12,6 +14,10 @@ public class OtherResearchProduct extends Result implements Serializable {
private List<Field<String>> tool; private List<Field<String>> tool;
public OtherResearchProduct() {
setResulttype(ModelConstants.ORP_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getContactperson() { public List<Field<String>> getContactperson() {
return contactperson; return contactperson;
} }
@ -51,20 +57,4 @@ public class OtherResearchProduct extends Result implements Serializable {
tool = mergeLists(tool, o.getTool()); tool = mergeLists(tool, o.getTool());
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
OtherResearchProduct that = (OtherResearchProduct) o;
return Objects.equals(contactperson, that.contactperson) &&
Objects.equals(contactgroup, that.contactgroup) &&
Objects.equals(tool, that.tool);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), contactperson, contactgroup, tool);
}
} }

View File

@ -1,8 +1,8 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Project extends OafEntity implements Serializable { public class Project extends OafEntity implements Serializable {
@ -266,7 +266,6 @@ public class Project extends OafEntity implements Serializable {
this.fundedamount = fundedamount; this.fundedamount = fundedamount;
} }
@Override @Override
public void mergeFrom(OafEntity e) { public void mergeFrom(OafEntity e) {
super.mergeFrom(e); super.mergeFrom(e);
@ -283,65 +282,44 @@ public class Project extends OafEntity implements Serializable {
title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title; title = p.getTitle() != null && compareTrust(this, e) < 0 ? p.getTitle() : title;
startdate = p.getStartdate() != null && compareTrust(this, e) < 0 ? p.getStartdate() : startdate; startdate = p.getStartdate() != null && compareTrust(this, e) < 0 ? p.getStartdate() : startdate;
enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate; enddate = p.getEnddate() != null && compareTrust(this, e) < 0 ? p.getEnddate() : enddate;
callidentifier= p.getCallidentifier()!=null && compareTrust(this,e)<0?p.getCallidentifier():callidentifier; callidentifier = p.getCallidentifier() != null && compareTrust(this, e) < 0
? p.getCallidentifier()
: callidentifier;
keywords = p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords; keywords = p.getKeywords() != null && compareTrust(this, e) < 0 ? p.getKeywords() : keywords;
duration = p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration; duration = p.getDuration() != null && compareTrust(this, e) < 0 ? p.getDuration() : duration;
ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39; ecsc39 = p.getEcsc39() != null && compareTrust(this, e) < 0 ? p.getEcsc39() : ecsc39;
oamandatepublications= p.getOamandatepublications()!=null && compareTrust(this,e)<0?p.getOamandatepublications():oamandatepublications; oamandatepublications = p.getOamandatepublications() != null && compareTrust(this, e) < 0
ecarticle29_3= p.getEcarticle29_3()!=null && compareTrust(this,e)<0?p.getEcarticle29_3():ecarticle29_3; ? p.getOamandatepublications()
: oamandatepublications;
ecarticle29_3 = p.getEcarticle29_3() != null && compareTrust(this, e) < 0
? p.getEcarticle29_3()
: ecarticle29_3;
subjects = mergeLists(subjects, p.getSubjects()); subjects = mergeLists(subjects, p.getSubjects());
fundingtree = mergeLists(fundingtree, p.getFundingtree()); fundingtree = mergeLists(fundingtree, p.getFundingtree());
contracttype= p.getContracttype()!=null && compareTrust(this,e)<0?p.getContracttype():contracttype; contracttype = p.getContracttype() != null && compareTrust(this, e) < 0
? p.getContracttype()
: contracttype;
optional1 = p.getOptional1() != null && compareTrust(this, e) < 0 ? p.getOptional1() : optional1; optional1 = p.getOptional1() != null && compareTrust(this, e) < 0 ? p.getOptional1() : optional1;
optional2 = p.getOptional2() != null && compareTrust(this, e) < 0 ? p.getOptional2() : optional2; optional2 = p.getOptional2() != null && compareTrust(this, e) < 0 ? p.getOptional2() : optional2;
jsonextrainfo= p.getJsonextrainfo()!=null && compareTrust(this,e)<0?p.getJsonextrainfo():jsonextrainfo; jsonextrainfo = p.getJsonextrainfo() != null && compareTrust(this, e) < 0
contactfullname= p.getContactfullname()!=null && compareTrust(this,e)<0?p.getContactfullname():contactfullname; ? p.getJsonextrainfo()
: jsonextrainfo;
contactfullname = p.getContactfullname() != null && compareTrust(this, e) < 0
? p.getContactfullname()
: contactfullname;
contactfax = p.getContactfax() != null && compareTrust(this, e) < 0 ? p.getContactfax() : contactfax; contactfax = p.getContactfax() != null && compareTrust(this, e) < 0 ? p.getContactfax() : contactfax;
contactphone= p.getContactphone()!=null && compareTrust(this,e)<0?p.getContactphone():contactphone; contactphone = p.getContactphone() != null && compareTrust(this, e) < 0
contactemail= p.getContactemail()!=null && compareTrust(this,e)<0?p.getContactemail():contactemail; ? p.getContactphone()
: contactphone;
contactemail = p.getContactemail() != null && compareTrust(this, e) < 0
? p.getContactemail()
: contactemail;
summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary; summary = p.getSummary() != null && compareTrust(this, e) < 0 ? p.getSummary() : summary;
currency = p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency; currency = p.getCurrency() != null && compareTrust(this, e) < 0 ? p.getCurrency() : currency;
totalcost = p.getTotalcost() != null && compareTrust(this, e) < 0 ? p.getTotalcost() : totalcost; totalcost = p.getTotalcost() != null && compareTrust(this, e) < 0 ? p.getTotalcost() : totalcost;
fundedamount= p.getFundedamount()!= null && compareTrust(this,e)<0?p.getFundedamount():fundedamount; fundedamount = p.getFundedamount() != null && compareTrust(this, e) < 0
? p.getFundedamount()
: fundedamount;
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Project project = (Project) o;
return Objects.equals(websiteurl, project.websiteurl) &&
Objects.equals(code, project.code) &&
Objects.equals(acronym, project.acronym) &&
Objects.equals(title, project.title) &&
Objects.equals(startdate, project.startdate) &&
Objects.equals(enddate, project.enddate) &&
Objects.equals(callidentifier, project.callidentifier) &&
Objects.equals(keywords, project.keywords) &&
Objects.equals(duration, project.duration) &&
Objects.equals(ecsc39, project.ecsc39) &&
Objects.equals(oamandatepublications, project.oamandatepublications) &&
Objects.equals(ecarticle29_3, project.ecarticle29_3) &&
Objects.equals(subjects, project.subjects) &&
Objects.equals(fundingtree, project.fundingtree) &&
Objects.equals(contracttype, project.contracttype) &&
Objects.equals(optional1, project.optional1) &&
Objects.equals(optional2, project.optional2) &&
Objects.equals(jsonextrainfo, project.jsonextrainfo) &&
Objects.equals(contactfullname, project.contactfullname) &&
Objects.equals(contactfax, project.contactfax) &&
Objects.equals(contactphone, project.contactphone) &&
Objects.equals(contactemail, project.contactemail) &&
Objects.equals(summary, project.summary) &&
Objects.equals(currency, project.currency) &&
Objects.equals(totalcost, project.totalcost) &&
Objects.equals(fundedamount, project.fundedamount);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), websiteurl, code, acronym, title, startdate, enddate, callidentifier, keywords, duration, ecsc39, oamandatepublications, ecarticle29_3, subjects, fundingtree, contracttype, optional1, optional2, jsonextrainfo, contactfullname, contactfax, contactphone, contactemail, summary, currency, totalcost, fundedamount);
}
} }

View File

@ -1,13 +1,19 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.Objects;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Publication extends Result implements Serializable { public class Publication extends Result implements Serializable {
// publication specific // publication specific
private Journal journal; private Journal journal;
public Publication() {
setResulttype(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE);
}
public Journal getJournal() { public Journal getJournal() {
return journal; return journal;
} }
@ -30,18 +36,4 @@ public class Publication extends Result implements Serializable {
journal = p.getJournal(); journal = p.getJournal();
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Publication that = (Publication) o;
return Objects.equals(journal, that.journal);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), journal);
}
} }

View File

@ -1,9 +1,11 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import com.fasterxml.jackson.annotation.JsonIgnore; import java.io.Serializable;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
import java.io.Serializable; import com.fasterxml.jackson.annotation.JsonIgnore;
public class Qualifier implements Serializable { public class Qualifier implements Serializable {
@ -45,7 +47,11 @@ public class Qualifier implements Serializable {
} }
public String toComparableString() { public String toComparableString() {
return isBlank()?"": String.format("%s::%s::%s::%s", return isBlank()
? ""
: String
.format(
"%s::%s::%s::%s",
classid != null ? classid : "", classid != null ? classid : "",
classname != null ? classname : "", classname != null ? classname : "",
schemeid != null ? schemeid : "", schemeid != null ? schemeid : "",
@ -54,11 +60,12 @@ public class Qualifier implements Serializable {
@JsonIgnore @JsonIgnore
public boolean isBlank() { public boolean isBlank() {
return StringUtils.isBlank(classid) && return StringUtils.isBlank(classid)
StringUtils.isBlank(classname) && && StringUtils.isBlank(classname)
StringUtils.isBlank(schemeid) && && StringUtils.isBlank(schemeid)
StringUtils.isBlank(schemename); && StringUtils.isBlank(schemename);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return toComparableString().hashCode(); return toComparableString().hashCode();
@ -75,7 +82,6 @@ public class Qualifier implements Serializable {
Qualifier other = (Qualifier) obj; Qualifier other = (Qualifier) obj;
return toComparableString() return toComparableString().equals(other.toComparableString());
.equals(other.toComparableString());
} }
} }

