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dnet-hadoop
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[stats wf] indicators across stats dbs & updates in the org ids #248

Closed
dimitris.pierrakos wants to merge 1742 commits from beta into beta2master_sept_2022
pull from: beta
merge into: D-Net:beta2master_sept_2022
Conversation 3 Commits 1742 Files Changed 1525 +237844 -42922
1525 changed files with 237844 additions and 42922 deletions
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5
.gitignore vendored
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@ -3,8 +3,6 @@
*.iws
*.ipr
*.iml
*.ipr
*.iws
*~
.vscode
.metals
@ -27,4 +25,5 @@ spark-warehouse
/**/job-override.properties
/**/*.log
/**/.factorypath
/**/.scalafmt.conf
/.java-version

21
.scalafmt.conf Normal file
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@ -0,0 +1,21 @@
style = defaultWithAlign
align.openParenCallSite = false
align.openParenDefnSite = false
align.tokens = [{code = "->"}, {code = "<-"}, {code = "=>", owner = "Case"}]
continuationIndent.callSite = 2
continuationIndent.defnSite = 2
danglingParentheses = true
indentOperator = spray
maxColumn = 120
newlines.alwaysBeforeTopLevelStatements = true
project.excludeFilters = [".*\\.sbt"]
rewrite.rules = [AvoidInfix]
rewrite.rules = [ExpandImportSelectors]
rewrite.rules = [RedundantBraces]
rewrite.rules = [RedundantParens]
rewrite.rules = [SortImports]
rewrite.rules = [SortModifiers]
rewrite.rules = [PreferCurlyFors]
spaces.inImportCurlyBraces = false
unindentTopLevelOperators = true

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CODE_OF_CONDUCT.md Normal file
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@ -0,0 +1,43 @@
# Contributor Code of Conduct
Openness, transparency and our community-driven participatory approach guide us in our day-to-day interactions and decision-making. Our open source projects are no exception. Trust, respect, collaboration and transparency are core values we believe should live and breathe within our projects. Our community welcomes participants from around the world with different experiences, unique perspectives, and great ideas to share.
## Our Pledge
In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
## Our Standards
Examples of behavior that contributes to creating a positive environment include:
- Using welcoming and inclusive language
- Being respectful of differing viewpoints and experiences
- Gracefully accepting constructive criticism
- Attempting collaboration before conflict
- Focusing on what is best for the community
- Showing empathy towards other community members
Examples of unacceptable behavior by participants include:
- Violence, threats of violence, or inciting others to commit self-harm
- The use of sexualized language or imagery and unwelcome sexual attention or advances
- Trolling, intentionally spreading misinformation, insulting/derogatory comments, and personal or political attacks
- Public or private harassment
- Publishing others' private information, such as a physical or electronic address, without explicit permission
- Abuse of the reporting process to intentionally harass or exclude others
- Advocating for, or encouraging, any of the above behavior
- Other conduct which could reasonably be considered inappropriate in a professional setting
## Our Responsibilities
Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
## Scope
This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
## Attribution
This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org/), [version 1.4](https://www.contributor-covenant.org/version/1/4/code-of-conduct.html).

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CONTRIBUTING.md Normal file
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@ -0,0 +1,10 @@
# Contributing to D-Net Hadoop
:+1::tada: First off, thanks for taking the time to contribute! :tada::+1:
This project and everyone participating in it is governed by our [Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [dnet-team@isti.cnr.it](mailto:dnet-team@isti.cnr.it).
The following is a set of guidelines for contributing to this project and its packages. These are mostly guidelines, not rules, which applies to this project as a while, including all its sub-modules.
Use your best judgment, and feel free to propose changes to this document in a pull request.
All contributions are welcome, all contributions will be considered to be contributed under the [project license](LICENSE.md).

0
LICENSE → LICENSE.md
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133
README.md
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@ -1,2 +1,133 @@
# dnet-hadoop
Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning.
Dnet-hadoop is the project that defined all the [OOZIE workflows](https://oozie.apache.org/) for the OpenAIRE Graph construction, processing, provisioning.
This project adheres to the Contributor Covenant [code of conduct](CODE_OF_CONDUCT.md).
By participating, you are expected to uphold this code. Please report unacceptable behavior to [dnet-team@isti.cnr.it](mailto:dnet-team@isti.cnr.it).
This project is licensed under the [AGPL v3 or later version](#LICENSE.md).
How to build, package and run oozie workflows
====================
Oozie-installer is a utility allowing building, uploading and running oozie workflows. In practice, it creates a `*.tar.gz`
package that contains resources that define a workflow and some helper scripts.
This module is automatically executed when running:
`mvn package -Poozie-package -Dworkflow.source.dir=classpath/to/parent/directory/of/oozie_app`
on module having set:
```
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-workflows</artifactId>
</parent>
```
in `pom.xml` file. `oozie-package` profile initializes oozie workflow packaging, `workflow.source.dir` property points to
a workflow (notice: this is not a relative path but a classpath to directory usually holding `oozie_app` subdirectory).
The outcome of this packaging is `oozie-package.tar.gz` file containing inside all the resources required to run Oozie workflow:
- jar packages
- workflow definitions
- job properties
- maintenance scripts
Required properties
====================
In order to include proper workflow within package, `workflow.source.dir` property has to be set. It could be provided
by setting `-Dworkflow.source.dir=some/job/dir` maven parameter.
In oder to define full set of cluster environment properties one should create `~/.dhp/application.properties` file with
the following properties:
- `dhp.hadoop.frontend.user.name` - your user name on hadoop cluster and frontend machine
- `dhp.hadoop.frontend.host.name` - frontend host name
- `dhp.hadoop.frontend.temp.dir` - frontend directory for temporary files
- `dhp.hadoop.frontend.port.ssh` - frontend machine ssh port
- `oozieServiceLoc` - oozie service location required by run_workflow.sh script executing oozie job
- `nameNode` - name node address
- `jobTracker` - job tracker address
- `oozie.execution.log.file.location` - location of file that will be created when executing oozie job, it contains output
produced by `run_workflow.sh` script (needed to obtain oozie job id)
- `maven.executable` - mvn command location, requires parameterization due to a different setup of CI cluster
- `sparkDriverMemory` - amount of memory assigned to spark jobs driver
- `sparkExecutorMemory` - amount of memory assigned to spark jobs executors
- `sparkExecutorCores` - number of cores assigned to spark jobs executors
All values will be overriden with the ones from `job.properties` and eventually `job-override.properties` stored in module's
main folder.
When overriding properties from `job.properties`, `job-override.properties` file can be created in main module directory
(the one containing `pom.xml` file) and define all new properties which will override existing properties.
One can provide those properties one by one as command line `-D` arguments.
Properties overriding order is the following:
1. `pom.xml` defined properties (located in the project root dir)
2. `~/.dhp/application.properties` defined properties
3. `${workflow.source.dir}/job.properties`
4. `job-override.properties` (located in the project root dir)
5. `maven -Dparam=value`
where the maven `-Dparam` property is overriding all the other ones.
Workflow definition requirements
====================
`workflow.source.dir` property should point to the following directory structure:
[${workflow.source.dir}]
|
|-job.properties (optional)
|
\-[oozie_app]
|
\-workflow.xml
This property can be set using maven `-D` switch.
`[oozie_app]` is the default directory name however it can be set to any value as soon as `oozieAppDir` property is
provided with directory name as value.
Sub-workflows are supported as well and sub-workflow directories should be nested within `[oozie_app]` directory.
Creating oozie installer step-by-step
=====================================
Automated oozie-installer steps are the following:
1. creating jar packages: `*.jar` and `*tests.jar` along with copying all dependencies in `target/dependencies`
2. reading properties from maven, `~/.dhp/application.properties`, `job.properties`, `job-override.properties`
3. invoking priming mechanism linking resources from import.txt file (currently resolving subworkflow resources)
4. assembling shell scripts for preparing Hadoop filesystem, uploading Oozie application and starting workflow
5. copying whole `${workflow.source.dir}` content to `target/${oozie.package.file.name}`
6. generating updated `job.properties` file in `target/${oozie.package.file.name}` based on maven,
`~/.dhp/application.properties`, `job.properties` and `job-override.properties`
7. creating `lib` directory (or multiple directories for sub-workflows for each nested directory) and copying jar packages
created at step (1) to each one of them
8. bundling whole `${oozie.package.file.name}` directory into single tar.gz package
Uploading oozie package and running workflow on cluster
=======================================================
In order to simplify deployment and execution process two dedicated profiles were introduced:
- `deploy`
- `run`
to be used along with `oozie-package` profile e.g. by providing `-Poozie-package,deploy,run` maven parameters.
The `deploy` profile supplements packaging process with:
1) uploading oozie-package via scp to `/home/${user.name}/oozie-packages` directory on `${dhp.hadoop.frontend.host.name}` machine
2) extracting uploaded package
3) uploading oozie content to hadoop cluster HDFS location defined in `oozie.wf.application.path` property (generated dynamically by maven build process, based on `${dhp.hadoop.frontend.user.name}` and `workflow.source.dir` properties)
The `run` profile introduces:
1) executing oozie application uploaded to HDFS cluster using `deploy` command. Triggers `run_workflow.sh` script providing runtime properties defined in `job.properties` file.
Notice: ssh access to frontend machine has to be configured on system level and it is preferable to set key-based authentication in order to simplify remote operations.

2
dhp-build/dhp-build-assembly-resources/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-build</artifactId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-assembly-resources</artifactId>

2
dhp-build/dhp-build-properties-maven-plugin/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-build</artifactId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
</parent>
<artifactId>dhp-build-properties-maven-plugin</artifactId>

20
dhp-build/dhp-code-style/pom.xml
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@ -5,7 +5,7 @@
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-code-style</artifactId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
<packaging>jar</packaging>
@ -22,9 +22,20 @@
<id>dnet45-releases</id>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
</repository>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-build/dhp-code-style</url>
</site>
</distributionManagement>
<build>
<extensions>
<extension>
<groupId>org.apache.maven.wagon</groupId>
<artifactId>wagon-ssh</artifactId>
<version>2.10</version>
</extension>
</extensions>
<pluginManagement>
<plugins>
<plugin>
@ -35,14 +46,19 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-site-plugin</artifactId>
<version>3.7.1</version>
<version>3.9.1</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</pluginManagement>
</build>
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
</properties>
</project>

21
dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf Normal file
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@ -0,0 +1,21 @@
style = defaultWithAlign
align.openParenCallSite = false
align.openParenDefnSite = false
align.tokens = [{code = "->"}, {code = "<-"}, {code = "=>", owner = "Case"}]
continuationIndent.callSite = 2
continuationIndent.defnSite = 2
danglingParentheses = true
indentOperator = spray
maxColumn = 120
newlines.alwaysBeforeTopLevelStatements = true
project.excludeFilters = [".*\\.sbt"]
rewrite.rules = [AvoidInfix]
rewrite.rules = [ExpandImportSelectors]
rewrite.rules = [RedundantBraces]
rewrite.rules = [RedundantParens]
rewrite.rules = [SortImports]
rewrite.rules = [SortModifiers]
rewrite.rules = [PreferCurlyFors]
spaces.inImportCurlyBraces = false
unindentTopLevelOperators = true

21
dhp-build/dhp-code-style/src/site/site.xml Normal file
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@ -0,0 +1,21 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
name="DHP-Aggregation">
<skin>
<groupId>org.apache.maven.skins</groupId>
<artifactId>maven-fluido-skin</artifactId>
<version>1.8</version>
</skin>
<poweredBy>
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
</poweredBy>
<body>
<links>
<item name="Code" href="https://code-repo.d4science.org/" />
</links>
<menu ref="modules" />
<menu ref="reports"/>
</body>
</project>

13
dhp-build/pom.xml
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@ -4,12 +4,15 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
</parent>
<artifactId>dhp-build</artifactId>
<packaging>pom</packaging>
<description>This module is a container for the build tools used in dnet-hadoop</description>
<properties>
<maven.javadoc.skip>true</maven.javadoc.skip>
</properties>
<modules>
<module>dhp-code-style</module>
@ -17,4 +20,12 @@
<module>dhp-build-properties-maven-plugin</module>
</modules>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-build/</url>
</site>
</distributionManagement>
</project>

22
dhp-build/src/site/site.xml Normal file
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@ -0,0 +1,22 @@
<?xml version="1.0" encoding="ISO-8859-1"?>
<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
name="DHP-Aggregation">
<skin>
<groupId>org.apache.maven.skins</groupId>
<artifactId>maven-fluido-skin</artifactId>
<version>1.8</version>
</skin>
<poweredBy>
<logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
</poweredBy>
<body>
<links>
<item name="Code" href="https://code-repo.d4science.org/" />
</links>
<menu ref="modules" />
<menu ref="reports"/>
</body>
</project>

64
dhp-common/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.4-SNAPSHOT</version>
<version>1.2.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -13,9 +13,60 @@
<artifactId>dhp-common</artifactId>
<packaging>jar</packaging>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>${dhp.site.stage.path}/dhp-common</url>
</site>
</distributionManagement>
<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>${net.alchim31.maven.version}</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
<execution>
<id>scala-doc</id>
<phase>process-resources</phase> <!-- or wherever -->
<goals>
<goal>doc</goal>
</goals>
</execution>
</executions>
<configuration>
<failOnMultipleScalaVersions>true</failOnMultipleScalaVersions>
<scalaCompatVersion>${scala.binary.version}</scalaCompatVersion>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-pace-core</artifactId>
<version>${project.version}</version>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
@ -32,11 +83,11 @@
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
<dependency>
@ -98,11 +149,6 @@
<artifactId>okhttp</artifactId>
</dependency>
<dependency>
<groupId>eu.dnetlib</groupId>
<artifactId>dnet-pace-core</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
@ -115,7 +161,7 @@
<dependency>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-schemas</artifactId>
<artifactId>${dhp-schemas.artifact}</artifactId>
</dependency>
<dependency>

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
View File

@ -10,6 +10,12 @@ public class Constants {
public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
public static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
public static final String ROR_NS_PREFIX = "ror_________";
public static final String ROR_OPENAIRE_ID = "10|openaire____::993a7ae7a863813cf95028b50708e222";
public static final String ROR_DATASOURCE_NAME = "Research Organization Registry (ROR)";
public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
private Constants() {
@ -45,6 +51,7 @@ public class Constants {
public static final String RETRY_DELAY = "retryDelay";
public static final String CONNECT_TIMEOUT = "connectTimeOut";
public static final String READ_TIMEOUT = "readTimeOut";
public static final String REQUEST_METHOD = "requestMethod";
public static final String FROM_DATE_OVERRIDE = "fromDateOverride";
public static final String UNTIL_DATE_OVERRIDE = "untilDateOverride";