View File

@ -1,14 +1,15 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import static com.google.common.base.Preconditions.checkArgument;
import java.util.*; import java.util.*;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import java.util.stream.Stream; import java.util.stream.Stream;
import static com.google.common.base.Preconditions.checkArgument;
/** /**
* Relation aims to model any edge between two nodes in the OpenAIRE graph. It has a source id and a target id * Relation models any edge between two nodes in the OpenAIRE graph. It has a source id and a target id
* pointing to graph node identifiers and it is further characterised by the semantic of the link throught the fields * pointing to graph node identifiers and it is further characterised by the semantic of the link through the fields
* relType, subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom, * relType, subRelType and relClass. Provenance information is modeled according to the dataInfo element and collectedFrom,
* while individual relationship types can provide extra information via the properties field. * while individual relationship types can provide extra information via the properties field.
*/ */
@ -39,16 +40,6 @@ public class Relation extends Oaf {
*/ */
private String target; private String target;
/**
* The list of datasource id/name pairs providing this relationship.
*/
private List<KeyValue> collectedFrom = new ArrayList<>();
/**
* List of relation specific properties. Values include 'similarityLevel', indicating the similarity score between a pair of publications.
*/
private List<KeyValue> properties = new ArrayList<>();
public String getRelType() { public String getRelType() {
return relType; return relType;
} }
@ -89,53 +80,46 @@ public class Relation extends Oaf {
this.target = target; this.target = target;
} }
public List<KeyValue> getCollectedFrom() {
return collectedFrom;
}
public void setCollectedFrom(final List<KeyValue> collectedFrom) {
this.collectedFrom = collectedFrom;
}
public List<KeyValue> getProperties() {
return properties;
}
public void setProperties(List<KeyValue> properties) {
this.properties = properties;
}
public void mergeFrom(final Relation r) { public void mergeFrom(final Relation r) {
checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal"); checkArgument(Objects.equals(getSource(), r.getSource()), "source ids must be equal");
checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal"); checkArgument(Objects.equals(getTarget(), r.getTarget()), "target ids must be equal");
checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal"); checkArgument(Objects.equals(getRelType(), r.getRelType()), "relType(s) must be equal");
checkArgument(Objects.equals(getSubRelType(), r.getSubRelType()),"subRelType(s) must be equal"); checkArgument(
Objects.equals(getSubRelType(), r.getSubRelType()), "subRelType(s) must be equal");
checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal"); checkArgument(Objects.equals(getRelClass(), r.getRelClass()), "relClass(es) must be equal");
setCollectedFrom( setCollectedfrom(
Stream Stream
.concat(Optional.ofNullable(getCollectedFrom()).map(Collection::stream).orElse(Stream.empty()), .concat(
Optional.ofNullable(r.getCollectedFrom()).map(Collection::stream).orElse(Stream.empty())) Optional
.ofNullable(getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()),
Optional
.ofNullable(r.getCollectedfrom())
.map(Collection::stream)
.orElse(Stream.empty()))
.distinct() // relies on KeyValue.equals .distinct() // relies on KeyValue.equals
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
@Override @Override
public boolean equals(Object o) { public boolean equals(Object o) {
if (this == o) return true; if (this == o)
if (o == null || getClass() != o.getClass()) return false; return true;
if (o == null || getClass() != o.getClass())
return false;
Relation relation = (Relation) o; Relation relation = (Relation) o;
return relType.equals(relation.relType) && return relType.equals(relation.relType)
subRelType.equals(relation.subRelType) && && subRelType.equals(relation.subRelType)
relClass.equals(relation.relClass) && && relClass.equals(relation.relClass)
source.equals(relation.source) && && source.equals(relation.source)
target.equals(relation.target); && target.equals(relation.target);
} }
@Override @Override
public int hashCode() { public int hashCode() {
return Objects.hash(relType, subRelType, relClass, source, target, collectedFrom); return Objects.hash(relType, subRelType, relClass, source, target, collectedfrom);
} }
} }

View File

@ -1,9 +1,9 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.Comparator; import java.util.Comparator;
import java.util.List; import java.util.List;
import java.util.Objects;
public class Result extends OafEntity implements Serializable { public class Result extends OafEntity implements Serializable {
@ -231,6 +231,9 @@ public class Result extends OafEntity implements Serializable {
instance = mergeLists(instance, r.getInstance()); instance = mergeLists(instance, r.getInstance());
if (r.getBestaccessright() != null && compareTrust(this, r) < 0)
bestaccessright = r.getBestaccessright();
if (r.getResulttype() != null && compareTrust(this, r) < 0) if (r.getResulttype() != null && compareTrust(this, r) < 0)
resulttype = r.getResulttype(); resulttype = r.getResulttype();
@ -271,49 +274,24 @@ public class Result extends OafEntity implements Serializable {
externalReference = mergeLists(externalReference, r.getExternalReference()); externalReference = mergeLists(externalReference, r.getExternalReference());
} }
private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) { private List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
if (a == null || b == null) if (a == null || b == null)
return a == null ? b : a; return a == null ? b : a;
if (a.size() == b.size()) { if (a.size() == b.size()) {
int msa = a.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0); int msa = a
int msb = b.stream().filter(i -> i.getValue() != null).map(i -> i.getValue().length()).max(Comparator.naturalOrder()).orElse(0); .stream()
.filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
int msb = b
.stream()
.filter(i -> i.getValue() != null)
.map(i -> i.getValue().length())
.max(Comparator.naturalOrder())
.orElse(0);
return msa > msb ? a : b; return msa > msb ? a : b;
} }
return a.size() > b.size() ? a : b; return a.size() > b.size() ? a : b;
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Result result = (Result) o;
return Objects.equals(author, result.author) &&
Objects.equals(resulttype, result.resulttype) &&
Objects.equals(language, result.language) &&
Objects.equals(country, result.country) &&
Objects.equals(subject, result.subject) &&
Objects.equals(title, result.title) &&
Objects.equals(relevantdate, result.relevantdate) &&
Objects.equals(description, result.description) &&
Objects.equals(dateofacceptance, result.dateofacceptance) &&
Objects.equals(publisher, result.publisher) &&
Objects.equals(embargoenddate, result.embargoenddate) &&
Objects.equals(source, result.source) &&
Objects.equals(fulltext, result.fulltext) &&
Objects.equals(format, result.format) &&
Objects.equals(contributor, result.contributor) &&
Objects.equals(resourcetype, result.resourcetype) &&
Objects.equals(coverage, result.coverage) &&
Objects.equals(bestaccessright, result.bestaccessright) &&
Objects.equals(context, result.context) &&
Objects.equals(externalReference, result.externalReference) &&
Objects.equals(instance, result.instance);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), author, resulttype, language, country, subject, title, relevantdate, description, dateofacceptance, publisher, embargoenddate, source, fulltext, format, contributor, resourcetype, coverage, bestaccessright, context, externalReference, instance);
}
} }

View File

@ -1,8 +1,10 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
import java.util.List; import java.util.List;
import java.util.Objects;
import eu.dnetlib.dhp.schema.common.ModelConstants;
public class Software extends Result implements Serializable { public class Software extends Result implements Serializable {
@ -14,6 +16,10 @@ public class Software extends Result implements Serializable {
private Qualifier programmingLanguage; private Qualifier programmingLanguage;
public Software() {
setResulttype(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE);
}
public List<Field<String>> getDocumentationUrl() { public List<Field<String>> getDocumentationUrl() {
return documentationUrl; return documentationUrl;
} }
@ -59,27 +65,14 @@ public class Software extends Result implements Serializable {
license = mergeLists(license, s.getLicense()); license = mergeLists(license, s.getLicense());
codeRepositoryUrl = s.getCodeRepositoryUrl()!= null && compareTrust(this, s)<0?s.getCodeRepositoryUrl():codeRepositoryUrl; codeRepositoryUrl = s.getCodeRepositoryUrl() != null && compareTrust(this, s) < 0
? s.getCodeRepositoryUrl()
: codeRepositoryUrl;
programmingLanguage= s.getProgrammingLanguage()!= null && compareTrust(this, s)<0?s.getProgrammingLanguage():programmingLanguage; programmingLanguage = s.getProgrammingLanguage() != null && compareTrust(this, s) < 0
? s.getProgrammingLanguage()
: programmingLanguage;
mergeOAFDataInfo(e); mergeOAFDataInfo(e);
} }
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
if (!super.equals(o)) return false;
Software software = (Software) o;
return Objects.equals(documentationUrl, software.documentationUrl) &&
Objects.equals(license, software.license) &&
Objects.equals(codeRepositoryUrl, software.codeRepositoryUrl) &&
Objects.equals(programmingLanguage, software.programmingLanguage);
}
@Override
public int hashCode() {
return Objects.hash(super.hashCode(), documentationUrl, license, codeRepositoryUrl, programmingLanguage);
}
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import java.io.Serializable; import java.io.Serializable;
@ -54,7 +55,6 @@ public class StructuredProperty implements Serializable {
StructuredProperty other = (StructuredProperty) obj; StructuredProperty other = (StructuredProperty) obj;
return toComparableString() return toComparableString().equals(other.toComparableString());
.equals(other.toComparableString());
} }
} }

View File

@ -1,14 +1,16 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Dataset; package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import org.apache.commons.lang3.StringUtils;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.HashMap; import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
public class DLIDataset extends Dataset { public class DLIDataset extends Dataset {
private String originalObjIdentifier; private String originalObjIdentifier;
@ -52,12 +54,16 @@ public class DLIDataset extends Dataset {
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
} }
private List<ProvenaceInfo> mergeProvenance(final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) { private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>(); Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null) if (a != null)
a.forEach(p -> { a
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p); result.put(p.getId(), p);
} }
@ -65,9 +71,12 @@ public class DLIDataset extends Dataset {
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
if (b != null) if (b != null)
b.forEach(p -> { b
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p); result.put(p.getId(), p);
} }

View File

@ -1,10 +1,13 @@
package eu.dnetlib.dhp.schema.scholexplorer; package eu.dnetlib.dhp.schema.scholexplorer;
import java.io.Serializable;
import java.util.*;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Publication; import eu.dnetlib.dhp.schema.oaf.Publication;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable;
import java.util.*;
public class DLIPublication extends Publication implements Serializable { public class DLIPublication extends Publication implements Serializable {
@ -49,12 +52,16 @@ public class DLIPublication extends Publication implements Serializable {
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
} }
private List<ProvenaceInfo> mergeProvenance(final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) { private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>(); Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null) if (a != null)
a.forEach(p -> { a
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p); result.put(p.getId(), p);
} }
@ -62,9 +69,12 @@ public class DLIPublication extends Publication implements Serializable {
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
if (b != null) if (b != null)
b.forEach(p -> { b
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p); result.put(p.getId(), p);
} }

View File

@ -0,0 +1,16 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Relation;
public class DLIRelation extends Relation {
private String dateOfCollection;
public String getDateOfCollection() {
return dateOfCollection;
}
public void setDateOfCollection(String dateOfCollection) {
this.dateOfCollection = dateOfCollection;
}
}

View File

@ -1,9 +1,5 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.Oaf; package eu.dnetlib.dhp.schema.scholexplorer;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.lang3.StringUtils;
import java.io.Serializable; import java.io.Serializable;
import java.util.ArrayList; import java.util.ArrayList;
@ -11,6 +7,11 @@ import java.util.HashMap;
import java.util.List; import java.util.List;
import java.util.Map; import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class DLIUnknown extends Oaf implements Serializable { public class DLIUnknown extends Oaf implements Serializable {
private String id; private String id;
@ -49,7 +50,6 @@ public class DLIUnknown extends Oaf implements Serializable {
this.id = id; this.id = id;
} }
public List<StructuredProperty> getPid() { public List<StructuredProperty> getPid() {
return pid; return pid;
} }
@ -80,12 +80,16 @@ public class DLIUnknown extends Oaf implements Serializable {
dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom()); dlicollectedfrom = mergeProvenance(dlicollectedfrom, p.getDlicollectedfrom());
} }
private List<ProvenaceInfo> mergeProvenance(final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) { private List<ProvenaceInfo> mergeProvenance(
final List<ProvenaceInfo> a, final List<ProvenaceInfo> b) {
Map<String, ProvenaceInfo> result = new HashMap<>(); Map<String, ProvenaceInfo> result = new HashMap<>();
if (a != null) if (a != null)
a.forEach(p -> { a
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p); result.put(p.getId(), p);
} }
@ -93,9 +97,12 @@ public class DLIUnknown extends Oaf implements Serializable {
result.put(p.getId(), p); result.put(p.getId(), p);
}); });
if (b != null) if (b != null)
b.forEach(p -> { b
.forEach(
p -> {
if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) { if (p != null && StringUtils.isNotBlank(p.getId()) && result.containsKey(p.getId())) {
if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus()) && StringUtils.isNotBlank(p.getCompletionStatus())) { if ("incomplete".equalsIgnoreCase(result.get(p.getId()).getCompletionStatus())
&& StringUtils.isNotBlank(p.getCompletionStatus())) {
result.put(p.getId(), p); result.put(p.getId(), p);
} }