413
dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java
View File

@ -1,413 +0,0 @@
package eu.dnetlib.dhp.common;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.dump.oaf.*;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance;
import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class GraphResultMapper implements Serializable {
public static <E extends eu.dnetlib.dhp.schema.oaf.OafEntity> Result map(
E in) {
CommunityResult out = new CommunityResult();
eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in;
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> ort = Optional.ofNullable(input.getResulttype());
if (ort.isPresent()) {
switch (ort.get().getClassid()) {
case "publication":
Optional<Journal> journal = Optional
.ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal());
if (journal.isPresent()) {
Journal j = journal.get();
Container c = new Container();
c.setConferencedate(j.getConferencedate());
c.setConferenceplace(j.getConferenceplace());
c.setEdition(j.getEdition());
c.setEp(j.getEp());
c.setIss(j.getIss());
c.setIssnLinking(j.getIssnLinking());
c.setIssnOnline(j.getIssnOnline());
c.setIssnPrinted(j.getIssnPrinted());
c.setName(j.getName());
c.setSp(j.getSp());
c.setVol(j.getVol());
out.setContainer(c);
out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname());
}
break;
case "dataset":
eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input;
Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue()));
Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue()));
out
.setGeolocation(
Optional
.ofNullable(id.getGeolocation())
.map(
igl -> igl
.stream()
.filter(Objects::nonNull)
.map(gli -> {
GeoLocation gl = new GeoLocation();
gl.setBox(gli.getBox());
gl.setPlace(gli.getPlace());
gl.setPoint(gli.getPoint());
return gl;
})
.collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname());
break;
case "software":
eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input;
Optional
.ofNullable(is.getCodeRepositoryUrl())
.ifPresent(value -> out.setCodeRepositoryUrl(value.getValue()));
Optional
.ofNullable(is.getDocumentationUrl())
.ifPresent(
value -> out
.setDocumentationUrl(
value
.stream()
.map(Field::getValue)
.collect(Collectors.toList())));
Optional
.ofNullable(is.getProgrammingLanguage())
.ifPresent(value -> out.setProgrammingLanguage(value.getClassid()));
out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname());
break;
case "other":
eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input;
out
.setContactgroup(
Optional
.ofNullable(ir.getContactgroup())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setContactperson(
Optional
.ofNullable(ir.getContactperson())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out
.setTool(
Optional
.ofNullable(ir.getTool())
.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
.orElse(null));
out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
break;
}
Optional
.ofNullable(input.getAuthor())
.ifPresent(
ats -> out.setAuthor(ats.stream().map(GraphResultMapper::getAuthor).collect(Collectors.toList())));
// I do not map Access Right UNKNOWN or OTHER
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oar = Optional.ofNullable(input.getBestaccessright());
if (oar.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(oar.get().getClassid());
out
.setBestaccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
final List<String> contributorList = new ArrayList<>();
Optional
.ofNullable(input.getContributor())
.ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue())));
out.setContributor(contributorList);
Optional
.ofNullable(input.getCountry())
.ifPresent(
value -> out
.setCountry(
value
.stream()
.map(
c -> {
if (c.getClassid().equals((ModelConstants.UNKNOWN))) {
return null;
}
Country country = new Country();
country.setCode(c.getClassid());
country.setLabel(c.getClassname());
Optional
.ofNullable(c.getDataInfo())
.ifPresent(
provenance -> country
.setProvenance(
Provenance
.newInstance(
provenance
.getProvenanceaction()
.getClassname(),
c.getDataInfo().getTrust())));
return country;
})
.filter(Objects::nonNull)
.collect(Collectors.toList())));
final List<String> coverageList = new ArrayList<>();
Optional
.ofNullable(input.getCoverage())
.ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue())));
out.setCoverage(coverageList);
out.setDateofcollection(input.getDateofcollection());
final List<String> descriptionList = new ArrayList<>();
Optional
.ofNullable(input.getDescription())
.ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue())));
out.setDescription(descriptionList);
Optional<Field<String>> oStr = Optional.ofNullable(input.getEmbargoenddate());
if (oStr.isPresent()) {
out.setEmbargoenddate(oStr.get().getValue());
}
final List<String> formatList = new ArrayList<>();
Optional
.ofNullable(input.getFormat())
.ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue())));
out.setFormat(formatList);
out.setId(input.getId());
out.setOriginalId(input.getOriginalId());
Optional<List<eu.dnetlib.dhp.schema.oaf.Instance>> oInst = Optional
.ofNullable(input.getInstance());
if (oInst.isPresent()) {
out
.setInstance(
oInst.get().stream().map(GraphResultMapper::getInstance).collect(Collectors.toList()));
}
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> oL = Optional.ofNullable(input.getLanguage());
if (oL.isPresent()) {
eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get();
out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname()));
}
Optional<Long> oLong = Optional.ofNullable(input.getLastupdatetimestamp());
if (oLong.isPresent()) {
out.setLastupdatetimestamp(oLong.get());
}
Optional<List<StructuredProperty>> otitle = Optional.ofNullable(input.getTitle());
if (otitle.isPresent()) {
List<StructuredProperty> iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setMaintitle(iTitle.get(0).getValue());
}
iTitle = otitle
.get()
.stream()
.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
.collect(Collectors.toList());
if (!iTitle.isEmpty()) {
out.setSubtitle(iTitle.get(0).getValue());
}
}
List<ControlledField> pids = new ArrayList<>();
Optional
.ofNullable(input.getPid())
.ifPresent(
value -> value
.stream()
.forEach(
p -> pids
.add(
ControlledField
.newInstance(p.getQualifier().getClassid(), p.getValue()))));
out.setPid(pids);
oStr = Optional.ofNullable(input.getDateofacceptance());
if (oStr.isPresent()) {
out.setPublicationdate(oStr.get().getValue());
}
oStr = Optional.ofNullable(input.getPublisher());
if (oStr.isPresent()) {
out.setPublisher(oStr.get().getValue());
}
List<String> sourceList = new ArrayList<>();
Optional
.ofNullable(input.getSource())
.ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue())));
// out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList()));
List<Subject> subjectList = new ArrayList<>();
Optional
.ofNullable(input.getSubject())
.ifPresent(
value -> value
.forEach(s -> subjectList.add(getSubject(s))));
out.setSubjects(subjectList);
out.setType(input.getResulttype().getClassid());
}
out
.setCollectedfrom(
input
.getCollectedfrom()
.stream()
.map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue()))
.collect(Collectors.toList()));
return out;
}
private static CommunityInstance getInstance(eu.dnetlib.dhp.schema.oaf.Instance i) {
CommunityInstance instance = new CommunityInstance();
setCommonValue(i, instance);
instance
.setCollectedfrom(
KeyValue
.newInstance(i.getCollectedfrom().getKey(), i.getCollectedfrom().getValue()));
instance
.setHostedby(
KeyValue.newInstance(i.getHostedby().getKey(), i.getHostedby().getValue()));
return instance;
}
private static <I extends Instance> void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) {
Optional<eu.dnetlib.dhp.schema.oaf.Qualifier> opAr = Optional
.ofNullable(i.getAccessright());
if (opAr.isPresent()) {
if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) {
String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid());
instance
.setAccessright(
AccessRight
.newInstance(
code,
Constants.coarCodeLabelMap.get(code),
Constants.COAR_ACCESS_RIGHT_SCHEMA));
}
}
Optional
.ofNullable(i.getLicense())
.ifPresent(value -> instance.setLicense(value.getValue()));
Optional
.ofNullable(i.getDateofacceptance())
.ifPresent(value -> instance.setPublicationdate(value.getValue()));
Optional
.ofNullable(i.getRefereed())
.ifPresent(value -> instance.setRefereed(value.getClassname()));
Optional
.ofNullable(i.getInstancetype())
.ifPresent(value -> instance.setType(value.getClassname()));
Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value));
}
private static Subject getSubject(StructuredProperty s) {
Subject subject = new Subject();
subject.setSubject(ControlledField.newInstance(s.getQualifier().getClassid(), s.getValue()));
Optional<DataInfo> di = Optional.ofNullable(s.getDataInfo());
if (di.isPresent()) {
Provenance p = new Provenance();
p.setProvenance(di.get().getProvenanceaction().getClassname());
p.setTrust(di.get().getTrust());
subject.setProvenance(p);
}
return subject;
}
private static Author getAuthor(eu.dnetlib.dhp.schema.oaf.Author oa) {
Author a = new Author();
a.setFullname(oa.getFullname());
a.setName(oa.getName());
a.setSurname(oa.getSurname());
a.setRank(oa.getRank());
Optional<List<StructuredProperty>> oPids = Optional
.ofNullable(oa.getPid());
if (oPids.isPresent()) {
Pid pid = getOrcid(oPids.get());
if (pid != null) {
a.setPid(pid);
}
}
return a;
}
private static Pid getOrcid(List<StructuredProperty> p) {
for (StructuredProperty pid : p) {
if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) {
Optional<DataInfo> di = Optional.ofNullable(pid.getDataInfo());
if (di.isPresent()) {
return Pid
.newInstance(
ControlledField
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue()),
Provenance
.newInstance(
di.get().getProvenanceaction().getClassname(),
di.get().getTrust()));
} else {
return Pid
.newInstance(
ControlledField
.newInstance(
pid.getQualifier().getClassid(),
pid.getValue())
);
}
}
}
return null;
}
}

100
dhp-common/src/main/java/eu/dnetlib/dhp/common/MDStoreInfo.java Normal file
View File

@ -0,0 +1,100 @@
package eu.dnetlib.dhp.common;
/**
* This utility represent the Metadata Store information
* needed during the migration from mongo to HDFS to store
*/
public class MDStoreInfo {
private String mdstore;
private String currentId;
private Long latestTimestamp;
/**
* Instantiates a new Md store info.
*/
public MDStoreInfo() {
}
/**
* Instantiates a new Md store info.
*
* @param mdstore the mdstore
* @param currentId the current id
* @param latestTimestamp the latest timestamp
*/
public MDStoreInfo(String mdstore, String currentId, Long latestTimestamp) {
this.mdstore = mdstore;
this.currentId = currentId;
this.latestTimestamp = latestTimestamp;
}
/**
* Gets mdstore.
*
* @return the mdstore
*/
public String getMdstore() {
return mdstore;
}
/**
* Sets mdstore.
*
* @param mdstore the mdstore
* @return the mdstore
*/
public MDStoreInfo setMdstore(String mdstore) {
this.mdstore = mdstore;
return this;
}
/**
* Gets current id.
*
* @return the current id
*/
public String getCurrentId() {
return currentId;
}
/**
* Sets current id.
*
* @param currentId the current id
* @return the current id
*/
public MDStoreInfo setCurrentId(String currentId) {
this.currentId = currentId;
return this;
}
/**
* Gets latest timestamp.
*
* @return the latest timestamp
*/
public Long getLatestTimestamp() {
return latestTimestamp;
}
/**
* Sets latest timestamp.
*
* @param latestTimestamp the latest timestamp
* @return the latest timestamp
*/
public MDStoreInfo setLatestTimestamp(Long latestTimestamp) {
this.latestTimestamp = latestTimestamp;
return this;
}
@Override
public String toString() {
return "MDStoreInfo{" +
"mdstore='" + mdstore + '\'' +
", currentId='" + currentId + '\'' +
", latestTimestamp=" + latestTimestamp +
'}';
}
}

96
dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java
View File

@ -5,13 +5,71 @@ import java.io.BufferedInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.Serializable;
import java.util.Optional;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class MakeTarArchive implements Serializable {
private static final Logger log = LoggerFactory.getLogger(MakeTarArchive.class);
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
MakeTarArchive.class
.getResourceAsStream(
"/eu/dnetlib/dhp/common/input_maketar_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
final String outputPath = parser.get("hdfsPath");
log.info("hdfsPath: {}", outputPath);
final String hdfsNameNode = parser.get("nameNode");
log.info("nameNode: {}", hdfsNameNode);
final String inputPath = parser.get("sourcePath");
log.info("input path : {}", inputPath);
final int gBperSplit = Optional
.ofNullable(parser.get("splitSize"))
.map(Integer::valueOf)
.orElse(10);
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
makeTArArchive(fileSystem, inputPath, outputPath, gBperSplit);
}
public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit)
throws IOException {
RemoteIterator<LocatedFileStatus> dirIterator = fileSystem.listLocatedStatus(new Path(inputPath));
while (dirIterator.hasNext()) {
LocatedFileStatus fileStatus = dirIterator.next();
Path p = fileStatus.getPath();
String pathString = p.toString();
String entity = pathString.substring(pathString.lastIndexOf("/") + 1);
MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit);
}
}
private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException {
Path hdfsWritePath = new Path(outputPath);
if (fileSystem.exists(hdfsWritePath)) {
@ -21,7 +79,7 @@ public class MakeTarArchive implements Serializable {
return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream());
}
private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dirName)
throws IOException {
Path hdfsWritePath = new Path(outputPath);
@ -37,7 +95,7 @@ public class MakeTarArchive implements Serializable {
new Path(inputPath), true);
while (iterator.hasNext()) {
writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
writeCurrentFile(fileSystem, dirName, iterator, ar, 0);
}
}
@ -59,32 +117,30 @@ public class MakeTarArchive implements Serializable {
new Path(inputPath), true);
boolean next = fileStatusListIterator.hasNext();
while (next) {
TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar");
try (TarArchiveOutputStream ar = getTar(fileSystem, outputPath + "_" + (partNum + 1) + ".tar")) {
long current_size = 0;
while (next && current_size < bytesPerSplit) {
current_size = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, current_size);
next = fileStatusListIterator.hasNext();
long currentSize = 0;
while (next && currentSize < bytesPerSplit) {
currentSize = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, currentSize);
next = fileStatusListIterator.hasNext();
}
partNum += 1;
}
partNum += 1;
ar.close();
}
}
}
private static long writeCurrentFile(FileSystem fileSystem, String dir_name,
private static long writeCurrentFile(FileSystem fileSystem, String dirName,
RemoteIterator<LocatedFileStatus> fileStatusListIterator,
TarArchiveOutputStream ar, long current_size) throws IOException {
TarArchiveOutputStream ar, long currentSize) throws IOException {
LocatedFileStatus fileStatus = fileStatusListIterator.next();
Path p = fileStatus.getPath();
String p_string = p.toString();
if (!p_string.endsWith("_SUCCESS")) {
String name = p_string.substring(p_string.lastIndexOf("/") + 1);
String pString = p.toString();
if (!pString.endsWith("_SUCCESS")) {
String name = pString.substring(pString.lastIndexOf("/") + 1);
if (name.startsWith("part-") & name.length() > 10) {
String tmp = name.substring(0, 10);
if (name.contains(".")) {
@ -92,9 +148,9 @@ public class MakeTarArchive implements Serializable {
}
name = tmp;
}
TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
TarArchiveEntry entry = new TarArchiveEntry(dirName + "/" + name);
entry.setSize(fileStatus.getLen());
current_size += fileStatus.getLen();
currentSize += fileStatus.getLen();
ar.putArchiveEntry(entry);
InputStream is = fileSystem.open(fileStatus.getPath());
@ -110,7 +166,7 @@ public class MakeTarArchive implements Serializable {
ar.closeArchiveEntry();
}
return current_size;
return currentSize;
}
}

38
dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreClient.java
View File

@ -1,12 +1,12 @@
package eu.dnetlib.dhp.common;
import static com.mongodb.client.model.Sorts.descending;
import java.io.Closeable;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
import org.apache.commons.lang3.StringUtils;
@ -38,6 +38,26 @@ public class MdstoreClient implements Closeable {
this.db = getDb(client, dbName);
}
private Long parseTimestamp(Document f) {
if (f == null || !f.containsKey("timestamp"))
return null;
Object ts = f.get("timestamp");
return Long.parseLong(ts.toString());
}
public Long getLatestTimestamp(final String collectionId) {
MongoCollection<Document> collection = db.getCollection(collectionId);
FindIterable<Document> result = collection.find().sort(descending("timestamp")).limit(1);
if (result == null) {
return null;
}
Document f = result.first();
return parseTimestamp(f);
}
public MongoCollection<Document> mdStore(final String mdId) {
BasicDBObject query = (BasicDBObject) QueryBuilder.start("mdId").is(mdId).get();
@ -54,6 +74,16 @@ public class MdstoreClient implements Closeable {
return getColl(db, currentId, true);
}
public List<MDStoreInfo> mdStoreWithTimestamp(final String mdFormat, final String mdLayout,
final String mdInterpretation) {
Map<String, String> res = validCollections(mdFormat, mdLayout, mdInterpretation);
return res
.entrySet()
.stream()
.map(e -> new MDStoreInfo(e.getKey(), e.getValue(), getLatestTimestamp(e.getValue())))
.collect(Collectors.toList());
}
public Map<String, String> validCollections(
final String mdFormat, final String mdLayout, final String mdInterpretation) {

74
dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java
View File

@ -1,18 +1,18 @@
package eu.dnetlib.dhp.common;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.text.Normalizer;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.text.WordUtils;
import com.ctc.wstx.dtd.LargePrefixedNameSet;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Lists;
import com.google.common.hash.Hashing;
@ -29,7 +29,19 @@ public class PacePerson {
private List<String> fullname = Lists.newArrayList();
private final String original;
private static Set<String> particles = null;
private static Set<String> particles;
static {
try {
particles = new HashSet<>(IOUtils
.readLines(
PacePerson.class
.getResourceAsStream(
"/eu/dnetlib/dhp/common/name_particles.txt")));
} catch (IOException e) {
throw new RuntimeException(e);
}
}
/**
* Capitalizes a string
@ -37,29 +49,20 @@ public class PacePerson {
* @param s the string to capitalize
* @return the input string with capital letter
*/
public static final String capitalize(final String s) {
public static String capitalize(final String s) {
if (particles.contains(s)) {
return s;
}
return WordUtils.capitalize(s.toLowerCase(), ' ', '-');
}
/**
* Adds a dot to a string with length equals to 1
*/
public static final String dotAbbreviations(final String s) {
public static String dotAbbreviations(final String s) {
return s.length() == 1 ? s + "." : s;
}
public static Set<String> loadFromClasspath(final String classpath) {
final Set<String> h = new HashSet<>();
try {
for (final String s : IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) {
h.add(s);
}
} catch (final Throwable e) {
return new HashSet<>();
}
return h;
}
/**
* The constructor of the class. It fills the fields of the class basing on the input fullname.
*
@ -128,10 +131,6 @@ public class PacePerson {
}
private List<String> splitTerms(final String s) {
if (particles == null) {
particles = loadFromClasspath("/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt");
}
final List<String> list = Lists.newArrayList();
for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) {
if (!particles.contains(part.toLowerCase())) {
@ -187,17 +186,36 @@ public class PacePerson {
}
public List<String> getCapitalFirstnames() {
return Lists
.newArrayList(
Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize));
return Optional
.ofNullable(getNameWithAbbreviations())
.map(
name -> name
.stream()
.map(PacePerson::capitalize)
.collect(Collectors.toList()))
.orElse(new ArrayList<>());
}
public List<String> getCapitalSurname() {
return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize));
return Optional
.ofNullable(getSurname())
.map(
surname -> surname
.stream()
.map(PacePerson::capitalize)
.collect(Collectors.toList()))
.orElse(new ArrayList<>());
}
public List<String> getNameWithAbbreviations() {
return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations));
return Optional
.ofNullable(getName())
.map(
name -> name
.stream()
.map(PacePerson::dotAbbreviations)
.collect(Collectors.toList()))
.orElse(new ArrayList<>());
}
public boolean isAccurate() {

81
dhp-common/src/main/java/eu/dnetlib/dhp/common/action/ReadDatasourceMasterDuplicateFromDB.java Normal file
View File

@ -0,0 +1,81 @@
package eu.dnetlib.dhp.common.action;
import java.io.BufferedWriter;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.nio.charset.StandardCharsets;
import java.sql.ResultSet;
import java.sql.SQLException;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.DbClient;
import eu.dnetlib.dhp.common.action.model.MasterDuplicate;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class ReadDatasourceMasterDuplicateFromDB {
private static final Logger log = LoggerFactory.getLogger(ReadDatasourceMasterDuplicateFromDB.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
private static final String QUERY = "SELECT distinct dd.id as masterId, d.officialname as masterName, dd.duplicate as duplicateId "
+
"FROM dsm_dedup_services dd join dsm_services d on (dd.id = d.id);";
public static int execute(String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode)
throws IOException {
int count = 0;
try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
Configuration conf = new Configuration();
conf.set("fs.defaultFS", hdfsNameNode);
FileSystem fileSystem = FileSystem.get(conf);
FSDataOutputStream fos = fileSystem.create(new Path(hdfsPath));
log.info("running query: {}", QUERY);
log.info("storing results in: {}", hdfsPath);
try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
dbClient.processResults(QUERY, rs -> writeMap(datasourceMasterMap(rs), writer));
count++;
}
}
return count;
}
private static MasterDuplicate datasourceMasterMap(ResultSet rs) {
try {
final MasterDuplicate md = new MasterDuplicate();
final String duplicateId = rs.getString("duplicateId");
final String masterId = rs.getString("masterId");
final String masterName = rs.getString("masterName");
md.setDuplicateId(OafMapperUtils.createOpenaireId(10, duplicateId, true));
md.setMasterId(OafMapperUtils.createOpenaireId(10, masterId, true));
md.setMasterName(masterName);
return md;
} catch (final SQLException e) {
throw new RuntimeException(e);
}
}
private static void writeMap(final MasterDuplicate dm, final BufferedWriter writer) {
try {
writer.write(OBJECT_MAPPER.writeValueAsString(dm));
writer.newLine();
} catch (final IOException e) {
throw new RuntimeException(e);
}
}
}

38
dhp-common/src/main/java/eu/dnetlib/dhp/common/action/model/MasterDuplicate.java Normal file
View File

@ -0,0 +1,38 @@
package eu.dnetlib.dhp.common.action.model;
import java.io.Serializable;
/**
* @author miriam.baglioni
* @Date 21/07/22
*/
public class MasterDuplicate implements Serializable {
private String duplicateId;
private String masterId;
private String masterName;
public String getDuplicateId() {
return duplicateId;
}
public void setDuplicateId(String duplicateId) {
this.duplicateId = duplicateId;
}
public String getMasterId() {
return masterId;
}
public void setMasterId(String masterId) {
this.masterId = masterId;
}
public String getMasterName() {
return masterName;
}
public void setMasterName(String masterName) {
this.masterName = masterName;
}
}

295
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java
View File

@ -3,10 +3,13 @@ package eu.dnetlib.dhp.common.api;
import java.io.*;
import java.io.IOException;
import java.net.HttpURLConnection;
import java.net.URL;
import java.util.concurrent.TimeUnit;
import org.apache.http.HttpHeaders;
import org.apache.http.entity.ContentType;
import org.jetbrains.annotations.NotNull;
import com.google.gson.Gson;
@ -60,33 +63,31 @@ public class ZenodoAPIClient implements Serializable {
*/
public int newDeposition() throws IOException {
String json = "{}";
OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
Request request = new Request.Builder()
.url(urlString)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.post(body)
.build();
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
// Get response body
json = response.body().string();
ZenodoModel newSubmission = new Gson().fromJson(json, ZenodoModel.class);
this.bucket = newSubmission.getLinks().getBucket();
this.deposition_id = newSubmission.getId();
return response.code();
URL url = new URL(urlString);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setRequestMethod("POST");
conn.setDoOutput(true);
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
}
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class);
this.bucket = newSubmission.getLinks().getBucket();
this.deposition_id = newSubmission.getId();
return responseCode;
}
/**
@ -94,28 +95,48 @@ public class ZenodoAPIClient implements Serializable {
*
* @param is the inputStream for the file to upload
* @param file_name the name of the file as it will appear on Zenodo
* @param len the size of the file
* @return the response code
*/
public int uploadIS(InputStream is, String file_name, long len) throws IOException {
OkHttpClient httpClient = new OkHttpClient.Builder()
.writeTimeout(600, TimeUnit.SECONDS)
.readTimeout(600, TimeUnit.SECONDS)
.connectTimeout(600, TimeUnit.SECONDS)
.build();
public int uploadIS(InputStream is, String file_name) throws IOException {
Request request = new Request.Builder()
.url(bucket + "/" + file_name)
.addHeader(HttpHeaders.CONTENT_TYPE, "application/zip") // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.put(InputStreamRequestBody.create(MEDIA_TYPE_ZIP, is, len))
.build();
URL url = new URL(bucket + "/" + file_name);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, "application/zip");
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("PUT");
byte[] buf = new byte[8192];
int length;
try (OutputStream os = conn.getOutputStream()) {
while ((length = is.read(buf)) != -1) {
os.write(buf, 0, length);
}
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
return response.code();
}
int responseCode = conn.getResponseCode();
if (!checkOKStatus(responseCode)) {
throw new IOException("Unexpected code " + responseCode + getBody(conn));
}
return responseCode;
}
@NotNull
private String getBody(HttpURLConnection conn) throws IOException {
String body = "{}";
try (BufferedReader br = new BufferedReader(
new InputStreamReader(conn.getInputStream(), "utf-8"))) {
StringBuilder response = new StringBuilder();
String responseLine = null;
while ((responseLine = br.readLine()) != null) {
response.append(responseLine.trim());
}
body = response.toString();
}
return body;
}
/**
@ -127,26 +148,34 @@ public class ZenodoAPIClient implements Serializable {
*/
public int sendMretadata(String metadata) throws IOException {
OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
URL url = new URL(urlString + "/" + deposition_id);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("PUT");
RequestBody body = RequestBody.create(metadata, MEDIA_TYPE_JSON);
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.put(body)
.build();
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
return response.code();
try (OutputStream os = conn.getOutputStream()) {
byte[] input = metadata.getBytes("utf-8");
os.write(input, 0, input.length);
}
final int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + getBody(conn));
return responseCode;
}
private boolean checkOKStatus(int responseCode) {
if (HttpURLConnection.HTTP_OK != responseCode ||
HttpURLConnection.HTTP_CREATED != responseCode)
return true;
return false;
}
/**
@ -155,6 +184,7 @@ public class ZenodoAPIClient implements Serializable {
* @return response code
* @throws IOException
*/
@Deprecated
public int publish() throws IOException {
String json = "{}";
@ -191,31 +221,37 @@ public class ZenodoAPIClient implements Serializable {
* @throws MissingConceptDoiException
*/
public int newVersion(String concept_rec_id) throws IOException, MissingConceptDoiException {
setDepositionId(concept_rec_id);
setDepositionId(concept_rec_id, 1);
String json = "{}";
OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
URL url = new URL(urlString + "/" + deposition_id + "/actions/newversion");
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
RequestBody body = RequestBody.create(json, MEDIA_TYPE_JSON);
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("POST");
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id + "/actions/newversion")
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.post(body)
.build();
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
String latest_draft = zenodoModel.getLinks().getLatest_draft();
deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1);
bucket = getBucket(latest_draft);
return response.code();
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
}
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
String latest_draft = zenodoModel.getLinks().getLatest_draft();
deposition_id = latest_draft.substring(latest_draft.lastIndexOf("/") + 1);
bucket = getBucket(latest_draft);
return responseCode;
}
/**
@ -233,29 +269,38 @@ public class ZenodoAPIClient implements Serializable {
this.deposition_id = deposition_id;
OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
String json = "{}";
Request request = new Request.Builder()
.url(urlString + "/" + deposition_id)
.addHeader("Authorization", "Bearer " + access_token)
.build();
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
bucket = zenodoModel.getLinks().getBucket();
return response.code();
URL url = new URL(urlString + "/" + deposition_id);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setRequestMethod("POST");
conn.setDoOutput(true);
try (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
}
String body = getBody(conn);
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
bucket = zenodoModel.getLinks().getBucket();
return responseCode;
}
private void setDepositionId(String concept_rec_id) throws IOException, MissingConceptDoiException {
private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException {
ZenodoModelList zenodoModelList = new Gson().fromJson(getPrevDepositions(), ZenodoModelList.class);
ZenodoModelList zenodoModelList = new Gson()
.fromJson(getPrevDepositions(String.valueOf(page)), ZenodoModelList.class);
for (ZenodoModel zm : zenodoModelList) {
if (zm.getConceptrecid().equals(concept_rec_id)) {
@ -263,55 +308,57 @@ public class ZenodoAPIClient implements Serializable {
return;
}
}
throw new MissingConceptDoiException("The concept record id specified was missing in the list of depositions");
if (zenodoModelList.size() == 0)
throw new MissingConceptDoiException(
"The concept record id specified was missing in the list of depositions");
setDepositionId(concept_rec_id, page + 1);
}
private String getPrevDepositions() throws IOException {
OkHttpClient httpClient = new OkHttpClient.Builder().connectTimeout(600, TimeUnit.SECONDS).build();
private String getPrevDepositions(String page) throws IOException {
Request request = new Request.Builder()
.url(urlString)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.get()
.build();
HttpUrl.Builder urlBuilder = HttpUrl.parse(urlString).newBuilder();
urlBuilder.addQueryParameter("page", page);
try (Response response = httpClient.newCall(request).execute()) {
URL url = new URL(urlBuilder.build().toString());
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("GET");
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
String body = getBody(conn);
return response.body().string();
int responseCode = conn.getResponseCode();
}
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
return body;
}
private String getBucket(String url) throws IOException {
OkHttpClient httpClient = new OkHttpClient.Builder()
.connectTimeout(600, TimeUnit.SECONDS)
.build();
private String getBucket(String inputUurl) throws IOException {
Request request = new Request.Builder()
.url(url)
.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
.get()
.build();
URL url = new URL(inputUurl);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString());
conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + access_token);
conn.setDoOutput(true);
conn.setRequestMethod("GET");
try (Response response = httpClient.newCall(request).execute()) {
String body = getBody(conn);
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
int responseCode = conn.getResponseCode();
// Get response body
ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
return zenodoModel.getLinks().getBucket();
ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
}
return zenodoModel.getLinks().getBucket();
}

39
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummary.java Normal file
View File