View File

@ -1,3 +1,4 @@
package eu.dnetlib.dhp.schema.scholexplorer; package eu.dnetlib.dhp.schema.scholexplorer;
import java.io.Serializable; import java.io.Serializable;

View File

@ -1,18 +1,18 @@
package eu.dnetlib.dhp.schema.action; package eu.dnetlib.dhp.schema.action;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.Test;
import java.io.IOException;
import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.*;
/** import java.io.IOException;
* @author claudio.atzori
*/ import org.apache.commons.lang3.StringUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Relation;
/** @author claudio.atzori */
public class AtomicActionTest { public class AtomicActionTest {
@Test @Test
@ -36,7 +36,5 @@ public class AtomicActionTest {
assertEquals(aa1.getClazz(), aa2.getClazz()); assertEquals(aa1.getClazz(), aa2.getClazz());
assertEquals(aa1.getPayload(), aa2.getPayload()); assertEquals(aa1.getPayload(), aa2.getPayload());
} }
} }

View File

@ -1,13 +1,15 @@
package eu.dnetlib.dhp.schema.common; package eu.dnetlib.dhp.schema.common;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result; import eu.dnetlib.dhp.schema.oaf.Result;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
public class ModelSupportTest { public class ModelSupportTest {

View File

@ -0,0 +1,4 @@
package eu.dnetlib.dhp.schema.oaf;
public class MeasureTest {
}

View File

@ -1,12 +1,14 @@
package eu.dnetlib.dhp.schema.oaf; package eu.dnetlib.dhp.schema.oaf;
import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
public class MergeTest { public class MergeTest {
OafEntity oaf; OafEntity oaf;
@ -44,7 +46,6 @@ public class MergeTest {
assertNotNull(a.getCollectedfrom()); assertNotNull(a.getCollectedfrom());
assertEquals(3, a.getCollectedfrom().size()); assertEquals(3, a.getCollectedfrom().size());
} }
@Test @Test
@ -60,7 +61,6 @@ public class MergeTest {
assertNotNull(a.getSubject()); assertNotNull(a.getSubject());
assertEquals(3, a.getSubject().size()); assertEquals(3, a.getSubject().size());
} }
private KeyValue setKV(final String key, final String value) { private KeyValue setKV(final String key, final String value) {
@ -73,7 +73,8 @@ public class MergeTest {
return k; return k;
} }
private StructuredProperty setSP(final String value, final String schema, final String classname) { private StructuredProperty setSP(
final String value, final String schema, final String classname) {
StructuredProperty s = new StructuredProperty(); StructuredProperty s = new StructuredProperty();
s.setValue(value); s.setValue(value);
Qualifier q = new Qualifier(); Qualifier q = new Qualifier();

View File

@ -1,19 +1,21 @@
package eu.dnetlib.dhp.schema.scholexplorer;
import com.fasterxml.jackson.core.JsonProcessingException; package eu.dnetlib.dhp.schema.scholexplorer;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.junit.jupiter.api.Test;
import java.io.IOException; import java.io.IOException;
import java.util.Arrays; import java.util.Arrays;
import java.util.Collections; import java.util.Collections;
public class DLItest { import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class DLItest {
@Test @Test
public void testMergePublication() throws JsonProcessingException { public void testMergePublication() throws JsonProcessingException {
@ -24,26 +26,27 @@ public class DLItest {
a1.setCompletionStatus("complete"); a1.setCompletionStatus("complete");
DLIPublication a = new DLIPublication(); DLIPublication a = new DLIPublication();
a.setPid(Arrays.asList(createSP("10.11","doi","dnet:pid_types"), createSP("123456","pdb","dnet:pid_types"))); a
.setPid(
Arrays
.asList(
createSP("10.11", "doi", "dnet:pid_types"),
createSP("123456", "pdb", "dnet:pid_types")));
a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle"))); a.setTitle(Collections.singletonList(createSP("A Title", "title", "dnetTitle")));
a.setDlicollectedfrom(Arrays.asList(createCollectedFrom("dct","datacite","complete"),createCollectedFrom("dct","datacite","incomplete"))); a
.setDlicollectedfrom(
Arrays
.asList(
createCollectedFrom("dct", "datacite", "complete"),
createCollectedFrom("dct", "datacite", "incomplete")));
a.setCompletionStatus("incomplete"); a.setCompletionStatus("incomplete");
a.mergeFrom(a1); a.mergeFrom(a1);
ObjectMapper mapper = new ObjectMapper(); ObjectMapper mapper = new ObjectMapper();
System.out.println(mapper.writeValueAsString(a)); System.out.println(mapper.writeValueAsString(a));
} }
@Test @Test
public void testDeserialization() throws IOException { public void testDeserialization() throws IOException {
@ -56,7 +59,8 @@ public class DLItest {
System.out.println(mapper.writeValueAsString(dliDataset)); System.out.println(mapper.writeValueAsString(dliDataset));
} }
private ProvenaceInfo createCollectedFrom(final String id, final String name, final String completionStatus) { private ProvenaceInfo createCollectedFrom(
final String id, final String name, final String completionStatus) {
ProvenaceInfo p = new ProvenaceInfo(); ProvenaceInfo p = new ProvenaceInfo();
p.setId(id); p.setId(id);
p.setName(name); p.setName(name);
@ -64,8 +68,8 @@ public class DLItest {
return p; return p;
} }
private StructuredProperty createSP(
private StructuredProperty createSP(final String value, final String className, final String schemeName) { final String value, final String className, final String schemeName) {
StructuredProperty p = new StructuredProperty(); StructuredProperty p = new StructuredProperty();
p.setValue(value); p.setValue(value);
Qualifier schema = new Qualifier(); Qualifier schema = new Qualifier();
@ -76,6 +80,4 @@ public class DLItest {
p.setQualifier(schema); p.setQualifier(schema);
return p; return p;
} }
} }

View File

@ -47,6 +47,16 @@
<artifactId>jaxen</artifactId> <artifactId>jaxen</artifactId>
</dependency> </dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-distcp</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-openaire-data-protos</artifactId>
</dependency>
<dependency> <dependency>
<groupId>eu.dnetlib.dhp</groupId> <groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId> <artifactId>dhp-schemas</artifactId>
@ -57,6 +67,44 @@
<groupId>eu.dnetlib</groupId> <groupId>eu.dnetlib</groupId>
<artifactId>dnet-actionmanager-api</artifactId> <artifactId>dnet-actionmanager-api</artifactId>
</dependency> </dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-actionmanager-common</artifactId>
<exclusions>
<exclusion>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-openaireplus-mapping-utils</artifactId>
</exclusion>
<exclusion>
<groupId>saxonica</groupId>
<artifactId>saxon</artifactId>
</exclusion>
<exclusion>
<groupId>saxonica</groupId>
<artifactId>saxon-dom</artifactId>
</exclusion>
<exclusion>
<groupId>jgrapht</groupId>
<artifactId>jgrapht</artifactId>
</exclusion>
<exclusion>
<groupId>net.sf.ehcache</groupId>
<artifactId>ehcache</artifactId>
</exclusion>
<exclusion>
<groupId>org.springframework</groupId>
<artifactId>spring-test</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.*</groupId>
<artifactId>*</artifactId>
</exclusion>
<exclusion>
<groupId>apache</groupId>
<artifactId>*</artifactId>
</exclusion>
</exclusions>
</dependency>
</dependencies> </dependencies>
</project> </project>

View File

@ -1,20 +1,5 @@
package eu.dnetlib.dhp.actionmanager;
import com.google.common.base.Splitter; package eu.dnetlib.dhp.actionmanager;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
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 org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable; import java.io.Serializable;
import java.io.StringReader; import java.io.StringReader;
@ -23,23 +8,49 @@ import java.util.List;
import java.util.NoSuchElementException; import java.util.NoSuchElementException;
import java.util.stream.Collectors; import java.util.stream.Collectors;
import org.dom4j.Document;
import org.dom4j.Element;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
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;
public class ISClient implements Serializable { public class ISClient implements Serializable {
private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final String INPUT_ACTION_SET_ID_SEPARATOR = ","; private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
public static List<String> getLatestRawsetPaths(String isLookupUrl, String setIds) { private final ISLookUpService isLookup;
ISLookUpService isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl); public ISClient(String isLookupUrl) {
ISClient isClient = new ISClient(); isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
List<String> ids = Lists.newArrayList(Splitter.on(INPUT_ACTION_SET_ID_SEPARATOR) }
public List<String> getLatestRawsetPaths(String setIds) {
List<String> ids = Lists
.newArrayList(
Splitter
.on(INPUT_ACTION_SET_ID_SEPARATOR)
.omitEmptyStrings() .omitEmptyStrings()
.trimResults() .trimResults()
.split(setIds)); .split(setIds));
return ids.stream() return ids
.map(id -> isClient.getSet(isLookup, id)) .stream()
.map(id -> getSet(isLookup, id))
.map(as -> as.getPathToLatest()) .map(as -> as.getPathToLatest())
.collect(Collectors.toCollection(ArrayList::new)); .collect(Collectors.toCollection(ArrayList::new));
} }
@ -47,7 +58,9 @@ public class ISClient implements Serializable {
private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) { private ActionManagerSet getSet(ISLookUpService isLookup, final String setId) {
final String q = "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') " final String q = "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') "
+ "where $x//SET/@id = '" + setId + "' return $x"; + "where $x//SET/@id = '"
+ setId
+ "' return $x";
try { try {
final String basePath = getBasePathHDFS(isLookup); final String basePath = getBasePathHDFS(isLookup);
@ -58,7 +71,8 @@ public class ISClient implements Serializable {
} }
} }
private ActionManagerSet getActionManagerSet(final String basePath, final String profile) throws ActionManagerException { private ActionManagerSet getActionManagerSet(final String basePath, final String profile)
throws ActionManagerException {
final SAXReader reader = new SAXReader(); final SAXReader reader = new SAXReader();
final ActionManagerSet set = new ActionManagerSet(); final ActionManagerSet set = new ActionManagerSet();
@ -68,13 +82,21 @@ public class ISClient implements Serializable {
set.setId(doc.valueOf("//SET/@id").trim()); set.setId(doc.valueOf("//SET/@id").trim());
set.setName(doc.valueOf("//SET").trim()); set.setName(doc.valueOf("//SET").trim());
set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim())); set.setImpact(ImpactTypes.valueOf(doc.valueOf("//IMPACT").trim()));
set.setLatest(doc.valueOf("//RAW_SETS/LATEST/@id"), doc.valueOf("//RAW_SETS/LATEST/@creationDate"), doc.valueOf("//RAW_SETS/LATEST/@lastUpdate")); set
.setLatest(
doc.valueOf("//RAW_SETS/LATEST/@id"),
doc.valueOf("//RAW_SETS/LATEST/@creationDate"),
doc.valueOf("//RAW_SETS/LATEST/@lastUpdate"));
set.setDirectory(doc.valueOf("//SET/@directory")); set.setDirectory(doc.valueOf("//SET/@directory"));
final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED"); final List expiredNodes = doc.selectNodes("//RAW_SETS/EXPIRED");
if (expiredNodes != null) { if (expiredNodes != null) {
for (int i = 0; i < expiredNodes.size(); i++) { for (int i = 0; i < expiredNodes.size(); i++) {
Element ex = (Element) expiredNodes.get(i); Element ex = (Element) expiredNodes.get(i);
set.addExpired(ex.attributeValue("id"), ex.attributeValue("creationDate"), ex.attributeValue("lastUpdate")); set
.addExpired(
ex.attributeValue("id"),
ex.attributeValue("creationDate"),
ex.attributeValue("lastUpdate"));
} }
} }
@ -96,9 +118,11 @@ public class ISClient implements Serializable {
return queryServiceProperty(isLookup, "basePath"); return queryServiceProperty(isLookup, "basePath");
} }
private String queryServiceProperty(ISLookUpService isLookup, final String propertyName) throws ActionManagerException { private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
throws ActionManagerException {
final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='" final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
+ propertyName + "']/@value/string()"; + propertyName
+ "']/@value/string()";
log.debug("quering for service property: " + q); log.debug("quering for service property: " + q);
try { try {
final List<String> value = isLookup.quickSearchProfile(q); final List<String> value = isLookup.quickSearchProfile(q);
@ -117,6 +141,4 @@ public class ISClient implements Serializable {
throw new ActionManagerException(msg, e); throw new ActionManagerException(msg, e);
} }
} }
} }

View File

@ -0,0 +1,69 @@
package eu.dnetlib.dhp.actionmanager.migration;
import java.util.Comparator;
import eu.dnetlib.data.proto.FieldTypeProtos.Qualifier;
public class LicenseComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if (lClass.equals("OPEN SOURCE"))
return -1;
if (rClass.equals("OPEN SOURCE"))
return 1;
if (lClass.equals("OPEN"))
return -1;
if (rClass.equals("OPEN"))
return 1;
if (lClass.equals("6MONTHS"))
return -1;
if (rClass.equals("6MONTHS"))
return 1;
if (lClass.equals("12MONTHS"))
return -1;
if (rClass.equals("12MONTHS"))
return 1;
if (lClass.equals("EMBARGO"))
return -1;
if (rClass.equals("EMBARGO"))
return 1;
if (lClass.equals("RESTRICTED"))
return -1;
if (rClass.equals("RESTRICTED"))
return 1;
if (lClass.equals("CLOSED"))
return -1;
if (rClass.equals("CLOSED"))
return 1;
if (lClass.equals("UNKNOWN"))
return -1;
if (rClass.equals("UNKNOWN"))
return 1;
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
}

View File

@ -0,0 +1,194 @@
package eu.dnetlib.dhp.actionmanager.migration;
import java.io.File;
import java.io.FileOutputStream;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.tools.DistCp;
import org.apache.hadoop.tools.DistCpOptions;
import org.apache.hadoop.util.ToolRunner;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
public class MigrateActionSet {
private static final Logger log = LoggerFactory.getLogger(MigrateActionSet.class);
private static final String SEPARATOR = "/";
private static final String TARGET_PATHS = "target_paths";
private static final String RAWSET_PREFIX = "rawset_";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
MigrateActionSet.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/migrate_actionsets_parameters.json")));
parser.parseArgument(args);
new MigrateActionSet().run(parser);
}
private void run(ArgumentApplicationParser parser) throws Exception {
final String isLookupUrl = parser.get("isLookupUrl");
final String sourceNN = parser.get("sourceNameNode");
final String targetNN = parser.get("targetNameNode");
final String workDir = parser.get("workingDirectory");
final Integer distcp_num_maps = Integer.parseInt(parser.get("distcp_num_maps"));
final String distcp_memory_mb = parser.get("distcp_memory_mb");
final String distcp_task_timeout = parser.get("distcp_task_timeout");
final String transform_only_s = parser.get("transform_only");
log.info("transform only param: {}", transform_only_s);
final Boolean transformOnly = Boolean.valueOf(parser.get("transform_only"));
log.info("transform only: {}", transformOnly);
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
Configuration conf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
FileSystem targetFS = FileSystem.get(conf);
Configuration sourceConf = getConfiguration(distcp_task_timeout, distcp_memory_mb, distcp_num_maps);
sourceConf.set(FileSystem.FS_DEFAULT_NAME_KEY, sourceNN);
FileSystem sourceFS = FileSystem.get(sourceConf);
Properties props = new Properties();
List<Path> targetPaths = new ArrayList<>();
final List<Path> sourcePaths = getSourcePaths(sourceNN, isLookUp);
log
.info(
"paths to process:\n{}",
sourcePaths.stream().map(p -> p.toString()).collect(Collectors.joining("\n")));
for (Path source : sourcePaths) {
if (!sourceFS.exists(source)) {
log.warn("skipping unexisting path: {}", source);
} else {
LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(source.toUri().getPath()));
final String rawSet = pathQ.pollLast();
log.info("got RAWSET: {}", rawSet);
if (StringUtils.isNotBlank(rawSet) && rawSet.startsWith(RAWSET_PREFIX)) {
final String actionSetDirectory = pathQ.pollLast();
final Path targetPath = new Path(
targetNN + workDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawSet);
log.info("using TARGET PATH: {}", targetPath);
if (!transformOnly) {
if (targetFS.exists(targetPath)) {
targetFS.delete(targetPath, true);
}
runDistcp(
distcp_num_maps, distcp_memory_mb, distcp_task_timeout, conf, source, targetPath);
}
targetPaths.add(targetPath);
}
}
}
props
.setProperty(
TARGET_PATHS, targetPaths.stream().map(p -> p.toString()).collect(Collectors.joining(",")));
File file = new File(System.getProperty("oozie.action.output.properties"));
try (OutputStream os = new FileOutputStream(file)) {
props.store(os, "");
}
System.out.println(file.getAbsolutePath());
}
private void runDistcp(
Integer distcp_num_maps,
String distcp_memory_mb,
String distcp_task_timeout,
Configuration conf,
Path source,
Path targetPath)
throws Exception {
final DistCpOptions op = new DistCpOptions(source, targetPath);
op.setMaxMaps(distcp_num_maps);
op.preserve(DistCpOptions.FileAttribute.BLOCKSIZE);
op.preserve(DistCpOptions.FileAttribute.REPLICATION);
op.preserve(DistCpOptions.FileAttribute.CHECKSUMTYPE);
int res = ToolRunner
.run(
new DistCp(conf, op),
new String[] {
"-Dmapred.task.timeout=" + distcp_task_timeout,
"-Dmapreduce.map.memory.mb=" + distcp_memory_mb,
"-pb",
"-m " + distcp_num_maps,
source.toString(),
targetPath.toString()
});
if (res != 0) {
throw new RuntimeException(String.format("distcp exited with code %s", res));
}
}
private Configuration getConfiguration(
String distcp_task_timeout, String distcp_memory_mb, Integer distcp_num_maps) {
final Configuration conf = new Configuration();
conf.set("dfs.webhdfs.socket.connect-timeout", distcp_task_timeout);
conf.set("dfs.webhdfs.socket.read-timeout", distcp_task_timeout);
conf.set("dfs.http.client.retry.policy.enabled", "true");
conf.set("mapred.task.timeout", distcp_task_timeout);
conf.set("mapreduce.map.memory.mb", distcp_memory_mb);
conf.set("mapred.map.tasks", String.valueOf(distcp_num_maps));
return conf;
}
private List<Path> getSourcePaths(String sourceNN, ISLookUpService isLookUp)
throws ISLookUpException {
String XQUERY = "distinct-values(\n"
+ "let $basePath := collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()\n"
+ "for $x in collection('/db/DRIVER/ActionManagerSetDSResources/ActionManagerSetDSResourceType') \n"
+ "let $setDir := $x//SET/@directory/string()\n"
+ "let $rawSet := $x//RAW_SETS/LATEST/@id/string()\n"
+ "return concat($basePath, '/', $setDir, '/', $rawSet))";
log.info(String.format("running xquery:\n%s", XQUERY));
return isLookUp
.quickSearchProfile(XQUERY)
.stream()
.map(p -> sourceNN + p)
.map(Path::new)
.collect(Collectors.toList());
}
}