@ -0,0 +1,39 @@
package eu.dnetlib.dhp.common.api.context;
public class CategorySummary {
private String id;
private String label;
private boolean hasConcept;
public String getId() {
return id;
}
public String getLabel() {
return label;
}
public boolean isHasConcept() {
return hasConcept;
}
public CategorySummary setId(final String id) {
this.id = id;
return this;
}
public CategorySummary setLabel(final String label) {
this.label = label;
return this;
}
public CategorySummary setHasConcept(final boolean hasConcept) {
this.hasConcept = hasConcept;
return this;
}
}

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/CategorySummaryList.java Normal file
View File

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

52
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummary.java Normal file
View File

@ -0,0 +1,52 @@
package eu.dnetlib.dhp.common.api.context;
import java.util.List;
public class ConceptSummary {
private String id;
private String label;
public boolean hasSubConcept;
private List<ConceptSummary> concepts;
public String getId() {
return id;
}
public String getLabel() {
return label;
}
public List<ConceptSummary> getConcepts() {
return concepts;
}
public ConceptSummary setId(final String id) {
this.id = id;
return this;
}
public ConceptSummary setLabel(final String label) {
this.label = label;
return this;
}
public boolean isHasSubConcept() {
return hasSubConcept;
}
public ConceptSummary setHasSubConcept(final boolean hasSubConcept) {
this.hasSubConcept = hasSubConcept;
return this;
}
public ConceptSummary setConcept(final List<ConceptSummary> concepts) {
this.concepts = concepts;
return this;
}
}

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ConceptSummaryList.java Normal file
View File

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

50
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummary.java Normal file
View File

@ -0,0 +1,50 @@
package eu.dnetlib.dhp.common.api.context;
public class ContextSummary {
private String id;
private String label;
private String type;
private String status;
public String getId() {
return id;
}
public String getLabel() {
return label;
}
public String getType() {
return type;
}
public String getStatus() {
return status;
}
public ContextSummary setId(final String id) {
this.id = id;
return this;
}
public ContextSummary setLabel(final String label) {
this.label = label;
return this;
}
public ContextSummary setType(final String type) {
this.type = type;
return this;
}
public ContextSummary setStatus(final String status) {
this.status = status;
return this;
}
}

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/api/context/ContextSummaryList.java Normal file
View File

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

40
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/DecompressTarGz.java Normal file
View File

@ -0,0 +1,40 @@
package eu.dnetlib.dhp.common.collection;
import java.io.BufferedOutputStream;
import java.io.IOException;
import java.util.zip.GZIPOutputStream;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FSDataInputStream;
import org.apache.hadoop.fs.FSDataOutputStream;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
public class DecompressTarGz {
public static void doExtract(FileSystem fs, String outputPath, String tarGzPath) throws IOException {
FSDataInputStream inputFileStream = fs.open(new Path(tarGzPath));
try (TarArchiveInputStream tais = new TarArchiveInputStream(
new GzipCompressorInputStream(inputFileStream))) {
TarArchiveEntry entry = null;
while ((entry = tais.getNextTarEntry()) != null) {
if (!entry.isDirectory()) {
try (
FSDataOutputStream out = fs
.create(new Path(outputPath.concat(entry.getName()).concat(".gz")));
GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
IOUtils.copy(tais, gzipOs);
}
}
}
}
}
}

37
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpClientParams.java
View File

@ -1,6 +1,9 @@
package eu.dnetlib.dhp.common.collection;
import java.util.HashMap;
import java.util.Map;
/**
* Bundles the http connection parameters driving the client behaviour.
*/
@ -13,6 +16,8 @@ public class HttpClientParams {
public static int _connectTimeOut = 10; // seconds
public static int _readTimeOut = 30; // seconds
public static String _requestMethod = "GET";
/**
* Maximum number of allowed retires before failing
*/
@ -38,17 +43,30 @@ public class HttpClientParams {
*/
private int readTimeOut;
/**
* Custom http headers
*/
private Map<String, String> headers;
/**
* Request method (i.e., GET, POST etc)
*/
private String requestMethod;
public HttpClientParams() {
this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut);
this(_maxNumberOfRetry, _requestDelay, _retryDelay, _connectTimeOut, _readTimeOut, new HashMap<>(),
_requestMethod);
}
public HttpClientParams(int maxNumberOfRetry, int requestDelay, int retryDelay, int connectTimeOut,
int readTimeOut) {
int readTimeOut, Map<String, String> headers, String requestMethod) {
this.maxNumberOfRetry = maxNumberOfRetry;
this.requestDelay = requestDelay;
this.retryDelay = retryDelay;
this.connectTimeOut = connectTimeOut;
this.readTimeOut = readTimeOut;
this.headers = headers;
this.requestMethod = requestMethod;
}
public int getMaxNumberOfRetry() {
@ -91,4 +109,19 @@ public class HttpClientParams {
this.readTimeOut = readTimeOut;
}
public Map<String, String> getHeaders() {
return headers;
}
public void setHeaders(Map<String, String> headers) {
this.headers = headers;
}
public String getRequestMethod() {
return requestMethod;
}
public void setRequestMethod(String requestMethod) {
this.requestMethod = requestMethod;
}
}

78
dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
View File

@ -8,10 +8,13 @@ import java.io.InputStream;
import java.net.*;
import java.util.List;
import java.util.Map;
import java.util.concurrent.TimeUnit;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.http.HttpHeaders;
import org.joda.time.Instant;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -94,24 +97,32 @@ public class HttpConnector2 {
throw new CollectorException(msg);
}
log.info("Request attempt {} [{}]", retryNumber, requestUrl);
InputStream input = null;
long start = System.currentTimeMillis();
try {
if (getClientParams().getRequestDelay() > 0) {
backoffAndSleep(getClientParams().getRequestDelay());
}
log.info("Request attempt {} [{}]", retryNumber, requestUrl);
final HttpURLConnection urlConn = (HttpURLConnection) new URL(requestUrl).openConnection();
urlConn.setInstanceFollowRedirects(false);
urlConn.setReadTimeout(getClientParams().getReadTimeOut() * 1000);
urlConn.setConnectTimeout(getClientParams().getConnectTimeOut() * 1000);
urlConn.addRequestProperty(HttpHeaders.USER_AGENT, userAgent);
urlConn.setRequestMethod(getClientParams().getRequestMethod());
if (log.isDebugEnabled()) {
logHeaderFields(urlConn);
// if provided, add custom headers
if (!getClientParams().getHeaders().isEmpty()) {
for (Map.Entry<String, String> headerEntry : getClientParams().getHeaders().entrySet()) {
urlConn.addRequestProperty(headerEntry.getKey(), headerEntry.getValue());
}
}
logHeaderFields(urlConn);
int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
String rateLimit = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT);
String rateRemaining = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_REMAINING);
@ -125,9 +136,7 @@ public class HttpConnector2 {
}
if (is2xx(urlConn.getResponseCode())) {
input = urlConn.getInputStream();
responseType = urlConn.getContentType();
return input;
return getInputStream(urlConn, start);
}
if (is3xx(urlConn.getResponseCode())) {
// REDIRECTS
@ -137,6 +146,7 @@ public class HttpConnector2 {
.put(
REPORT_PREFIX + urlConn.getResponseCode(),
String.format("Moved to: %s", newUrl));
logRequestTime(start);
urlConn.disconnect();
if (retryAfter > 0) {
backoffAndSleep(retryAfter);
@ -152,26 +162,50 @@ public class HttpConnector2 {
if (retryAfter > 0) {
log
.warn(
"{} - waiting and repeating request after suggested retry-after {} sec.",
requestUrl, retryAfter);
"waiting and repeating request after suggested retry-after {} sec for URL {}",
retryAfter, requestUrl);
backoffAndSleep(retryAfter * 1000);
} else {
log
.warn(
"{} - waiting and repeating request after default delay of {} sec.",
requestUrl, getClientParams().getRetryDelay());
backoffAndSleep(retryNumber * getClientParams().getRetryDelay() * 1000);
"waiting and repeating request after default delay of {} sec for URL {}",
getClientParams().getRetryDelay(), requestUrl);
backoffAndSleep(retryNumber * getClientParams().getRetryDelay());
}
report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
logRequestTime(start);
urlConn.disconnect();
return attemptDownload(requestUrl, retryNumber + 1, report);
case 422: // UNPROCESSABLE ENTITY
report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
log.warn("waiting and repeating request after 10 sec for URL {}", requestUrl);
backoffAndSleep(10000);
urlConn.disconnect();
logRequestTime(start);
try {
return getInputStream(urlConn, start);
} catch (IOException e) {
log
.error(
"server returned 422 and got IOException accessing the response body from URL {}",
requestUrl);
log.error("IOException:", e);
return attemptDownload(requestUrl, retryNumber + 1, report);
}
default:
log.error("gor error {} from URL: {}", urlConn.getResponseCode(), urlConn.getURL());
log.error("response message: {}", urlConn.getResponseMessage());
report
.put(
REPORT_PREFIX + urlConn.getResponseCode(),
String
.format(
"%s Error: %s", requestUrl, urlConn.getResponseMessage()));
logRequestTime(start);
urlConn.disconnect();
throw new CollectorException(urlConn.getResponseCode() + " error " + report);
}
}
@ -192,13 +226,27 @@ public class HttpConnector2 {
}
}
private InputStream getInputStream(HttpURLConnection urlConn, long start) throws IOException {
InputStream input = urlConn.getInputStream();
responseType = urlConn.getContentType();
logRequestTime(start);
return input;
}
private static void logRequestTime(long start) {
log
.info(
"request time elapsed: {}sec",
TimeUnit.MILLISECONDS.toSeconds(System.currentTimeMillis() - start));
}
private void logHeaderFields(final HttpURLConnection urlConn) throws IOException {
log.debug("StatusCode: {}", urlConn.getResponseMessage());
log.info("Response: {} - {}", urlConn.getResponseCode(), urlConn.getResponseMessage());
for (Map.Entry<String, List<String>> e : urlConn.getHeaderFields().entrySet()) {
if (e.getKey() != null) {
for (String v : e.getValue()) {
log.debug(" key: {} - value: {}", e.getKey(), v);
log.info(" key: {} - value: {}", e.getKey(), v);
}
}
}
@ -218,7 +266,7 @@ public class HttpConnector2 {
for (String key : headerMap.keySet()) {
if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (!headerMap.get(key).isEmpty())
&& NumberUtils.isCreatable(headerMap.get(key).get(0))) {
return Integer.parseInt(headerMap.get(key).get(0)) + 10;
return Integer.parseInt(headerMap.get(key).get(0));
}
}
return -1;

34
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java
View File

@ -4,6 +4,7 @@ package eu.dnetlib.dhp.common.vocabulary;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import org.apache.commons.lang3.StringUtils;
@ -62,25 +63,46 @@ public class Vocabulary implements Serializable {
}
public VocabularyTerm getTermBySynonym(final String syn) {
return getTerm(synonyms.get(syn.toLowerCase()));
return Optional
.ofNullable(syn)
.map(s -> getTerm(synonyms.get(s.toLowerCase())))
.orElse(null);
}
public Qualifier getTermAsQualifier(final String termId) {
if (StringUtils.isBlank(termId)) {
return getTermAsQualifier(termId, false);
}
public Qualifier getTermAsQualifier(final String termId, boolean strict) {
final VocabularyTerm term = getTerm(termId);
if (Objects.nonNull(term)) {
return OafMapperUtils.qualifier(term.getId(), term.getName(), getId(), getName());
} else if (Objects.isNull(term) && strict) {
return OafMapperUtils.unknown(getId(), getName());
} else if (termExists(termId)) {
final VocabularyTerm t = getTerm(termId);
return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName());
} else {
return OafMapperUtils.qualifier(termId, termId, getId(), getName());
}
}
public Qualifier getSynonymAsQualifier(final String syn) {
return getSynonymAsQualifier(syn, false);
}
public Qualifier getSynonymAsQualifier(final String syn, boolean strict) {
return Optional
.ofNullable(getTermBySynonym(syn))
.map(term -> getTermAsQualifier(term.getId()))
.map(term -> getTermAsQualifier(term.getId(), strict))
.orElse(null);
}
public Qualifier lookup(String id) {
return lookup(id, false);
}
public Qualifier lookup(String id, boolean strict) {
return Optional
.ofNullable(getSynonymAsQualifier(id, strict))
.orElse(getTermAsQualifier(id, strict));
}
}

33
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java
View File

@ -57,9 +57,17 @@ public class VocabularyGroup implements Serializable {
final String syn = arr[2].trim();
vocs.addSynonyms(vocId, termId, syn);
}
}
// add the term names as synonyms
vocs.vocs.values().forEach(voc -> {
voc.getTerms().values().forEach(term -> {
voc.addSynonym(term.getName().toLowerCase(), term.getId());
});
});
return vocs;
}
@ -73,6 +81,13 @@ public class VocabularyGroup implements Serializable {
vocs.put(id.toLowerCase(), new Vocabulary(id, name));
}
public Optional<Vocabulary> find(final String vocId) {
return Optional
.ofNullable(vocId)
.map(String::toLowerCase)
.map(vocs::get);
}
public void addTerm(final String vocId, final String id, final String name) {
if (vocabularyExists(vocId)) {
vocs.get(vocId.toLowerCase()).addTerm(id, name);
@ -120,6 +135,24 @@ public class VocabularyGroup implements Serializable {
return vocs.get(vocId.toLowerCase()).getSynonymAsQualifier(syn);
}
public Qualifier lookupTermBySynonym(final String vocId, final String syn) {
return find(vocId)
.map(
vocabulary -> Optional
.ofNullable(vocabulary.getTerm(syn))
.map(
term -> OafMapperUtils
.qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName()))
.orElse(
Optional
.ofNullable(vocabulary.getTermBySynonym(syn))
.map(
term -> OafMapperUtils
.qualifier(term.getId(), term.getName(), vocabulary.getId(), vocabulary.getName()))
.orElse(null)))
.orElse(null);
}
/**
* getSynonymAsQualifierCaseSensitive
*

28
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
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@ -119,6 +119,32 @@ public class AuthorMerger {
});
}
public static String normalizeFullName(final String fullname) {
return nfd(fullname)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
// of large input strings
.replaceAll("(\\W)+", " ")
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
}
private static String authorFieldToBeCompared(Author author) {
if (StringUtils.isNotBlank(author.getSurname())) {
return author.getSurname();
}
if (StringUtils.isNotBlank(author.getFullname())) {
return author.getFullname();
}
return null;
}
public static String pidToComparableString(StructuredProperty pid) {
final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
: "";
@ -171,7 +197,7 @@ public class AuthorMerger {
}
}
private static String normalize(final String s) {
public static String normalize(final String s) {
String[] normalized = nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError

194
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java Normal file
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@ -0,0 +1,194 @@
package eu.dnetlib.dhp.oa.merge;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
import static org.apache.spark.sql.functions.col;
import static org.apache.spark.sql.functions.when;
import java.util.Map;
import java.util.Optional;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.ForkJoinPool;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.api.java.function.MapGroupsFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.common.HdfsSupport;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
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;
/**
* Groups the graph content by entity identifier to ensure ID uniqueness
*/
public class GroupEntitiesSparkJob {
private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC = Encoders.kryo(OafEntity.class);
private ArgumentApplicationParser parser;
public GroupEntitiesSparkJob(ArgumentApplicationParser parser) {
this.parser = parser;
}
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
GroupEntitiesSparkJob.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String isLookupUrl = parser.get("isLookupUrl");
log.info("isLookupUrl: {}", isLookupUrl);
final ISLookUpService isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl);
new GroupEntitiesSparkJob(parser).run(isSparkSessionManaged, isLookupService);
}
public void run(Boolean isSparkSessionManaged, ISLookUpService isLookUpService)
throws ISLookUpException {
String graphInputPath = parser.get("graphInputPath");
log.info("graphInputPath: {}", graphInputPath);
String checkpointPath = parser.get("checkpointPath");
log.info("checkpointPath: {}", checkpointPath);
String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
boolean filterInvisible = Boolean.parseBoolean(parser.get("filterInvisible"));
log.info("filterInvisible: {}", filterInvisible);
SparkConf conf = new SparkConf();
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
final VocabularyGroup vocs = VocabularyGroup.loadVocsFromIS(isLookUpService);
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
HdfsSupport.remove(checkpointPath, spark.sparkContext().hadoopConfiguration());
groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible, vocs);
});
}
private static void groupEntities(
SparkSession spark,
String inputPath,
String checkpointPath,
String outputPath,
boolean filterInvisible, VocabularyGroup vocs) {
Dataset<OafEntity> allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC);
for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
String entity = e.getKey().name();
Class<? extends OafEntity> entityClass = e.getValue();
String entityInputPath = inputPath + "/" + entity;
if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) {
continue;
}
allEntities = allEntities
.union(
((Dataset<OafEntity>) spark
.read()
.schema(Encoders.bean(entityClass).schema())
.json(entityInputPath)
.filter("length(id) > 0")
.as(Encoders.bean(entityClass)))
.map((MapFunction<OafEntity, OafEntity>) r -> r, OAFENTITY_KRYO_ENC));
}
Dataset<?> groupedEntities = allEntities
.map(
(MapFunction<OafEntity, OafEntity>) entity -> GraphCleaningFunctions
.applyCoarVocabularies(entity, vocs),
OAFENTITY_KRYO_ENC)
.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
.mapGroups((MapGroupsFunction<String, OafEntity, OafEntity>) MergeUtils::mergeGroup, OAFENTITY_KRYO_ENC)
.map(
(MapFunction<OafEntity, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
t.getClass().getName(), t),
Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
// pivot on "_1" (classname of the entity)
// created columns containing only entities of the same class
for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
String entity = e.getKey().name();
Class<? extends OafEntity> entityClass = e.getValue();
groupedEntities = groupedEntities
.withColumn(
entity,
when(col("_1").equalTo(entityClass.getName()), col("_2")));
}
groupedEntities
.drop("_1", "_2")
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.save(checkpointPath);
ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size());
ModelSupport.entityTypes
.entrySet()
.stream()
.map(e -> parPool.submit(() -> {
String entity = e.getKey().name();
Class<? extends OafEntity> entityClass = e.getValue();
spark
.read()
.load(checkpointPath)
.select(col(entity).as("value"))
.filter("value IS NOT NULL")
.as(OAFENTITY_KRYO_ENC)
.map((MapFunction<OafEntity, OafEntity>) r -> r, (Encoder<OafEntity>) Encoders.bean(entityClass))
.filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE")
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.json(outputPath + "/" + entity);
}))
.collect(Collectors.toList())
.forEach(t -> {
try {
t.get();
} catch (InterruptedException | ExecutionException e) {
throw new RuntimeException(e);
}
});
}
}

77
dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java Normal file
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@ -0,0 +1,77 @@
package eu.dnetlib.dhp.oozie;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
import java.net.URL;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.Optional;
import org.apache.commons.lang3.time.DurationFormatUtils;
import org.apache.commons.text.StringSubstitutor;
import org.apache.spark.SparkConf;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.common.io.Resources;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
public class RunSQLSparkJob {
private static final Logger log = LoggerFactory.getLogger(RunSQLSparkJob.class);
private final ArgumentApplicationParser parser;
public RunSQLSparkJob(ArgumentApplicationParser parser) {
this.parser = parser;
}
public static void main(String[] args) throws Exception {
Map<String, String> params = new HashMap<>();
for (int i = 0; i < args.length - 1; i++) {
if (args[i].startsWith("--")) {
params.put(args[i].substring(2), args[++i]);
}
}
/*
* String jsonConfiguration = IOUtils .toString( Objects .requireNonNull( RunSQLSparkJob.class
* .getResourceAsStream( "/eu/dnetlib/dhp/oozie/run_sql_parameters.json"))); final ArgumentApplicationParser
* parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args);
*/
Boolean isSparkSessionManaged = Optional
.ofNullable(params.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
URL url = com.google.common.io.Resources.getResource(params.get("sql"));
String raw_sql = Resources.toString(url, StandardCharsets.UTF_8);
String sql = StringSubstitutor.replace(raw_sql, params);
log.info("sql: {}", sql);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", params.get("hiveMetastoreUris"));
runWithSparkHiveSession(
conf,
isSparkSessionManaged,
spark -> {
for (String statement : sql.split(";\\s*/\\*\\s*EOS\\s*\\*/\\s*")) {
log.info("executing: {}", statement);
long startTime = System.currentTimeMillis();
spark.sql(statement).show();
log
.info(
"executed in {}",
DurationFormatUtils.formatDuration(System.currentTimeMillis() - startTime, "HH:mm:ss.S"));
}
});
}
}

76
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java Normal file
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@ -0,0 +1,76 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashSet;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class CleaningFunctions {
public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
public static final String DOI_PREFIX = "10.";
public static final Set<String> PID_BLACKLIST = new HashSet<>();
static {
PID_BLACKLIST.add("none");
PID_BLACKLIST.add("na");
}
public CleaningFunctions() {
}
/**
* Utility method that filter PID values on a per-type basis.
* @param s the PID whose value will be checked.
* @return false if the pid matches the filter criteria, true otherwise.
*/
public static boolean pidFilter(StructuredProperty s) {
final String pidValue = s.getValue();
if (Objects.isNull(s.getQualifier()) ||
StringUtils.isBlank(pidValue) ||
StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
return false;
}
if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
return false;
}
return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
}
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
pid
.setValue(
normalizePidValue(
pid.getQualifier().getClassid(),
pid.getValue()));
return pid;
}
public static String normalizePidValue(String pidType, String pidValue) {
String value = Optional
.ofNullable(pidValue)
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pidType) {
// TODO add cleaning for more PID types as needed
case "doi":
return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
}
return value;
}
}

38
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java Normal file
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@ -0,0 +1,38 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import org.apache.commons.lang3.StringUtils;
public class DoiCleaningRule {
public static String clean(final String doi) {
return doi
.toLowerCase()
.replaceAll("\\s", "")
.replaceAll("^doi:", "")
.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
}
public static String normalizeDoi(final String input) {
if (input == null)
return null;
final String replaced = input
.replaceAll("\\n|\\r|\\t|\\s", "")
.toLowerCase()
.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
if (StringUtils.isEmpty(replaced))
return null;
if (!replaced.contains("10."))
return null;
final String ret = replaced.substring(replaced.indexOf("10."));
if (!ret.startsWith(CleaningFunctions.DOI_PREFIX))
return null;
return ret;
}
}

25
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/FundRefCleaningRule.java Normal file
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@ -0,0 +1,25 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class FundRefCleaningRule {
public static final Pattern PATTERN = Pattern.compile("\\d+");
public static String clean(final String fundRefId) {
String s = fundRefId
.toLowerCase()
.replaceAll("\\s", "");
Matcher m = PATTERN.matcher(s);
if (m.find()) {
return m.group();
} else {
return "";
}
}
}

1143
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
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File diff suppressed because it is too large Load Diff

24
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRule.java Normal file
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@ -0,0 +1,24 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class GridCleaningRule {
public static final Pattern PATTERN = Pattern.compile("(?<grid>\\d{4,6}\\.[0-9a-z]{1,2})");
public static String clean(String grid) {
String s = grid
.replaceAll("\\s", "")
.toLowerCase();
Matcher m = PATTERN.matcher(s);
if (m.find()) {
return "grid." + m.group("grid");
}
return "";
}
}

21
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ISNICleaningRule.java Normal file
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@ -0,0 +1,21 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
// https://www.wikidata.org/wiki/Property:P213
public class ISNICleaningRule {
public static final Pattern PATTERN = Pattern.compile("([0]{4}) ?([0-9]{4}) ?([0-9]{4}) ?([0-9]{3}[0-9X])");
public static String clean(final String isni) {
Matcher m = PATTERN.matcher(isni);
if (m.find()) {
return String.join("", m.group(1), m.group(2), m.group(3), m.group(4));
} else {
return "";
}
}
}

294
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java Normal file
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@ -0,0 +1,294 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static com.google.common.base.Preconditions.checkArgument;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.security.MessageDigest;
import java.util.*;
import java.util.function.Function;
import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.HashBiMap;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
/**
* Factory class for OpenAIRE identifiers in the Graph
*/
public class IdentifierFactory implements Serializable {
public static final String ID_SEPARATOR = "::";
public static final String ID_PREFIX_SEPARATOR = "|";
public static final int ID_PREFIX_LEN = 12;
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE.
* The id of the record (source_::id) will be rewritten as pidType_::id)
*/
public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
static {
PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
PID_AUTHORITY.put(PidType.w3id, HashBiMap.create());
PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ROHub");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
*
* If a record with the same id (same pid) comes from 2 data sources, the one coming from a delegated source wins. E.g. Zenodo records win over those from Datacite.
* See also https://code-repo.d4science.org/D-Net/dnet-hadoop/pulls/187 and the class dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
*/
public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
static {
DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
DELEGATED_PID_AUTHORITY.put(PidType.w3id, new HashMap<>());
DELEGATED_PID_AUTHORITY.get(PidType.w3id).put(ROHUB_ID, "ro-id");
}
/**
* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
* the same OpenAIRE id.
*/
public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
static {
ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
}
public static Set<String> delegatedAuthorityDatasourceIds() {
return DELEGATED_PID_AUTHORITY
.values()
.stream()
.flatMap(m -> m.keySet().stream())
.collect(Collectors.toCollection(HashSet::new));
}
public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
}
public static <T extends Result> String createDOIBoostIdentifier(T entity) {
if (entity == null)
return null;
StructuredProperty pid = null;
if (entity.getPid() != null) {
pid = entity
.getPid()
.stream()
.filter(Objects::nonNull)
.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
} else {
if (entity.getInstance() != null) {
pid = entity
.getInstance()
.stream()
.filter(i -> i.getPid() != null)
.flatMap(i -> i.getPid().stream())
.filter(CleaningFunctions::pidFilter)
.findAny()
.orElse(null);
}
}
if (pid != null)
return idFromPid(entity, pid, true);
return null;
}
/**
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
*
* @param entity the entity providing PIDs and a default ID.
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
* @param md5 indicates whether should hash the PID value or not.
* @return an identifier from the most relevant PID, entity.id otherwise
*/
public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
return pids
.values()
.stream()
.flatMap(Set::stream)
.min(new PidComparator<>(entity))
.map(
min -> Optional
.ofNullable(pids.get(min.getQualifier().getClassid()))
.map(
p -> p
.stream()
.sorted(new PidValueComparator())
.findFirst()
.map(s -> idFromPid(entity, s, md5))
.orElseGet(entity::getId))
.orElseGet(entity::getId))
.orElseGet(entity::getId);
}
private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
if (entity instanceof Result) {
return Optional
.ofNullable(((Result) entity).getInstance())
.map(IdentifierFactory::mapPids)
.orElse(new HashMap<>());
} else {
return entity
.getPid()
.stream()
.map(CleaningFunctions::normalizePidValue)
.filter(CleaningFunctions::pidFilter)
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
}
private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
return instance
.stream()
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
.flatMap(Function.identity())
.collect(
Collectors
.groupingBy(
p -> p.getQualifier().getClassid(),
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
}
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
boolean mapHandles) {
return Optional
.ofNullable(pid)
.map(
pp -> pp
.stream()
// filter away PIDs provided by a DS that is not considered an authority for the
// given PID Type
.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
.map(CleaningFunctions::normalizePidValue)
.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
.filter(CleaningFunctions::pidFilter))
.orElse(Stream.empty());
}
private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
if (Objects.isNull(collectedFrom)) {
return false;
}
boolean isEnrich = Optional
.ofNullable(ENRICHMENT_PROVIDER.get(pType))
.map(
enrich -> enrich.containsKey(collectedFrom.getKey())
|| enrich.containsValue(collectedFrom.getValue()))
.orElse(false);
boolean isAuthority = Optional
.ofNullable(PID_AUTHORITY.get(pType))
.map(
authorities -> authorities.containsKey(collectedFrom.getKey())
|| authorities.containsValue(collectedFrom.getValue()))
.orElse(false);
return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
}
private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
if (Objects.isNull(da)) {
return true;
}
if (!da.containsKey(collectedFrom.getKey())) {
return true;
}
return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
}
/**
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
*/
public static <T extends OafEntity> String createIdentifier(T entity) {
return createIdentifier(entity, true);
}
private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
}
public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
return new StringBuilder()
.append(numericPrefix)
.append(ID_PREFIX_SEPARATOR)
.append(createPrefix(pidType))
.append(ID_SEPARATOR)
.append(md5 ? md5(pidValue) : pidValue)
.toString();
}
// create the prefix (length = 12)
private static String createPrefix(String pidType) {
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
while (prefix.length() < ID_PREFIX_LEN) {
prefix.append("_");
}
return prefix.substring(0, ID_PREFIX_LEN);
}
public static String md5(final String s) {
try {
final MessageDigest md = MessageDigest.getInstance("MD5");
md.update(s.getBytes(StandardCharsets.UTF_8));
return new String(Hex.encodeHex(md.digest()));
} catch (final Exception e) {
return null;
}
}
}

78
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeComparator.java Normal file
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@ -0,0 +1,78 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
//
// Source code recreated from a .class file by IntelliJ IDEA
// (powered by FernFlower decompiler)
//
import eu.dnetlib.dhp.schema.common.EntityType;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Result;
public class MergeComparator implements Comparator<Oaf> {
public MergeComparator() {
}
public int compare(Oaf left, Oaf right) {
// nulls at the end
if (left == null && right == null) {
return 0;
} else if (left == null) {
return -1;
} else if (right == null) {
return 1;
}
// invisible
if (left.getDataInfo() != null && left.getDataInfo().getInvisible() == true) {
if (right.getDataInfo() != null && right.getDataInfo().getInvisible() == false) {
return -1;
}
}
// collectedfrom
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
&& !rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
return -1;
} else if (!lCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")
&& rCf.contains("10|openaire____::081b82f96300b6a6e3d282bad31cb6e2")) {
return 1;
}
SubEntityType lClass = SubEntityType.fromClass(left.getClass());
SubEntityType rClass = SubEntityType.fromClass(right.getClass());
return lClass.ordinal() - rClass.ordinal();
}
protected HashSet<String> getCollectedFromIds(Oaf left) {
return (HashSet) Optional.ofNullable(left.getCollectedfrom()).map((cf) -> {
return (HashSet) cf.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}).orElse(new HashSet());
}
enum SubEntityType {
publication, dataset, software, otherresearchproduct, datasource, organization, project;
/**
* Resolves the EntityType, given the relative class name
*
* @param clazz the given class name
* @param <T> actual OafEntity subclass
* @return the EntityType associated to the given class
*/
public static <T extends Oaf> SubEntityType fromClass(Class<T> clazz) {
return valueOf(clazz.getSimpleName().toLowerCase());
}
}
}