View File

@ -0,0 +1,664 @@
package eu.dnetlib.dhp.actionmanager.migration;
import static eu.dnetlib.data.proto.KindProtos.Kind.entity;
import static eu.dnetlib.data.proto.KindProtos.Kind.relation;
import static eu.dnetlib.data.proto.TypeProtos.*;
import static eu.dnetlib.data.proto.TypeProtos.Type.*;
import java.io.Serializable;
import java.util.List;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Lists;
import com.googlecode.protobuf.format.JsonFormat;
import eu.dnetlib.data.proto.*;
import eu.dnetlib.dhp.schema.oaf.*;
public class ProtoConverter implements Serializable {
public static final String UNKNOWN = "UNKNOWN";
public static final String NOT_AVAILABLE = "not available";
public static final String DNET_ACCESS_MODES = "dnet:access_modes";
public static Oaf convert(OafProtos.Oaf oaf) {
try {
switch (oaf.getKind()) {
case entity:
return convertEntity(oaf);
case relation:
return convertRelation(oaf);
default:
throw new IllegalArgumentException("invalid kind " + oaf.getKind());
}
} catch (Throwable e) {
throw new RuntimeException("error on getting " + JsonFormat.printToString(oaf), e);
}
}
private static Relation convertRelation(OafProtos.Oaf oaf) {
final OafProtos.OafRel r = oaf.getRel();
final Relation rel = new Relation();
rel.setDataInfo(mapDataInfo(oaf.getDataInfo()));
rel.setLastupdatetimestamp(oaf.getLastupdatetimestamp());
rel.setSource(r.getSource());
rel.setTarget(r.getTarget());
rel.setRelType(r.getRelType().toString());
rel.setSubRelType(r.getSubRelType().toString());
rel.setRelClass(r.getRelClass());
rel
.setCollectedfrom(
r.getCollectedfromCount() > 0
? r.getCollectedfromList().stream().map(kv -> mapKV(kv)).collect(Collectors.toList())
: null);
return rel;
}
private static OafEntity convertEntity(OafProtos.Oaf oaf) {
switch (oaf.getEntity().getType()) {
case result:
final Result r = convertResult(oaf);
r.setInstance(convertInstances(oaf));
return r;
case project:
return convertProject(oaf);
case datasource:
return convertDataSource(oaf);
case organization:
return convertOrganization(oaf);
default:
throw new RuntimeException("received unknown type");
}
}
private static List<Instance> convertInstances(OafProtos.Oaf oaf) {
final ResultProtos.Result r = oaf.getEntity().getResult();
if (r.getInstanceCount() > 0) {
return r.getInstanceList().stream().map(i -> convertInstance(i)).collect(Collectors.toList());
}
return Lists.newArrayList();
}
private static Instance convertInstance(ResultProtos.Result.Instance ri) {
final Instance i = new Instance();
i.setAccessright(mapQualifier(ri.getAccessright()));
i.setCollectedfrom(mapKV(ri.getCollectedfrom()));
i.setDateofacceptance(mapStringField(ri.getDateofacceptance()));
i.setDistributionlocation(ri.getDistributionlocation());
i.setHostedby(mapKV(ri.getHostedby()));
i.setInstancetype(mapQualifier(ri.getInstancetype()));
i.setLicense(mapStringField(ri.getLicense()));
i.setUrl(ri.getUrlList());
i.setRefereed(mapStringField(ri.getRefereed()));
i.setProcessingchargeamount(mapStringField(ri.getProcessingchargeamount()));
i.setProcessingchargecurrency(mapStringField(ri.getProcessingchargecurrency()));
return i;
}
private static Organization convertOrganization(OafProtos.Oaf oaf) {
final OrganizationProtos.Organization.Metadata m = oaf.getEntity().getOrganization().getMetadata();
final Organization org = setOaf(new Organization(), oaf);
setEntity(org, oaf);
org.setLegalshortname(mapStringField(m.getLegalshortname()));
org.setLegalname(mapStringField(m.getLegalname()));
org
.setAlternativeNames(
m
.getAlternativeNamesList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
org.setWebsiteurl(mapStringField(m.getWebsiteurl()));
org.setLogourl(mapStringField(m.getLogourl()));
org.setEclegalbody(mapStringField(m.getEclegalbody()));
org.setEclegalperson(mapStringField(m.getEclegalperson()));
org.setEcnonprofit(mapStringField(m.getEcnonprofit()));
org.setEcresearchorganization(mapStringField(m.getEcresearchorganization()));
org.setEchighereducation(mapStringField(m.getEchighereducation()));
org
.setEcinternationalorganizationeurinterests(
mapStringField(m.getEcinternationalorganizationeurinterests()));
org.setEcinternationalorganization(mapStringField(m.getEcinternationalorganization()));
org.setEcenterprise(mapStringField(m.getEcenterprise()));
org.setEcsmevalidated(mapStringField(m.getEcsmevalidated()));
org.setEcnutscode(mapStringField(m.getEcnutscode()));
org.setCountry(mapQualifier(m.getCountry()));
return org;
}
private static Datasource convertDataSource(OafProtos.Oaf oaf) {
final DatasourceProtos.Datasource.Metadata m = oaf.getEntity().getDatasource().getMetadata();
final Datasource datasource = setOaf(new Datasource(), oaf);
setEntity(datasource, oaf);
datasource
.setAccessinfopackage(
m
.getAccessinfopackageList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
datasource.setCertificates(mapStringField(m.getCertificates()));
datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl()));
datasource.setContactemail(mapStringField(m.getContactemail()));
datasource.setDatabaseaccessrestriction(mapStringField(m.getDatabaseaccessrestriction()));
datasource.setDatabaseaccesstype(mapStringField(m.getDatabaseaccesstype()));
datasource.setDataprovider(mapBoolField(m.getDataprovider()));
datasource.setDatasourcetype(mapQualifier(m.getDatasourcetype()));
datasource.setDatauploadrestriction(mapStringField(m.getDatauploadrestriction()));
datasource.setCitationguidelineurl(mapStringField(m.getCitationguidelineurl()));
datasource.setDatauploadtype(mapStringField(m.getDatauploadtype()));
datasource.setDateofvalidation(mapStringField(m.getDateofvalidation()));
datasource.setDescription(mapStringField(m.getDescription()));
datasource.setEnglishname(mapStringField(m.getEnglishname()));
datasource.setLatitude(mapStringField(m.getLatitude()));
datasource.setLongitude(mapStringField(m.getLongitude()));
datasource.setLogourl(mapStringField(m.getLogourl()));
datasource.setMissionstatementurl(mapStringField(m.getMissionstatementurl()));
datasource.setNamespaceprefix(mapStringField(m.getNamespaceprefix()));
datasource
.setOdcontenttypes(
m
.getOdcontenttypesList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
datasource
.setOdlanguages(
m
.getOdlanguagesList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
datasource.setOdnumberofitems(mapStringField(m.getOdnumberofitems()));
datasource.setOdnumberofitemsdate(mapStringField(m.getOdnumberofitemsdate()));
datasource.setOdpolicies(mapStringField(m.getOdpolicies()));
datasource.setOfficialname(mapStringField(m.getOfficialname()));
datasource.setOpenairecompatibility(mapQualifier(m.getOpenairecompatibility()));
datasource.setPidsystems(mapStringField(m.getPidsystems()));
datasource
.setPolicies(
m.getPoliciesList().stream().map(ProtoConverter::mapKV).collect(Collectors.toList()));
datasource.setQualitymanagementkind(mapStringField(m.getQualitymanagementkind()));
datasource.setReleaseenddate(mapStringField(m.getReleaseenddate()));
datasource.setServiceprovider(mapBoolField(m.getServiceprovider()));
datasource.setReleasestartdate(mapStringField(m.getReleasestartdate()));
datasource
.setSubjects(
m
.getSubjectsList()
.stream()
.map(ProtoConverter::mapStructuredProperty)
.collect(Collectors.toList()));
datasource.setVersioning(mapBoolField(m.getVersioning()));
datasource.setWebsiteurl(mapStringField(m.getWebsiteurl()));
datasource.setJournal(mapJournal(m.getJournal()));
return datasource;
}
private static Project convertProject(OafProtos.Oaf oaf) {
final ProjectProtos.Project.Metadata m = oaf.getEntity().getProject().getMetadata();
final Project project = setOaf(new Project(), oaf);
setEntity(project, oaf);
project.setAcronym(mapStringField(m.getAcronym()));
project.setCallidentifier(mapStringField(m.getCallidentifier()));
project.setCode(mapStringField(m.getCode()));
project.setContactemail(mapStringField(m.getContactemail()));
project.setContactfax(mapStringField(m.getContactfax()));
project.setContactfullname(mapStringField(m.getContactfullname()));
project.setContactphone(mapStringField(m.getContactphone()));
project.setContracttype(mapQualifier(m.getContracttype()));
project.setCurrency(mapStringField(m.getCurrency()));
project.setDuration(mapStringField(m.getDuration()));
project.setEcarticle29_3(mapStringField(m.getEcarticle293()));
project.setEcsc39(mapStringField(m.getEcsc39()));
project.setOamandatepublications(mapStringField(m.getOamandatepublications()));
project.setStartdate(mapStringField(m.getStartdate()));
project.setEnddate(mapStringField(m.getEnddate()));
project.setFundedamount(m.getFundedamount());
project.setTotalcost(m.getTotalcost());
project.setKeywords(mapStringField(m.getKeywords()));
project
.setSubjects(
m
.getSubjectsList()
.stream()
.map(sp -> mapStructuredProperty(sp))
.collect(Collectors.toList()));
project.setTitle(mapStringField(m.getTitle()));
project.setWebsiteurl(mapStringField(m.getWebsiteurl()));
project
.setFundingtree(
m.getFundingtreeList().stream().map(f -> mapStringField(f)).collect(Collectors.toList()));
project.setJsonextrainfo(mapStringField(m.getJsonextrainfo()));
project.setSummary(mapStringField(m.getSummary()));
project.setOptional1(mapStringField(m.getOptional1()));
project.setOptional2(mapStringField(m.getOptional2()));
return project;
}
private static Result convertResult(OafProtos.Oaf oaf) {
switch (oaf.getEntity().getResult().getMetadata().getResulttype().getClassid()) {
case "dataset":
return createDataset(oaf);
case "publication":
return createPublication(oaf);
case "software":
return createSoftware(oaf);
case "other":
return createORP(oaf);
default:
Result result = setOaf(new Result(), oaf);
setEntity(result, oaf);
return setResult(result, oaf);
}
}
private static Software createSoftware(OafProtos.Oaf oaf) {
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
Software software = setOaf(new Software(), oaf);
setEntity(software, oaf);
setResult(software, oaf);
software
.setDocumentationUrl(
m
.getDocumentationUrlList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
software
.setLicense(
m
.getLicenseList()
.stream()
.map(ProtoConverter::mapStructuredProperty)
.collect(Collectors.toList()));
software.setCodeRepositoryUrl(mapStringField(m.getCodeRepositoryUrl()));
software.setProgrammingLanguage(mapQualifier(m.getProgrammingLanguage()));
return software;
}
private static OtherResearchProduct createORP(OafProtos.Oaf oaf) {
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
OtherResearchProduct otherResearchProducts = setOaf(new OtherResearchProduct(), oaf);
setEntity(otherResearchProducts, oaf);
setResult(otherResearchProducts, oaf);
otherResearchProducts
.setContactperson(
m
.getContactpersonList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
otherResearchProducts
.setContactgroup(
m
.getContactgroupList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
otherResearchProducts
.setTool(
m.getToolList().stream().map(ProtoConverter::mapStringField).collect(Collectors.toList()));
return otherResearchProducts;
}
private static Publication createPublication(OafProtos.Oaf oaf) {
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
Publication publication = setOaf(new Publication(), oaf);
setEntity(publication, oaf);
setResult(publication, oaf);
publication.setJournal(mapJournal(m.getJournal()));
return publication;
}
private static Dataset createDataset(OafProtos.Oaf oaf) {
ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
Dataset dataset = setOaf(new Dataset(), oaf);
setEntity(dataset, oaf);
setResult(dataset, oaf);
dataset.setStoragedate(mapStringField(m.getStoragedate()));
dataset.setDevice(mapStringField(m.getDevice()));
dataset.setSize(mapStringField(m.getSize()));
dataset.setVersion(mapStringField(m.getVersion()));
dataset.setLastmetadataupdate(mapStringField(m.getLastmetadataupdate()));
dataset.setMetadataversionnumber(mapStringField(m.getMetadataversionnumber()));
dataset
.setGeolocation(
m
.getGeolocationList()
.stream()
.map(ProtoConverter::mapGeolocation)
.collect(Collectors.toList()));
return dataset;
}
public static <T extends Oaf> T setOaf(T oaf, OafProtos.Oaf o) {
oaf.setDataInfo(mapDataInfo(o.getDataInfo()));
oaf.setLastupdatetimestamp(o.getLastupdatetimestamp());
return oaf;
}
public static <T extends OafEntity> T setEntity(T entity, OafProtos.Oaf oaf) {
// setting Entity fields
final OafProtos.OafEntity e = oaf.getEntity();
entity.setId(e.getId());
entity.setOriginalId(e.getOriginalIdList());
entity
.setCollectedfrom(
e.getCollectedfromList().stream().map(ProtoConverter::mapKV).collect(Collectors.toList()));
entity
.setPid(
e
.getPidList()
.stream()
.map(ProtoConverter::mapStructuredProperty)
.collect(Collectors.toList()));
entity.setDateofcollection(e.getDateofcollection());
entity.setDateoftransformation(e.getDateoftransformation());
entity
.setExtraInfo(
e
.getExtraInfoList()
.stream()
.map(ProtoConverter::mapExtraInfo)
.collect(Collectors.toList()));
return entity;
}
public static <T extends Result> T setResult(T entity, OafProtos.Oaf oaf) {
// setting Entity fields
final ResultProtos.Result.Metadata m = oaf.getEntity().getResult().getMetadata();
entity
.setAuthor(
m.getAuthorList().stream().map(ProtoConverter::mapAuthor).collect(Collectors.toList()));
entity.setResulttype(mapQualifier(m.getResulttype()));
entity.setLanguage(mapQualifier(m.getLanguage()));
entity
.setCountry(
m
.getCountryList()
.stream()
.map(ProtoConverter::mapQualifierAsCountry)
.collect(Collectors.toList()));
entity
.setSubject(
m
.getSubjectList()
.stream()
.map(ProtoConverter::mapStructuredProperty)
.collect(Collectors.toList()));
entity
.setTitle(
m
.getTitleList()
.stream()
.map(ProtoConverter::mapStructuredProperty)
.collect(Collectors.toList()));
entity
.setRelevantdate(
m
.getRelevantdateList()
.stream()
.map(ProtoConverter::mapStructuredProperty)
.collect(Collectors.toList()));
entity
.setDescription(
m
.getDescriptionList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
entity.setDateofacceptance(mapStringField(m.getDateofacceptance()));
entity.setPublisher(mapStringField(m.getPublisher()));
entity.setEmbargoenddate(mapStringField(m.getEmbargoenddate()));
entity
.setSource(
m
.getSourceList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
entity
.setFulltext(
m
.getFulltextList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
entity
.setFormat(
m
.getFormatList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
entity
.setContributor(
m
.getContributorList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
entity.setResourcetype(mapQualifier(m.getResourcetype()));
entity
.setCoverage(
m
.getCoverageList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
entity
.setContext(
m.getContextList().stream().map(ProtoConverter::mapContext).collect(Collectors.toList()));
entity.setBestaccessright(getBestAccessRights(oaf.getEntity().getResult().getInstanceList()));
return entity;
}
private static Qualifier getBestAccessRights(List<ResultProtos.Result.Instance> instanceList) {
if (instanceList != null) {
final Optional<FieldTypeProtos.Qualifier> min = instanceList
.stream()
.map(i -> i.getAccessright())
.min(new LicenseComparator());
final Qualifier rights = min.isPresent() ? mapQualifier(min.get()) : new Qualifier();
if (StringUtils.isBlank(rights.getClassid())) {
rights.setClassid(UNKNOWN);
}
if (StringUtils.isBlank(rights.getClassname())
|| UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
rights.setClassname(NOT_AVAILABLE);
}
if (StringUtils.isBlank(rights.getSchemeid())) {
rights.setSchemeid(DNET_ACCESS_MODES);
}
if (StringUtils.isBlank(rights.getSchemename())) {
rights.setSchemename(DNET_ACCESS_MODES);
}
return rights;
}
return null;
}
private static Context mapContext(ResultProtos.Result.Context context) {
final Context entity = new Context();
entity.setId(context.getId());
entity
.setDataInfo(
context
.getDataInfoList()
.stream()
.map(ProtoConverter::mapDataInfo)
.collect(Collectors.toList()));
return entity;
}
public static KeyValue mapKV(FieldTypeProtos.KeyValue kv) {
final KeyValue keyValue = new KeyValue();
keyValue.setKey(kv.getKey());
keyValue.setValue(kv.getValue());
keyValue.setDataInfo(mapDataInfo(kv.getDataInfo()));
return keyValue;
}
public static DataInfo mapDataInfo(FieldTypeProtos.DataInfo d) {
final DataInfo dataInfo = new DataInfo();
dataInfo.setDeletedbyinference(d.getDeletedbyinference());
dataInfo.setInferenceprovenance(d.getInferenceprovenance());
dataInfo.setInferred(d.getInferred());
dataInfo.setInvisible(d.getInvisible());
dataInfo.setProvenanceaction(mapQualifier(d.getProvenanceaction()));
dataInfo.setTrust(d.getTrust());
return dataInfo;
}
public static Qualifier mapQualifier(FieldTypeProtos.Qualifier q) {
final Qualifier qualifier = new Qualifier();
qualifier.setClassid(q.getClassid());
qualifier.setClassname(q.getClassname());
qualifier.setSchemeid(q.getSchemeid());
qualifier.setSchemename(q.getSchemename());
return qualifier;
}
public static Country mapQualifierAsCountry(FieldTypeProtos.Qualifier q) {
final Country c = new Country();
c.setClassid(q.getClassid());
c.setClassname(q.getClassname());
c.setSchemeid(q.getSchemeid());
c.setSchemename(q.getSchemename());
c.setDataInfo(mapDataInfo(q.getDataInfo()));
return c;
}
public static StructuredProperty mapStructuredProperty(FieldTypeProtos.StructuredProperty sp) {
final StructuredProperty structuredProperty = new StructuredProperty();
structuredProperty.setValue(sp.getValue());
structuredProperty.setQualifier(mapQualifier(sp.getQualifier()));
structuredProperty.setDataInfo(mapDataInfo(sp.getDataInfo()));
return structuredProperty;
}
public static ExtraInfo mapExtraInfo(FieldTypeProtos.ExtraInfo extraInfo) {
final ExtraInfo entity = new ExtraInfo();
entity.setName(extraInfo.getName());
entity.setTypology(extraInfo.getTypology());
entity.setProvenance(extraInfo.getProvenance());
entity.setTrust(extraInfo.getTrust());
entity.setValue(extraInfo.getValue());
return entity;
}
public static OAIProvenance mapOAIProvenance(FieldTypeProtos.OAIProvenance oaiProvenance) {
final OAIProvenance entity = new OAIProvenance();
entity.setOriginDescription(mapOriginalDescription(oaiProvenance.getOriginDescription()));
return entity;
}
public static OriginDescription mapOriginalDescription(
FieldTypeProtos.OAIProvenance.OriginDescription originDescription) {
final OriginDescription originDescriptionResult = new OriginDescription();
originDescriptionResult.setHarvestDate(originDescription.getHarvestDate());
originDescriptionResult.setAltered(originDescription.getAltered());
originDescriptionResult.setBaseURL(originDescription.getBaseURL());
originDescriptionResult.setIdentifier(originDescription.getIdentifier());
originDescriptionResult.setDatestamp(originDescription.getDatestamp());
originDescriptionResult.setMetadataNamespace(originDescription.getMetadataNamespace());
return originDescriptionResult;
}
public static Field<String> mapStringField(FieldTypeProtos.StringField s) {
final Field<String> stringField = new Field<>();
stringField.setValue(s.getValue());
stringField.setDataInfo(mapDataInfo(s.getDataInfo()));
return stringField;
}
public static Field<Boolean> mapBoolField(FieldTypeProtos.BoolField b) {
final Field<Boolean> booleanField = new Field<>();
booleanField.setValue(b.getValue());
booleanField.setDataInfo(mapDataInfo(b.getDataInfo()));
return booleanField;
}
public static Field<Integer> mapIntField(FieldTypeProtos.IntField b) {
final Field<Integer> entity = new Field<>();
entity.setValue(b.getValue());
entity.setDataInfo(mapDataInfo(b.getDataInfo()));
return entity;
}
public static Journal mapJournal(FieldTypeProtos.Journal j) {
final Journal journal = new Journal();
journal.setConferencedate(j.getConferencedate());
journal.setConferenceplace(j.getConferenceplace());
journal.setEdition(j.getEdition());
journal.setEp(j.getEp());
journal.setIss(j.getIss());
journal.setIssnLinking(j.getIssnLinking());
journal.setIssnOnline(j.getIssnOnline());
journal.setIssnPrinted(j.getIssnPrinted());
journal.setName(j.getName());
journal.setSp(j.getSp());
journal.setVol(j.getVol());
journal.setDataInfo(mapDataInfo(j.getDataInfo()));
return journal;
}
public static Author mapAuthor(FieldTypeProtos.Author author) {
final Author entity = new Author();
entity.setFullname(author.getFullname());
entity.setName(author.getName());
entity.setSurname(author.getSurname());
entity.setRank(author.getRank());
entity
.setPid(
author
.getPidList()
.stream()
.map(
kv -> {
final StructuredProperty sp = new StructuredProperty();
sp.setValue(kv.getValue());
final Qualifier q = new Qualifier();
q.setClassid(kv.getKey());
q.setClassname(kv.getKey());
sp.setQualifier(q);
return sp;
})
.collect(Collectors.toList()));
entity
.setAffiliation(
author
.getAffiliationList()
.stream()
.map(ProtoConverter::mapStringField)
.collect(Collectors.toList()));
return entity;
}
public static GeoLocation mapGeolocation(ResultProtos.Result.GeoLocation geoLocation) {
final GeoLocation entity = new GeoLocation();
entity.setPoint(geoLocation.getPoint());
entity.setBox(geoLocation.getBox());
entity.setPlace(geoLocation.getPlace());
return entity;
}
}

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@ -0,0 +1,172 @@
package eu.dnetlib.dhp.actionmanager.migration;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import java.io.IOException;
import java.io.Serializable;
import java.util.LinkedList;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.apache.hadoop.io.Text;
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaSparkContext;
import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import com.google.protobuf.InvalidProtocolBufferException;
import eu.dnetlib.data.proto.OafProtos;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.action.AtomicAction;
import eu.dnetlib.dhp.schema.oaf.*;
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 TransformActions implements Serializable {
private static final Logger log = LoggerFactory.getLogger(TransformActions.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String SEPARATOR = "/";
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
IOUtils
.toString(
MigrateActionSet.class
.getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/migration/transform_actionsets_parameters.json")));
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final String inputPaths = parser.get("inputPaths");
if (StringUtils.isBlank(inputPaths)) {
throw new RuntimeException("empty inputPaths");
}
log.info("inputPaths: {}", inputPaths);
final String targetBaseDir = getTargetBaseDir(isLookupUrl);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf, isSparkSessionManaged, spark -> transformActions(inputPaths, targetBaseDir, spark));
}
private static void transformActions(String inputPaths, String targetBaseDir, SparkSession spark)
throws IOException {
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
final FileSystem fs = FileSystem.get(spark.sparkContext().hadoopConfiguration());
for (String sourcePath : Lists.newArrayList(Splitter.on(",").split(inputPaths))) {
LinkedList<String> pathQ = Lists.newLinkedList(Splitter.on(SEPARATOR).split(sourcePath));
final String rawset = pathQ.pollLast();
final String actionSetDirectory = pathQ.pollLast();
final Path targetDirectory = new Path(targetBaseDir + SEPARATOR + actionSetDirectory + SEPARATOR + rawset);
if (fs.exists(targetDirectory)) {
log.info("found target directory '{}", targetDirectory);
fs.delete(targetDirectory, true);
log.info("deleted target directory '{}", targetDirectory);
}
log.info("transforming actions from '{}' to '{}'", sourcePath, targetDirectory);
sc
.sequenceFile(sourcePath, Text.class, Text.class)
.map(a -> eu.dnetlib.actionmanager.actions.AtomicAction.fromJSON(a._2().toString()))
.map(TransformActions::doTransform)
.filter(Objects::nonNull)
.mapToPair(
a -> new Tuple2<>(a.getClazz().toString(), OBJECT_MAPPER.writeValueAsString(a)))
.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
.saveAsNewAPIHadoopFile(
targetDirectory.toString(),
Text.class,
Text.class,
SequenceFileOutputFormat.class,
sc.hadoopConfiguration());
}
}
private static AtomicAction doTransform(eu.dnetlib.actionmanager.actions.AtomicAction aa)
throws InvalidProtocolBufferException {
// dedup similarity relations had empty target value, don't migrate them
if (aa.getTargetValue().length == 0) {
return null;
}
final OafProtos.Oaf proto_oaf = OafProtos.Oaf.parseFrom(aa.getTargetValue());
final Oaf oaf = ProtoConverter.convert(proto_oaf);
switch (proto_oaf.getKind()) {
case entity:
switch (proto_oaf.getEntity().getType()) {
case datasource:
return new AtomicAction<>(Datasource.class, (Datasource) oaf);
case organization:
return new AtomicAction<>(Organization.class, (Organization) oaf);
case project:
return new AtomicAction<>(Project.class, (Project) oaf);
case result:
final String resulttypeid = proto_oaf
.getEntity()
.getResult()
.getMetadata()
.getResulttype()
.getClassid();
switch (resulttypeid) {
case "publication":
return new AtomicAction<>(Publication.class, (Publication) oaf);
case "software":
return new AtomicAction<>(Software.class, (Software) oaf);
case "other":
return new AtomicAction<>(OtherResearchProduct.class, (OtherResearchProduct) oaf);
case "dataset":
return new AtomicAction<>(Dataset.class, (Dataset) oaf);
default:
// can be an update, where the resulttype is not specified
return new AtomicAction<>(Result.class, (Result) oaf);
}
default:
throw new IllegalArgumentException(
"invalid entity type: " + proto_oaf.getEntity().getType());
}
case relation:
return new AtomicAction<>(Relation.class, (Relation) oaf);
default:
throw new IllegalArgumentException("invalid kind: " + proto_oaf.getKind());
}
}
private static String getTargetBaseDir(String isLookupUrl) throws ISLookUpException {
ISLookUpService isLookUp = ISLookupClientFactory.getLookUpService(isLookupUrl);
String XQUERY = "collection('/db/DRIVER/ServiceResources/ActionManagerServiceResourceType')//SERVICE_PROPERTIES/PROPERTY[@key = 'basePath']/@value/string()";
return isLookUp.getResourceProfileByQuery(XQUERY);
}
}