1032
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java Normal file
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27
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java Normal file
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@ -0,0 +1,27 @@
package eu.dnetlib.dhp.schema.oaf.utils;
public class ModelHardLimits {
private ModelHardLimits() {
}
public static final String LAYOUT = "index";
public static final String INTERPRETATION = "openaire";
public static final String SEPARATOR = "-";
public static final int MAX_EXTERNAL_ENTITIES = 50;
public static final int MAX_AUTHORS = 200;
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
public static final int MAX_TITLE_LENGTH = 5000;
public static final int MAX_TITLES = 10;
public static final int MAX_ABSTRACTS = 10;
public static final int MAX_ABSTRACT_LENGTH = 150000;
public static final int MAX_RELATED_ABSTRACT_LENGTH = 500;
public static final int MAX_INSTANCES = 10;
public static String getCollectionName(String format) {
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
}
}

183
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.sql.Array;
import java.sql.SQLException;
import java.util.*;
import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Function;
@ -12,7 +14,6 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
public class OafMapperUtils {
@ -20,42 +21,6 @@ public class OafMapperUtils {
private OafMapperUtils() {
}
public static Oaf merge(final Oaf left, final Oaf right) {
if (ModelSupport.isSubClass(left, OafEntity.class)) {
return mergeEntities((OafEntity) left, (OafEntity) right);
} else if (ModelSupport.isSubClass(left, Relation.class)) {
((Relation) left).mergeFrom((Relation) right);
} else {
throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName());
}
return left;
}
public static OafEntity mergeEntities(OafEntity left, OafEntity right) {
if (ModelSupport.isSubClass(left, Result.class)) {
return mergeResults((Result) left, (Result) right);
} else if (ModelSupport.isSubClass(left, Datasource.class)) {
left.mergeFrom(right);
} else if (ModelSupport.isSubClass(left, Organization.class)) {
left.mergeFrom(right);
} else if (ModelSupport.isSubClass(left, Project.class)) {
left.mergeFrom(right);
} else {
throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
}
return left;
}
public static Result mergeResults(Result left, Result right) {
if (new ResultTypeComparator().compare(left, right) < 0) {
left.mergeFrom(right);
return left;
} else {
right.mergeFrom(left);
return right;
}
}
public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue();
kv.setKey(k);
@ -95,6 +60,17 @@ public class OafMapperUtils {
.collect(Collectors.toList());
}
public static <T> List<T> listValues(Array values) throws SQLException {
if (Objects.isNull(values)) {
return null;
}
return Arrays
.stream((T[]) values.getArray())
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
return values
.stream()
@ -104,8 +80,30 @@ public class OafMapperUtils {
.collect(Collectors.toList());
}
public static InstanceTypeMapping instanceTypeMapping(String originalType, String code, String label,
String vocabularyName) {
final InstanceTypeMapping m = new InstanceTypeMapping();
m.setVocabularyName(vocabularyName);
m.setOriginalType(originalType);
m.setTypeCode(code);
m.setTypeLabel(label);
return m;
}
public static InstanceTypeMapping instanceTypeMapping(String originalType, Qualifier term) {
return instanceTypeMapping(originalType, term.getClassid(), term.getClassname(), term.getSchemeid());
}
public static InstanceTypeMapping instanceTypeMapping(String originalType) {
return instanceTypeMapping(originalType, null, null, null);
}
public static InstanceTypeMapping instanceTypeMapping(String originalType, String vocabularyName) {
return instanceTypeMapping(originalType, null, null, vocabularyName);
}
public static Qualifier unknown(final String schemeid, final String schemename) {
return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
return qualifier(UNKNOWN, "Unknown", schemeid, schemename);
}
public static AccessRight accessRight(
@ -153,6 +151,17 @@ public class OafMapperUtils {
return q;
}
public static Subject subject(
final String value,
final String classid,
final String classname,
final String schemeid,
final String schemename,
final DataInfo dataInfo) {
return subject(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
}
public static StructuredProperty structuredProperty(
final String value,
final String classid,
@ -164,6 +173,20 @@ public class OafMapperUtils {
return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
}
public static Subject subject(
final String value,
final Qualifier qualifier,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final Subject s = new Subject();
s.setValue(value);
s.setQualifier(qualifier);
s.setDataInfo(dataInfo);
return s;
}
public static StructuredProperty structuredProperty(
final String value,
final Qualifier qualifier,
@ -368,4 +391,88 @@ public class OafMapperUtils {
}
return null;
}
public static KeyValue newKeyValueInstance(String key, String value, DataInfo dataInfo) {
KeyValue kv = new KeyValue();
kv.setDataInfo(dataInfo);
kv.setKey(key);
kv.setValue(value);
return kv;
}
public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) {
Measure m = new Measure();
m.setId(id);
m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo)));
return m;
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity) {
return getRelation(source, target, relType, subRelType, relClass, entity, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final OafEntity entity,
final String validationDate) {
return getRelation(
source, target, relType, subRelType, relClass, entity.getCollectedfrom(), entity.getDataInfo(),
entity.getLastupdatetimestamp(), validationDate, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final List<KeyValue> collectedfrom,
final DataInfo dataInfo,
final Long lastupdatetimestamp) {
return getRelation(
source, target, relType, subRelType, relClass, collectedfrom, dataInfo, lastupdatetimestamp, null, null);
}
public static Relation getRelation(final String source,
final String target,
final String relType,
final String subRelType,
final String relClass,
final List<KeyValue> collectedfrom,
final DataInfo dataInfo,
final Long lastupdatetimestamp,
final String validationDate,
final List<KeyValue> properties) {
final Relation rel = new Relation();
rel.setRelType(relType);
rel.setSubRelType(subRelType);
rel.setRelClass(relClass);
rel.setSource(source);
rel.setTarget(target);
rel.setCollectedfrom(collectedfrom);
rel.setDataInfo(dataInfo);
rel.setLastupdatetimestamp(lastupdatetimestamp);
rel.setValidated(StringUtils.isNotBlank(validationDate));
rel.setValidationDate(StringUtils.isNotBlank(validationDate) ? validationDate : null);
rel.setProperties(properties);
return rel;
}
public static String getProvenance(DataInfo dataInfo) {
return Optional
.ofNullable(dataInfo)
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
}
}

46
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OrganizationPidComparator.java Normal file
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@ -0,0 +1,46 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class OrganizationPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null) {
return right == null ? 0 : -1;
} else if (right == null) {
return 1;
}
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(rClass))
return 0;
if (lClass.equals(PidType.openorgs))
return -1;
if (rClass.equals(PidType.openorgs))
return 1;
if (lClass.equals(PidType.GRID))
return -1;
if (rClass.equals(PidType.GRID))
return 1;
if (lClass.equals(PidType.mag_id))
return -1;
if (rClass.equals(PidType.mag_id))
return 1;
if (lClass.equals(PidType.urn))
return -1;
if (rClass.equals(PidType.urn))
return 1;
return 0;
}
}

21
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRule.java Normal file
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@ -0,0 +1,21 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class PICCleaningRule {
public static final Pattern PATTERN = Pattern.compile("\\d{9}");
public static String clean(final String pic) {
Matcher m = PATTERN.matcher(pic);
if (m.find()) {
return m.group();
} else {
return "";
}
}
}

8
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklist.java Normal file
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@ -0,0 +1,8 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.HashMap;
import java.util.HashSet;
public class PidBlacklist extends HashMap<String, HashSet<String>> {
}

40
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidBlacklistProvider.java Normal file
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@ -0,0 +1,40 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.io.IOException;
import java.util.HashSet;
import java.util.Optional;
import java.util.Set;
import org.apache.commons.io.IOUtils;
import com.fasterxml.jackson.databind.ObjectMapper;
public class PidBlacklistProvider {
private static final PidBlacklist blacklist;
static {
try {
String json = IOUtils.toString(IdentifierFactory.class.getResourceAsStream("pid_blacklist.json"));
blacklist = new ObjectMapper().readValue(json, PidBlacklist.class);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
public static PidBlacklist getBlacklist() {
return blacklist;
}
public static Set<String> getBlacklist(String pidType) {
return Optional
.ofNullable(getBlacklist().get(pidType))
.orElse(new HashSet<>());
}
private PidBlacklistProvider() {
}
}

62
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidCleaner.java Normal file
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@ -0,0 +1,62 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class PidCleaner {
/**
* Utility method that normalises PID values on a per-type basis.
* @param pid the PID whose value will be normalised.
* @return the PID containing the normalised value.
*/
public static StructuredProperty normalizePidValue(StructuredProperty pid) {
pid
.setValue(
normalizePidValue(
pid.getQualifier().getClassid(),
pid.getValue()));
return pid;
}
public static String normalizePidValue(String pidType, String pidValue) {
String value = Optional
.ofNullable(pidValue)
.map(String::trim)
.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
switch (pidType) {
// TODO add cleaning for more PID types as needed
// Result
case "doi":
return DoiCleaningRule.clean(value);
case "pmid":
return PmidCleaningRule.clean(value);
case "pmc":
return PmcCleaningRule.clean(value);
case "handle":
case "arXiv":
return value;
// Organization
case "GRID":
return GridCleaningRule.clean(value);
case "ISNI":
return ISNICleaningRule.clean(value);
case "ROR":
return RorCleaningRule.clean(value);
case "PIC":
return PICCleaningRule.clean(value);
case "FundRef":
return FundRefCleaningRule.clean(value);
default:
return value;
}
}
}

48
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidComparator.java Normal file
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@ -0,0 +1,48 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class PidComparator<T extends OafEntity> implements Comparator<StructuredProperty> {
private final T entity;
public PidComparator(T entity) {
this.entity = entity;
}
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
if (ModelSupport.isSubClass(entity, Result.class)) {
return compareResultPids(left, right);
}
if (ModelSupport.isSubClass(entity, Organization.class)) {
return compareOrganizationtPids(left, right);
}
// Else (but unlikely), lexicographical ordering will do.
return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
}
private int compareResultPids(StructuredProperty left, StructuredProperty right) {
return new ResultPidComparator().compare(left, right);
}
private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
return new OrganizationPidComparator().compare(left, right);
}
}

79
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidType.java Normal file
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@ -0,0 +1,79 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import org.apache.commons.lang3.EnumUtils;
public enum PidType {
/**
* The DOI syntax shall be made up of a DOI prefix and a DOI suffix separated by a forward slash.
*
* There is no defined limit on the length of the DOI name, or of the DOI prefix or DOI suffix.
*
* The DOI name is case-insensitive and can incorporate any printable characters from the legal graphic characters
* of Unicode. Further constraints on character use (e.g. use of language-specific alphanumeric characters) can be
* defined for an application by the ISO 26324 Registration Authority.
*
*
* DOI prefix: The DOI prefix shall be composed of a directory indicator followed by a registrant code.
* These two components shall be separated by a full stop (period). The directory indicator shall be "10" and
* distinguishes the entire set of character strings (prefix and suffix) as digital object identifiers within the
* resolution system.
*
* Registrant code: The second element of the DOI prefix shall be the registrant code. The registrant code is a
* unique string assigned to a registrant.
*
* DOI suffix: The DOI suffix shall consist of a character string of any length chosen by the registrant.
* Each suffix shall be unique to the prefix element that precedes it. The unique suffix can be a sequential number,
* or it might incorporate an identifier generated from or based on another system used by the registrant
* (e.g. ISAN, ISBN, ISRC, ISSN, ISTC, ISNI; in such cases, a preferred construction for such a suffix can be
* specified, as in Example 1).
*
* Source: https://www.doi.org/doi_handbook/2_Numbering.html#2.2
*/
doi,
/**
* PubMed Unique Identifier (PMID)
*
* This field is a 1-to-8 digit accession number with no leading zeros. It is present on all records and is the
* accession number for managing and disseminating records. PMIDs are not reused after records are deleted.
*
* Beginning in February 2012 PMIDs include extensions following a decimal point to account for article versions
* (e.g., 21804956.2). All citations are considered version 1 until replaced. The extended PMID is not displayed
* on the MEDLINE format.
*
* View the citation in abstract format in PubMed to access additional versions when available (see the article in
* the Jan-Feb 2012 NLM Technical Bulletin).
*
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
*/
pmid,
/**
* This field contains the unique identifier for the cited article in PubMed Central. The identifier begins with the
* prefix PMC.
*
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
*/
pmc, handle, arXiv, nct, pdb, w3id,
// Organization
openorgs, ROR, GRID, PIC, ISNI, Wikidata, FundRef, corda, corda_h2020, mag_id, urn,
// Used by dedup
undefined, original;
public static boolean isValid(String type) {
return EnumUtils.isValidEnum(PidType.class, type);
}
public static PidType tryValueOf(String s) {
try {
return PidType.valueOf(s);
} catch (Exception e) {
return PidType.original;
}
}
}

33
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java Normal file
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@ -0,0 +1,33 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import java.util.Optional;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class PidValueComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
StructuredProperty l = CleaningFunctions.normalizePidValue(left);
StructuredProperty r = CleaningFunctions.normalizePidValue(right);
return Optional
.ofNullable(l.getValue())
.map(
lv -> Optional
.ofNullable(r.getValue())
.map(rv -> lv.compareTo(rv))
.orElse(-1))
.orElse(1);
}
}

24
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PmcCleaningRule.java Normal file
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@ -0,0 +1,24 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class PmcCleaningRule {
public static final Pattern PATTERN = Pattern.compile("PMC\\d{1,8}");
public static String clean(String pmc) {
String s = pmc
.replaceAll("\\s", "")
.toUpperCase();
final Matcher m = PATTERN.matcher(s);
if (m.find()) {
return m.group();
}
return "";
}
}

25
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PmidCleaningRule.java Normal file
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@ -0,0 +1,25 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
// https://researchguides.stevens.edu/c.php?g=442331&p=6577176
public class PmidCleaningRule {
public static final Pattern PATTERN = Pattern.compile("0*(\\d{1,8})");
public static String clean(String pmid) {
String s = pmid
.toLowerCase()
.replaceAll("\\s", "");
final Matcher m = PATTERN.matcher(s);
if (m.find()) {
return m.group(1);
}
return "";
}
}

46
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/RefereedComparator.java Normal file
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@ -0,0 +1,46 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
/**
* Comparator for sorting the values from the dnet:review_levels vocabulary, implements the following ordering
*
* peerReviewed (0001) > nonPeerReviewed (0002) > UNKNOWN (0000)
*/
public class RefereedComparator implements Comparator<Qualifier> {
@Override
public int compare(Qualifier left, Qualifier right) {
if (left == null || left.getClassid() == null) {
return (right == null || right.getClassid() == null) ? 0 : -1;
} else if (right == null || right.getClassid() == null) {
return 1;
}
String lClass = left.getClassid();
String rClass = right.getClassid();
if (lClass.equals(rClass))
return 0;
if ("0001".equals(lClass))
return -1;
if ("0001".equals(rClass))
return 1;
if ("0002".equals(lClass))
return -1;
if ("0002".equals(rClass))
return 1;
if ("0000".equals(lClass))
return -1;
if ("0000".equals(rClass))
return 1;
return 0;
}
}

56
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultPidComparator.java Normal file
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@ -0,0 +1,56 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
public class ResultPidComparator implements Comparator<StructuredProperty> {
@Override
public int compare(StructuredProperty left, StructuredProperty right) {
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
if (lClass.equals(rClass))
return 0;
if (lClass.equals(PidType.doi))
return -1;
if (rClass.equals(PidType.doi))
return 1;
if (lClass.equals(PidType.pmid))
return -1;
if (rClass.equals(PidType.pmid))
return 1;
if (lClass.equals(PidType.pmc))
return -1;
if (rClass.equals(PidType.pmc))
return 1;
if (lClass.equals(PidType.handle))
return -1;
if (rClass.equals(PidType.handle))
return 1;
if (lClass.equals(PidType.arXiv))
return -1;
if (rClass.equals(PidType.arXiv))
return 1;
if (lClass.equals(PidType.nct))
return -1;
if (rClass.equals(PidType.nct))
return 1;
if (lClass.equals(PidType.pdb))
return -1;
if (rClass.equals(PidType.pdb))
return 1;
return 0;
}
}

78
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java Normal file
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@ -0,0 +1,78 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
import java.util.Comparator;
import java.util.HashSet;
import java.util.Optional;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Result;
public class ResultTypeComparator implements Comparator<Result> {
public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
@Override
public int compare(Result left, Result right) {
if (left == null && right == null)
return 0;
if (left == null)
return 1;
if (right == null)
return -1;
HashSet<String> lCf = getCollectedFromIds(left);
HashSet<String> rCf = getCollectedFromIds(right);
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
return -1;
}
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
return 1;
}
String lClass = left.getResulttype().getClassid();
String rClass = right.getResulttype().getClassid();
if (!lClass.equals(rClass)) {
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
return 1;
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return -1;
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
return 1;
}
// Else (but unlikely), lexicographical ordering will do.
return lClass.compareTo(rClass);
}
protected HashSet<String> getCollectedFromIds(Result left) {
return Optional
.ofNullable(left.getCollectedfrom())
.map(
cf -> cf
.stream()
.map(KeyValue::getKey)
.collect(Collectors.toCollection(HashSet::new)))
.orElse(new HashSet<>());
}
}

27
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/RorCleaningRule.java Normal file
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@ -0,0 +1,27 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
// https://ror.readme.io/docs/ror-identifier-pattern
public class RorCleaningRule {
public static final String ROR_PREFIX = "https://ror.org/";
private static final Pattern PATTERN = Pattern.compile("(?<ror>0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2})");
public static String clean(String ror) {
String s = ror
.replaceAll("\\s", "")
.toLowerCase();
Matcher m = PATTERN.matcher(s);
if (m.find()) {
return ROR_PREFIX + m.group("ror");
}
return "";
}
}

46
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/SubjectProvenanceComparator.java Normal file
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@ -0,0 +1,46 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Subject;
public class SubjectProvenanceComparator implements Comparator<Subject> {
@Override
public int compare(Subject left, Subject right) {
String lProv = getProvenance(left.getDataInfo());
String rProv = getProvenance(right.getDataInfo());
if (isBlank(lProv) && isBlank(rProv))
return 0;
if (isBlank(lProv))
return 1;
if (isBlank(rProv))
return -1;
if (lProv.equals(rProv))
return 0;
if (lProv.toLowerCase().contains("crosswalk"))
return -1;
if (rProv.toLowerCase().contains("crosswalk"))
return 1;
if (lProv.toLowerCase().contains("user"))
return -1;
if (rProv.toLowerCase().contains("user"))
return 1;
if (lProv.toLowerCase().contains("propagation"))
return -1;
if (rProv.toLowerCase().contains("propagation"))
return 1;
if (lProv.toLowerCase().contains("iis"))
return -1;
if (rProv.toLowerCase().contains("iis"))
return 1;
return 0;
}
}

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

@ -75,9 +75,14 @@ public class DHPUtils {
final HttpGet req = new HttpGet(url);
log.info("MDStoreManager request: {}", req);
try (final CloseableHttpClient client = HttpClients.createDefault()) {
try (final CloseableHttpResponse response = client.execute(req)) {
final String json = IOUtils.toString(response.getEntity().getContent());
log.info("MDStoreManager response: {}", json);
final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
return Arrays
.stream(mdstores)

0
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_maketar_parameters.json → dhp-common/src/main/resources/eu/dnetlib/dhp/common/input_maketar_parameters.json
View File

8
dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt Normal file
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@ -0,0 +1,8 @@
van
von
der
de
dell
sig
mr
mrs

38
dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json Normal file
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@ -0,0 +1,38 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "gin",
"paramLongName": "graphInputPath",
"paramDescription": "the input graph root path",
"paramRequired": true
},
{
"paramName": "cp",
"paramLongName": "checkpointPath",
"paramDescription": "checkpoint directory",
"paramRequired": true
},
{
"paramName": "out",
"paramLongName": "outputPath",
"paramDescription": "the output graph root path",
"paramRequired": true
},
{
"paramName": "fi",
"paramLongName": "filterInvisible",
"paramDescription": "if true filters out invisible entities",
"paramRequired": true
},
{
"paramName": "isu",
"paramLongName": "isLookupUrl",
"paramDescription": "url to the ISLookup Service",
"paramRequired": true
}
]

20
dhp-common/src/main/resources/eu/dnetlib/dhp/oozie/run_sql_parameters.json Normal file
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@ -0,0 +1,20 @@
[
{
"paramName": "issm",
"paramLongName": "isSparkSessionManaged",
"paramDescription": "when true will stop SparkSession after job execution",
"paramRequired": false
},
{
"paramName": "hmu",
"paramLongName": "hiveMetastoreUris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{
"paramName": "sql",
"paramLongName": "sql",
"paramDescription": "sql script to execute",
"paramRequired": true
}
]

85
dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala Normal file
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@ -0,0 +1,85 @@
package eu.dnetlib.dhp.application
import eu.dnetlib.dhp.common.Constants
import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
import scala.io.Source
/** This is the main Interface SparkApplication
* where all the Spark Scala class should inherit
*/
trait SparkScalaApplication {
/** This is the path in the classpath of the json
* describes all the argument needed to run
*/
val propertyPath: String
/** Utility to parse the arguments using the
* property json in the classpath identified from
* the variable propertyPath
*
* @param args the list of arguments
*/
def parseArguments(args: Array[String]): ArgumentApplicationParser = {
val parser = new ArgumentApplicationParser(
Source.fromInputStream(getClass.getResourceAsStream(propertyPath)).mkString
)
parser.parseArgument(args)
parser
}
/** Here all the spark applications runs this method
* where the whole logic of the spark node is defined
*/
def run(): Unit
}
import org.apache.spark.SparkConf
import org.apache.spark.sql.SparkSession
import org.slf4j.Logger
abstract class AbstractScalaApplication(
val propertyPath: String,
val args: Array[String],
log: Logger
) extends SparkScalaApplication {
var parser: ArgumentApplicationParser = null
var spark: SparkSession = null
def initialize(): SparkScalaApplication = {
parser = parseArguments(args)
spark = createSparkSession()
this
}
/** Utility for creating a spark session starting from parser
*
* @return a spark Session
*/
private def createSparkSession(): SparkSession = {
require(parser != null)
val conf: SparkConf = new SparkConf()
val master = parser.get("master")
log.info(s"Creating Spark session: Master: $master")
SparkSession
.builder()
.config(conf)
.appName(getClass.getSimpleName)
.master(master)
.getOrCreate()
}
def reportTotalSize(targetPath: String, outputBasePath: String): Unit = {
val total_items = spark.read.text(targetPath).count()
writeHdfsFile(
spark.sparkContext.hadoopConfiguration,
s"$total_items",
outputBasePath + Constants.MDSTORE_SIZE_PATH
)
}
}

10
dhp-common/src/main/scala/eu/dnetlib/dhp/application/dedup/log/DedupLogModel.scala Normal file
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@ -0,0 +1,10 @@
package eu.dnetlib.dhp.application.dedup.log
case class DedupLogModel(
tag: String,
configuration: String,
entity: String,
startTS: Long,
endTS: Long,
totalMs: Long
) {}

14
dhp-common/src/main/scala/eu/dnetlib/dhp/application/dedup/log/DedupLogWriter.scala Normal file
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@ -0,0 +1,14 @@
package eu.dnetlib.dhp.application.dedup.log
import org.apache.spark.sql.{SaveMode, SparkSession}
class DedupLogWriter(path: String) {
def appendLog(dedupLogModel: DedupLogModel, spark: SparkSession): Unit = {
import spark.implicits._
val df = spark.createDataset[DedupLogModel](data = List(dedupLogModel))
df.write.mode(SaveMode.Append).save(path)
}
}

442
dhp-common/src/main/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala Normal file
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@ -0,0 +1,442 @@
package eu.dnetlib.dhp.sx.graph.scholix
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.scholix._
import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.spark.sql.expressions.Aggregator
import org.apache.spark.sql.{Encoder, Encoders}
import org.json4s
import org.json4s.DefaultFormats
import org.json4s.jackson.JsonMethods.parse
import scala.collection.JavaConverters._
import scala.io.Source
object ScholixUtils extends Serializable {
val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
val DATE_RELATION_KEY: String = "RelationDate"
case class RelationVocabulary(original: String, inverse: String) {}
case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
val relations: Map[String, RelationVocabulary] = {
val input = Source
.fromInputStream(
getClass.getResourceAsStream("/eu/dnetlib/scholexplorer/relation/relations.json")
)
.mkString
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
lazy val json: json4s.JValue = parse(input)
json.extract[Map[String, RelationVocabulary]]
}
def extractRelationDate(relation: Relation): String = {
if (relation.getProperties == null || !relation.getProperties.isEmpty)
null
else {
val date = relation.getProperties.asScala
.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey))
.map(p => p.getValue)
if (date.isDefined)
date.get
else
null
}
}
def extractRelationDate(summary: ScholixSummary): String = {
if (summary.getDate == null || summary.getDate.isEmpty)
null
else {
summary.getDate.get(0)
}
}
def inverseRelationShip(rel: ScholixRelationship): ScholixRelationship = {
new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
}
def generateScholixResourceFromResult(r: Result): ScholixResource = {
generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
}
val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
override def zero: RelatedEntities = null
override def reduce(b: RelatedEntities, a: (String, String, Long)): RelatedEntities = {
val relatedDataset = if ("dataset".equalsIgnoreCase(a._2)) a._3 else 0
val relatedPublication = if ("publication".equalsIgnoreCase(a._2)) a._3 else 0
if (b == null)
RelatedEntities(a._1, relatedDataset, relatedPublication)
else
RelatedEntities(
a._1,
b.relatedDataset + relatedDataset,
b.relatedPublication + relatedPublication
)
}
override def merge(b1: RelatedEntities, b2: RelatedEntities): RelatedEntities = {
if (b1 != null && b2 != null)
RelatedEntities(
b1.id,
b1.relatedDataset + b2.relatedDataset,
b1.relatedPublication + b2.relatedPublication
)
else if (b1 != null)
b1
else
b2
}
override def finish(reduction: RelatedEntities): RelatedEntities = reduction
override def bufferEncoder: Encoder[RelatedEntities] = Encoders.bean(classOf[RelatedEntities])
override def outputEncoder: Encoder[RelatedEntities] = Encoders.bean(classOf[RelatedEntities])
}
val scholixAggregator: Aggregator[(String, Scholix), Scholix, Scholix] =
new Aggregator[(String, Scholix), Scholix, Scholix] with Serializable {
override def zero: Scholix = null
def scholix_complete(s: Scholix): Boolean = {
if (s == null || s.getIdentifier == null) {
false
} else if (s.getSource == null || s.getTarget == null) {
false
} else if (s.getLinkprovider == null || s.getLinkprovider.isEmpty)
false
else
true
}
override def reduce(b: Scholix, a: (String, Scholix)): Scholix = {
if (scholix_complete(b)) b else a._2
}
override def merge(b1: Scholix, b2: Scholix): Scholix = {
if (scholix_complete(b1)) b1 else b2
}
override def finish(reduction: Scholix): Scholix = reduction
override def bufferEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
override def outputEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
}
def createInverseScholixRelation(scholix: Scholix): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(inverseRelationShip(scholix.getRelationship))
s.setSource(scholix.getTarget)
s.setTarget(scholix.getSource)
s.setIdentifier(
DHPUtils.md5(
s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"
)
)
s
}
def extractCollectedFrom(summary: ScholixResource): List[ScholixEntityId] = {
if (summary.getCollectedFrom != null && !summary.getCollectedFrom.isEmpty) {
val l: List[ScholixEntityId] = summary.getCollectedFrom.asScala.map { d =>
new ScholixEntityId(d.getProvider.getName, d.getProvider.getIdentifiers)
}(collection.breakOut)
l
} else List()
}
def extractCollectedFrom(summary: ScholixSummary): List[ScholixEntityId] = {
if (summary.getDatasources != null && !summary.getDatasources.isEmpty) {
val l: List[ScholixEntityId] = summary.getDatasources.asScala.map { d =>
new ScholixEntityId(
d.getDatasourceName,
List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava
)
}(collection.breakOut)
l
} else List()
}
def extractCollectedFrom(relation: Relation): List[ScholixEntityId] = {
if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map { c =>
new ScholixEntityId(
c.getValue,
List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava
)
}.toList
l
} else List()
}
def generateCompleteScholix(scholix: Scholix, target: ScholixSummary): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(scholix.getRelationship)
s.setSource(scholix.getSource)
s.setTarget(generateScholixResourceFromSummary(target))
s.setIdentifier(
DHPUtils.md5(
s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"
)
)
s
}
def generateCompleteScholix(scholix: Scholix, target: ScholixResource): Scholix = {
val s = new Scholix
s.setPublicationDate(scholix.getPublicationDate)
s.setPublisher(scholix.getPublisher)
s.setLinkprovider(scholix.getLinkprovider)
s.setRelationship(scholix.getRelationship)
s.setSource(scholix.getSource)
s.setTarget(target)
s.setIdentifier(
DHPUtils.md5(
s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"
)
)
s
}
def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
val r = new ScholixResource
r.setIdentifier(summaryObject.getLocalIdentifier)
r.setDnetIdentifier(summaryObject.getId)
r.setObjectType(summaryObject.getTypology.toString)
r.setObjectSubType(summaryObject.getSubType)
if (summaryObject.getTitle != null && !summaryObject.getTitle.isEmpty)
r.setTitle(summaryObject.getTitle.get(0))
if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
val l: List[ScholixEntityId] =
summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a, null)).toList
if (l.nonEmpty)
r.setCreator(l.asJava)
}
if (summaryObject.getDate != null && !summaryObject.getDate.isEmpty)
r.setPublicationDate(summaryObject.getDate.get(0))
if (summaryObject.getPublisher != null && !summaryObject.getPublisher.isEmpty) {
val plist: List[ScholixEntityId] =
summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
if (plist.nonEmpty)
r.setPublisher(plist.asJava)
}
if (summaryObject.getDatasources != null && !summaryObject.getDatasources.isEmpty) {
val l: List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala
.map(c =>
new ScholixCollectedFrom(
new ScholixEntityId(
c.getDatasourceName,
List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava
),
"collected",
"complete"
)
)
.toList
if (l.nonEmpty)
r.setCollectedFrom(l.asJava)
}
r
}
def scholixFromSource(relation: Relation, source: ScholixResource): Scholix = {
if (relation == null || source == null)
return null
val s = new Scholix
var l: List[ScholixEntityId] = extractCollectedFrom(relation)
if (l.isEmpty)
l = extractCollectedFrom(source)
if (l.isEmpty)
return null
s.setLinkprovider(l.asJava)
var d = extractRelationDate(relation)
if (d == null)
d = source.getPublicationDate
s.setPublicationDate(d)
if (source.getPublisher != null && !source.getPublisher.isEmpty) {
s.setPublisher(source.getPublisher)
}
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
if (semanticRelation == null)
return null
s.setRelationship(
new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
)
s.setSource(source)
s
}
def scholixFromSource(relation: Relation, source: ScholixSummary): Scholix = {
if (relation == null || source == null)
return null
val s = new Scholix
var l: List[ScholixEntityId] = extractCollectedFrom(relation)
if (l.isEmpty)
l = extractCollectedFrom(source)
if (l.isEmpty)
return null
s.setLinkprovider(l.asJava)
var d = extractRelationDate(relation)
if (d == null)
d = extractRelationDate(source)
s.setPublicationDate(d)
if (source.getPublisher != null && !source.getPublisher.isEmpty) {
val l: List[ScholixEntityId] = source.getPublisher.asScala
.map { p =>
new ScholixEntityId(p, null)
}(collection.breakOut)
if (l.nonEmpty)
s.setPublisher(l.asJava)
}
val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
if (semanticRelation == null)
return null
s.setRelationship(
new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
)
s.setSource(generateScholixResourceFromSummary(source))
s
}
def findURLForPID(
pidValue: List[StructuredProperty],
urls: List[String]
): List[(StructuredProperty, String)] = {
pidValue.map { p =>
val pv = p.getValue
val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase))
(p, r.orNull)
}
}
def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
if (r.getInstance() == null || r.getInstance().isEmpty)
return List()
r.getInstance()
.asScala
.filter(i => i.getUrl != null && !i.getUrl.isEmpty)
.filter(i => i.getPid != null && i.getUrl != null)
.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2))
.distinct
.toList
}
def resultToSummary(r: Result): ScholixSummary = {
val s = new ScholixSummary
s.setId(r.getId)
if (r.getPid == null || r.getPid.isEmpty)
return null
val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
if (persistentIdentifiers.isEmpty)
return null
s.setLocalIdentifier(persistentIdentifiers.asJava)
if (r.isInstanceOf[Publication])
s.setTypology(Typology.publication)
else
s.setTypology(Typology.dataset)
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
if (r.getTitle != null && r.getTitle.asScala.nonEmpty) {
val titles: List[String] = r.getTitle.asScala.map(t => t.getValue).toList
if (titles.nonEmpty)
s.setTitle(titles.asJava)
else
return null
}
if (r.getAuthor != null && !r.getAuthor.isEmpty) {
val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname).toList
if (authors.nonEmpty)
s.setAuthor(authors.asJava)
}
if (r.getInstance() != null) {
val dt: List[String] = r
.getInstance()
.asScala
.filter(i => i.getDateofacceptance != null)
.map(i => i.getDateofacceptance.getValue)
.toList
if (dt.nonEmpty)
s.setDate(dt.distinct.asJava)
}
if (r.getDescription != null && !r.getDescription.isEmpty) {
val d = r.getDescription.asScala.find(f => f != null && f.getValue != null)
if (d.isDefined)
s.setDescription(d.get.getValue)
}
if (r.getSubject != null && !r.getSubject.isEmpty) {
val subjects: List[SchemeValue] = r.getSubject.asScala
.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))
.toList
if (subjects.nonEmpty)
s.setSubject(subjects.asJava)
}
if (r.getPublisher != null)
s.setPublisher(List(r.getPublisher.getValue).asJava)
if (r.getCollectedfrom != null && !r.getCollectedfrom.isEmpty) {
val cf: List[CollectedFromType] = r.getCollectedfrom.asScala
.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))
.toList
if (cf.nonEmpty)
s.setDatasources(cf.distinct.asJava)
}
s.setRelatedDatasets(0)
s.setRelatedPublications(0)
s.setRelatedUnknown(0)
s
}
}