View File

@ -1,9 +1,13 @@
package eu.dnetlib.dhp.actionmanager.partition; package eu.dnetlib.dhp.actionmanager.partition;
import eu.dnetlib.dhp.actionmanager.ISClient; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.common.HdfsSupport; import static org.apache.spark.sql.functions.*;
import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.hadoop.io.Text; import org.apache.hadoop.io.Text;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
@ -14,37 +18,47 @@ import org.apache.spark.sql.types.*;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.util.Arrays; import eu.dnetlib.dhp.actionmanager.ISClient;
import java.util.Collections; import eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob;
import java.util.List; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import java.util.Optional; import eu.dnetlib.dhp.common.HdfsSupport;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; /** Partitions given set of action sets by payload type. */
import static org.apache.spark.sql.functions.*;
/**
* Partitions given set of action sets by payload type.
*/
public class PartitionActionSetsByPayloadTypeJob { public class PartitionActionSetsByPayloadTypeJob {
private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class); private static final Logger logger = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
private static final StructType KV_SCHEMA = StructType$.MODULE$.apply( private static final StructType KV_SCHEMA = StructType$.MODULE$
Arrays.asList( .apply(
Arrays
.asList(
StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()), StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty()) StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
));
private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$.apply( private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$
Arrays.asList( .apply(
Arrays
.asList(
StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()), StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
StructField$.MODULE$.apply("payload", DataTypes.StringType, false, Metadata.empty()) StructField$.MODULE$
)); .apply(
"payload", DataTypes.StringType, false, Metadata.empty())));
private ISClient isClient;
public PartitionActionSetsByPayloadTypeJob(String isLookupUrl) {
this.isClient = new ISClient(isLookupUrl);
}
public PartitionActionSetsByPayloadTypeJob() {
}
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils.toString( String jsonConfiguration = IOUtils
.toString(
PromoteActionPayloadForGraphTableJob.class PromoteActionPayloadForGraphTableJob.class
.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json")); .getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/partition/partition_action_sets_by_payload_type_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
@ -63,62 +77,68 @@ public class PartitionActionSetsByPayloadTypeJob {
String isLookupUrl = parser.get("isLookupUrl"); String isLookupUrl = parser.get("isLookupUrl");
logger.info("isLookupUrl: {}", isLookupUrl); logger.info("isLookupUrl: {}", isLookupUrl);
List<String> inputActionSetPaths = ISClient.getLatestRawsetPaths(isLookupUrl, inputActionSetIds); new PartitionActionSetsByPayloadTypeJob(isLookupUrl)
.run(isSparkSessionManaged, inputActionSetIds, outputPath);
}
protected void run(Boolean isSparkSessionManaged, String inputActionSetIds, String outputPath) {
List<String> inputActionSetPaths = getIsClient().getLatestRawsetPaths(inputActionSetIds);
logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths)); logger.info("inputActionSetPaths: {}", String.join(",", inputActionSetPaths));
SparkConf conf = new SparkConf(); SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
runWithSparkSession(conf, isSparkSessionManaged, runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputPath); removeOutputDir(spark, outputPath);
readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath); readAndWriteActionSetsFromPaths(spark, inputActionSetPaths, outputPath);
}); });
} }
private static void removeOutputDir(SparkSession spark, private static void removeOutputDir(SparkSession spark, String path) {
String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
private static void readAndWriteActionSetsFromPaths(SparkSession spark, private static void readAndWriteActionSetsFromPaths(
List<String> inputActionSetPaths, SparkSession spark, List<String> inputActionSetPaths, String outputPath) {
String outputPath) {
inputActionSetPaths inputActionSetPaths
.forEach(inputActionSetPath -> { .stream()
.filter(path -> HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration()))
.forEach(
inputActionSetPath -> {
Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath); Dataset<Row> actionDS = readActionSetFromPath(spark, inputActionSetPath);
saveActions(actionDS, outputPath); saveActions(actionDS, outputPath);
}); });
} }
private static Dataset<Row> readActionSetFromPath(SparkSession spark, private static Dataset<Row> readActionSetFromPath(SparkSession spark, String path) {
String path) {
logger.info("Reading actions from path: {}", path); logger.info("Reading actions from path: {}", path);
List<String> files = HdfsSupport.listFiles(path, spark.sparkContext().hadoopConfiguration());
logger.info("Found files: {}", String.join(",", files));
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
return files
.stream()
.map(file -> {
JavaRDD<Row> rdd = sc JavaRDD<Row> rdd = sc
.sequenceFile(file, Text.class, Text.class) .sequenceFile(path, Text.class, Text.class)
.map(x -> RowFactory.create(x._1().toString(), x._2().toString())); .map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
return spark.createDataFrame(rdd, KV_SCHEMA)
return spark
.createDataFrame(rdd, KV_SCHEMA)
.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA)) .withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
.select(expr("atomic_action.*")); .select(expr("atomic_action.*"));
})
.reduce(spark.createDataFrame(Collections.emptyList(), ATOMIC_ACTION_SCHEMA), Dataset::union);
} }
private static void saveActions(Dataset<Row> actionDS, private static void saveActions(Dataset<Row> actionDS, String path) {
String path) {
logger.info("Saving actions to path: {}", path); logger.info("Saving actions to path: {}", path);
actionDS actionDS.write().partitionBy("clazz").mode(SaveMode.Append).parquet(path);
.write() }
.partitionBy("clazz")
.mode(SaveMode.Append) public ISClient getIsClient() {
.parquet(path); return isClient;
}
public void setIsClient(ISClient isClient) {
this.isClient = isClient;
} }
} }

View File

@ -1,17 +1,16 @@
package eu.dnetlib.dhp.actionmanager.promote; package eu.dnetlib.dhp.actionmanager.promote;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import java.util.function.BiFunction;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.schema.oaf.Oaf; import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity; import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Relation;
import java.util.function.BiFunction; /** OAF model merging support. */
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
/**
* OAF model merging support.
*/
public class MergeAndGet { public class MergeAndGet {
private MergeAndGet() { private MergeAndGet() {
@ -20,8 +19,8 @@ public class MergeAndGet {
/** /**
* Strategy for merging OAF model objects. * Strategy for merging OAF model objects.
* <p> * <p>
* MERGE_FROM_AND_GET: use OAF 'mergeFrom' method * MERGE_FROM_AND_GET: use OAF 'mergeFrom' method SELECT_NEWER_AND_GET: use last update timestamp to return newer
* SELECT_NEWER_AND_GET: use last update timestamp to return newer instance * instance
*/ */
public enum Strategy { public enum Strategy {
MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET MERGE_FROM_AND_GET, SELECT_NEWER_AND_GET
@ -35,7 +34,8 @@ public class MergeAndGet {
* @param <A> Action payload type * @param <A> Action payload type
* @return BiFunction to be used to merge OAF objects * @return BiFunction to be used to merge OAF objects
*/ */
public static <G extends Oaf, A extends Oaf> SerializableSupplier<BiFunction<G, A, G>> functionFor(Strategy strategy) { public static <G extends Oaf, A extends Oaf> SerializableSupplier<BiFunction<G, A, G>> functionFor(
Strategy strategy) {
switch (strategy) { switch (strategy) {
case MERGE_FROM_AND_GET: case MERGE_FROM_AND_GET:
return () -> MergeAndGet::mergeFromAndGet; return () -> MergeAndGet::mergeFromAndGet;
@ -49,26 +49,39 @@ public class MergeAndGet {
if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) { if (isSubClass(x, Relation.class) && isSubClass(y, Relation.class)) {
((Relation) x).mergeFrom((Relation) y); ((Relation) x).mergeFrom((Relation) y);
return x; return x;
} else if (isSubClass(x, OafEntity.class) && isSubClass(y, OafEntity.class) && isSubClass(x, y)) { } else if (isSubClass(x, OafEntity.class)
&& isSubClass(y, OafEntity.class)
&& isSubClass(x, y)) {
((OafEntity) x).mergeFrom((OafEntity) y); ((OafEntity) x).mergeFrom((OafEntity) y);
return x; return x;
} }
throw new RuntimeException(String.format("MERGE_FROM_AND_GET incompatible types: %s, %s", throw new RuntimeException(
String
.format(
"MERGE_FROM_AND_GET incompatible types: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
} }
private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) { private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x; return x;
} else if (x.getClass().equals(y.getClass()) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { } else if (x.getClass().equals(y.getClass())
&& x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
return (G) y; return (G) y;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) { } else if (isSubClass(x, y) && x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {
return x; return x;
} else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) { } else if (isSubClass(x, y) && x.getLastupdatetimestamp() < y.getLastupdatetimestamp()) {
throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s", throw new RuntimeException(
String
.format(
"SELECT_NEWER_AND_GET cannot return right type when it is not the same as left type: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
} }
throw new RuntimeException(String.format("SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s", throw new RuntimeException(
String
.format(
"SELECT_NEWER_AND_GET cannot be used when left is not subtype of right: %s, %s",
x.getClass().getCanonicalName(), y.getClass().getCanonicalName())); x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
} }
} }

View File

@ -1,11 +1,14 @@
package eu.dnetlib.dhp.actionmanager.promote; package eu.dnetlib.dhp.actionmanager.promote;
import com.fasterxml.jackson.databind.ObjectMapper; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier; import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.application.ArgumentApplicationParser; import java.util.Objects;
import eu.dnetlib.dhp.schema.common.ModelSupport; import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.*; import java.util.function.BiFunction;
import java.util.function.Function;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf; import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.api.java.function.MapFunction;
@ -16,26 +19,26 @@ import org.apache.spark.sql.SparkSession;
import org.slf4j.Logger; import org.slf4j.Logger;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.util.Objects; import com.fasterxml.jackson.databind.ObjectMapper;
import java.util.Optional;
import java.util.function.BiFunction;
import java.util.function.Function;
import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass; import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableSupplier;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
/** /** Applies a given action payload file to graph table of compatible type. */
* Applies a given action payload file to graph table of compatible type.
*/
public class PromoteActionPayloadForGraphTableJob { public class PromoteActionPayloadForGraphTableJob {
private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class); private static final Logger logger = LoggerFactory.getLogger(PromoteActionPayloadForGraphTableJob.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception { public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils.toString( String jsonConfiguration = IOUtils
.toString(
PromoteActionPayloadForGraphTableJob.class PromoteActionPayloadForGraphTableJob.class
.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json")); .getResourceAsStream(
"/eu/dnetlib/dhp/actionmanager/promote/promote_action_payload_for_graph_table_input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args); parser.parseArgument(args);
@ -72,10 +75,13 @@ public class PromoteActionPayloadForGraphTableJob {
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses()); conf.registerKryoClasses(ModelSupport.getOafModelClasses());
runWithSparkSession(conf, isSparkSessionManaged, runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> { spark -> {
removeOutputDir(spark, outputGraphTablePath); removeOutputDir(spark, outputGraphTablePath);
promoteActionPayloadForGraphTable(spark, promoteActionPayloadForGraphTable(
spark,
inputGraphTablePath, inputGraphTablePath,
inputActionPayloadPath, inputActionPayloadPath,
outputGraphTablePath, outputGraphTablePath,
@ -85,21 +91,23 @@ public class PromoteActionPayloadForGraphTableJob {
}); });
} }
private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(Class<? extends Oaf> rowClazz, private static void throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(
Class<? extends Oaf> actionPayloadClazz) { Class<? extends Oaf> rowClazz, Class<? extends Oaf> actionPayloadClazz) {
if (!isSubClass(rowClazz, actionPayloadClazz)) { if (!isSubClass(rowClazz, actionPayloadClazz)) {
String msg = String.format("graph table class is not a subclass of action payload class: graph=%s, action=%s", String msg = String
.format(
"graph table class is not a subclass of action payload class: graph=%s, action=%s",
rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName()); rowClazz.getCanonicalName(), actionPayloadClazz.getCanonicalName());
throw new RuntimeException(msg); throw new RuntimeException(msg);
} }
} }
private static void removeOutputDir(SparkSession spark, private static void removeOutputDir(SparkSession spark, String path) {
String path) {
HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
} }
private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(SparkSession spark, private static <G extends Oaf, A extends Oaf> void promoteActionPayloadForGraphTable(
SparkSession spark,
String inputGraphTablePath, String inputGraphTablePath,
String inputActionPayloadPath, String inputActionPayloadPath,
String outputGraphTablePath, String outputGraphTablePath,
@ -109,42 +117,55 @@ public class PromoteActionPayloadForGraphTableJob {
Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz); Dataset<G> rowDS = readGraphTable(spark, inputGraphTablePath, rowClazz);
Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz); Dataset<A> actionPayloadDS = readActionPayload(spark, inputActionPayloadPath, actionPayloadClazz);
Dataset<G> result = promoteActionPayloadForGraphTable(rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz) Dataset<G> result = promoteActionPayloadForGraphTable(
rowDS, actionPayloadDS, strategy, rowClazz, actionPayloadClazz)
.map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz)); .map((MapFunction<G, G>) value -> value, Encoders.bean(rowClazz));
saveGraphTable(result, outputGraphTablePath); saveGraphTable(result, outputGraphTablePath);
} }
private static <G extends Oaf> Dataset<G> readGraphTable(SparkSession spark, private static <G extends Oaf> Dataset<G> readGraphTable(
String path, SparkSession spark, String path, Class<G> rowClazz) {
Class<G> rowClazz) {
logger.info("Reading graph table from path: {}", path); logger.info("Reading graph table from path: {}", path);
return spark return spark
.read() .read()
.parquet(path) .textFile(path)
.as(Encoders.bean(rowClazz)); .map(
(MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz),
Encoders.bean(rowClazz));
/*
* return spark .read() .parquet(path) .as(Encoders.bean(rowClazz));
*/
} }
private static <A extends Oaf> Dataset<A> readActionPayload(SparkSession spark, private static <A extends Oaf> Dataset<A> readActionPayload(
String path, SparkSession spark, String path, Class<A> actionPayloadClazz) {
Class<A> actionPayloadClazz) {
logger.info("Reading action payload from path: {}", path); logger.info("Reading action payload from path: {}", path);
return spark return spark
.read() .read()
.parquet(path) .parquet(path)
.map((MapFunction<Row, A>) value -> OBJECT_MAPPER.readValue(value.<String>getAs("payload"), .map(
actionPayloadClazz), Encoders.bean(actionPayloadClazz)); (MapFunction<Row, A>) value -> OBJECT_MAPPER
.readValue(value.<String> getAs("payload"), actionPayloadClazz),
Encoders.bean(actionPayloadClazz));
} }
private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(Dataset<G> rowDS, private static <G extends Oaf, A extends Oaf> Dataset<G> promoteActionPayloadForGraphTable(
Dataset<G> rowDS,
Dataset<A> actionPayloadDS, Dataset<A> actionPayloadDS,
MergeAndGet.Strategy strategy, MergeAndGet.Strategy strategy,
Class<G> rowClazz, Class<G> rowClazz,
Class<A> actionPayloadClazz) { Class<A> actionPayloadClazz) {
logger.info("Promoting action payload for graph table: payload={}, table={}", actionPayloadClazz.getSimpleName(), rowClazz.getSimpleName()); logger
.info(
"Promoting action payload for graph table: payload={}, table={}",
actionPayloadClazz.getSimpleName(),
rowClazz.getSimpleName());
SerializableSupplier<Function<G, String>> rowIdFn = PromoteActionPayloadForGraphTableJob::idFn; SerializableSupplier<Function<G, String>> rowIdFn = ModelSupport::idFn;
SerializableSupplier<Function<A, String>> actionPayloadIdFn = PromoteActionPayloadForGraphTableJob::idFn; SerializableSupplier<Function<A, String>> actionPayloadIdFn = ModelSupport::idFn;
SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy); SerializableSupplier<BiFunction<G, A, G>> mergeRowWithActionPayloadAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy); SerializableSupplier<BiFunction<G, G, G>> mergeRowsAndGetFn = MergeAndGet.functionFor(strategy);
SerializableSupplier<G> zeroFn = zeroFn(rowClazz); SerializableSupplier<G> zeroFn = zeroFn(rowClazz);
@ -162,44 +183,7 @@ public class PromoteActionPayloadForGraphTableJob {
return PromoteActionPayloadFunctions return PromoteActionPayloadFunctions
.groupGraphTableByIdAndMerge( .groupGraphTableByIdAndMerge(
joinedAndMerged, joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
rowIdFn,
mergeRowsAndGetFn,
zeroFn,
isNotZeroFn,
rowClazz);
}
private static <T extends Oaf> Function<T, String> idFn() {
return x -> {
if (isSubClass(x, Relation.class)) {
return idFnForRelation(x);
}
return idFnForOafEntity(x);
};
}
private static <T extends Oaf> String idFnForRelation(T t) {
Relation r = (Relation) t;
return Optional.ofNullable(r.getSource())
.map(source -> Optional.ofNullable(r.getTarget())
.map(target -> Optional.ofNullable(r.getRelType())
.map(relType -> Optional.ofNullable(r.getSubRelType())
.map(subRelType -> Optional.ofNullable(r.getRelClass())
.map(relClass -> String.join(source, target, relType, subRelType, relClass))
.orElse(String.join(source, target, relType, subRelType))
)
.orElse(String.join(source, target, relType))
)
.orElse(String.join(source, target))
)
.orElse(source)
)
.orElse(null);
}
private static <T extends Oaf> String idFnForOafEntity(T t) {
return ((OafEntity) t).getId();
} }
private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) { private static <T extends Oaf> SerializableSupplier<T> zeroFn(Class<T> clazz) {
@ -234,13 +218,8 @@ public class PromoteActionPayloadForGraphTableJob {
}; };
} }
private static <G extends Oaf> void saveGraphTable(Dataset<G> result, private static <G extends Oaf> void saveGraphTable(Dataset<G> result, String path) {
String path) {
logger.info("Saving graph table to path: {}", path); logger.info("Saving graph table to path: {}", path);
result result.toJSON().write().option("compression", "gzip").text(path);
.toJSON()
.write()
.option("compression", "gzip")
.text(path);
} }
} }

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