36
dhp-common/src/test/java/eu/dnetlib/dhp/common/MdStoreClientTest.java Normal file
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@ -0,0 +1,36 @@
package eu.dnetlib.dhp.common;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
public class MdStoreClientTest {
// @Test
public void testMongoCollection() throws IOException {
final MdstoreClient client = new MdstoreClient("mongodb://localhost:27017", "mdstore");
final ObjectMapper mapper = new ObjectMapper();
final List<MDStoreInfo> infos = client.mdStoreWithTimestamp("ODF", "store", "cleaned");
infos.forEach(System.out::println);
final String s = mapper.writeValueAsString(infos);
Path fileName = Paths.get("/Users/sandro/mdstore_info.json");
// Writing into the file
Files.write(fileName, s.getBytes(StandardCharsets.UTF_8));
}
}

8
dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java
View File

@ -33,7 +33,7 @@ class ZenodoAPIClientTest {
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz", file.length()));
Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz"));
String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json"));
@ -56,7 +56,7 @@ class ZenodoAPIClientTest {
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz", file.length()));
Assertions.assertEquals(200, client.uploadIS(is, "COVID-19.json.gz"));
String metadata = IOUtils.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/common/api/metadata.json"));
@ -80,7 +80,7 @@ class ZenodoAPIClientTest {
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition", file.length()));
Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition"));
Assertions.assertEquals(202, client.publish());
@ -100,7 +100,7 @@ class ZenodoAPIClientTest {
InputStream is = new FileInputStream(file);
Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition", file.length()));
Assertions.assertEquals(200, client.uploadIS(is, "newVersion_deposition"));
Assertions.assertEquals(202, client.publish());

100
dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java
View File

@ -1,100 +0,0 @@
package eu.dnetlib.dhp.oa.merge;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
class AuthorMergerTest {
private String publicationsBasePath;
private List<List<Author>> authors;
@BeforeEach
public void setUp() throws Exception {
publicationsBasePath = Paths
.get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI())
.toFile()
.getAbsolutePath();
authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
}
@Test
void mergeTest() { // used in the dedup: threshold set to 0.95
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));
for (Author author : authors1) {
System.out.println(authorToString(author));
}
}
List<Author> merge = AuthorMerger.merge(authors);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(7, merge.size());
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
public String authorToString(Author a) {
String print = "Fullname = ";
print += a.getFullname() + " pid = [";
if (a.getPid() != null)
for (StructuredProperty sp : a.getPid()) {
print += sp.toComparableString() + " ";
}
print += "]";
return print;
}
}

21
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/BlackListProviderTest.java Normal file
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@ -0,0 +1,21 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.Set;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
class BlackListProviderTest {
@Test
void blackListTest() {
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
Assertions.assertNotNull(xxx);
Assertions.assertEquals(0, xxx.size());
}
}

18
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRuleTest.java Normal file
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@ -0,0 +1,18 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class GridCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("grid.493784.5", GridCleaningRule.clean("grid.493784.5"));
assertEquals("grid.493784.5x", GridCleaningRule.clean("grid.493784.5x"));
assertEquals("grid.493784.5x", GridCleaningRule.clean("493784.5x"));
assertEquals("", GridCleaningRule.clean("493x784.5x"));
}
}

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/ISNICleaningRuleTest.java Normal file
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@ -0,0 +1,19 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class ISNICleaningRuleTest {
@Test
void testCleaning() {
assertEquals("0000000463436020", ISNICleaningRule.clean("0000 0004 6343 6020"));
assertEquals("0000000463436020", ISNICleaningRule.clean("0000000463436020"));
assertEquals("", ISNICleaningRule.clean("Q30256598"));
assertEquals("0000000493403529", ISNICleaningRule.clean("ISNI:0000000493403529"));
assertEquals("000000008614884X", ISNICleaningRule.clean("0000 0000 8614 884X"));
}
}

87
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java Normal file
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@ -0,0 +1,87 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import java.io.IOException;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Publication;
class IdentifierFactoryTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
void testCreateIdentifierForPublication() throws IOException {
verifyIdentifier(
"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
verifyIdentifier(
"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
verifyIdentifier(
"publication_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
verifyIdentifier(
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
verifyIdentifier(
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
verifyIdentifier(
"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, true);
verifyIdentifier("publication_4.json", defaultID, true);
verifyIdentifier("publication_5.json", defaultID, true);
}
@Test
void testCreateIdentifierForPublicationNoHash() throws IOException {
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
verifyIdentifier(
"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
verifyIdentifier("publication_3.json", defaultID, false);
verifyIdentifier("publication_4.json", defaultID, false);
verifyIdentifier("publication_5.json", defaultID, false);
}
@Test
void testCreateIdentifierForROHub() throws IOException {
verifyIdentifier(
"orp-rohub.json", "50|w3id________::afc7592914ae190a50570db90f55f9c2", true);
}
protected void verifyIdentifier(String filename, String expectedID, boolean md5) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class);
String id = IdentifierFactory.createIdentifier(pub, md5);
System.out.println(id);
assertNotNull(id);
assertEquals(expectedID, id);
}
}

130
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtilsTest.java Normal file
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@ -0,0 +1,130 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.*;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
import java.util.HashSet;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.commons.beanutils.BeanUtils;
import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.databind.DeserializationFeature;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
public class MergeUtilsTest {
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
@Test
void testMergePubs_new() throws IOException {
Publication pt = read("publication_test.json", Publication.class);
Publication p1 = read("publication_test.json", Publication.class);
assertEquals(1, pt.getCollectedfrom().size());
assertEquals(ModelConstants.CROSSREF_ID, pt.getCollectedfrom().get(0).getKey());
Instance i = new Instance();
i.setUrl(Lists.newArrayList("https://..."));
p1.getInstance().add(i);
Publication ptp1 = MergeUtils.mergePublication(pt, p1);
assertNotNull(ptp1.getInstance());
assertEquals(2, ptp1.getInstance().size());
}
@Test
void testMergePubs() throws IOException {
Publication p1 = read("publication_1.json", Publication.class);
Publication p2 = read("publication_2.json", Publication.class);
Dataset d1 = read("dataset_1.json", Dataset.class);
Dataset d2 = read("dataset_2.json", Dataset.class);
assertEquals(1, p1.getCollectedfrom().size());
assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
assertEquals(1, d2.getCollectedfrom().size());
assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertEquals(1, p2.getCollectedfrom().size());
assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
assertEquals(1, d1.getCollectedfrom().size());
assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
final Result p1d2 = MergeUtils.checkedMerge(p1, d2);
assertEquals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID, p1d2.getResulttype().getClassid());
assertTrue(p1d2 instanceof Publication);
assertEquals(p1.getId(), p1d2.getId());
}
@Test
void testMergePubs_1() throws IOException {
Publication p2 = read("publication_2.json", Publication.class);
Dataset d1 = read("dataset_1.json", Dataset.class);
final Result p2d1 = MergeUtils.checkedMerge(p2, d1);
assertEquals((ModelConstants.DATASET_RESULTTYPE_CLASSID), p2d1.getResulttype().getClassid());
assertTrue(p2d1 instanceof Dataset);
assertEquals(d1.getId(), p2d1.getId());
assertEquals(2, p2d1.getCollectedfrom().size());
}
@Test
void testMergePubs_2() throws IOException {
Publication p1 = read("publication_1.json", Publication.class);
Publication p2 = read("publication_2.json", Publication.class);
Result p1p2 = MergeUtils.checkedMerge(p1, p2);
assertTrue(p1p2 instanceof Publication);
assertEquals(p1.getId(), p1p2.getId());
assertEquals(2, p1p2.getCollectedfrom().size());
}
@Test
void testDelegatedAuthority_1() throws IOException {
Dataset d1 = read("dataset_2.json", Dataset.class);
Dataset d2 = read("dataset_delegated.json", Dataset.class);
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = (Result) MergeUtils.merge(d1, d2, true);
assertEquals(d2, res);
}
@Test
void testDelegatedAuthority_2() throws IOException {
Dataset p1 = read("publication_1.json", Dataset.class);
Dataset d2 = read("dataset_delegated.json", Dataset.class);
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = (Result) MergeUtils.merge(p1, d2, true);
assertEquals(d2, res);
}
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}
protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
return OBJECT_MAPPER.readValue(json, clazz);
}
}

215
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
View File

@ -44,105 +44,104 @@ class OafMapperUtilsTest {
@Test
void testDateValidation() {
assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z ").isPresent());
assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent());
assertTrue(GraphCleaningFunctions.doCleanDate(" 2016-04-05").isPresent());
assertNotNull(GraphCleaningFunctions.cleanDate("2016-05-07T12:41:19.202Z "));
assertNotNull(GraphCleaningFunctions.cleanDate("2020-09-10 11:08:52 "));
assertNotNull(GraphCleaningFunctions.cleanDate(" 2016-04-05"));
assertEquals("2016-04-05", GraphCleaningFunctions.doCleanDate("2016 Apr 05").get());
assertEquals("2016-04-05", GraphCleaningFunctions.cleanDate("2016 Apr 05"));
assertEquals("2009-05-08", GraphCleaningFunctions.doCleanDate("May 8, 2009 5:57:51 PM").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, 1970").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, '70").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 1970").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 70").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 2006").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 MST 2006").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 02 15:04:05 -0700 2006").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Monday, 02-Jan-06 15:04:05 MST").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 MST").get());
assertEquals("2017-07-11", GraphCleaningFunctions.doCleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 -0700").get());
assertEquals("2018-01-04", GraphCleaningFunctions.doCleanDate("Thu, 4 Jan 2018 17:53:36 +0000").get());
assertEquals("2015-08-10", GraphCleaningFunctions.doCleanDate("Mon Aug 10 15:44:11 UTC+0100 2015").get());
assertEquals("2009-05-08", GraphCleaningFunctions.cleanDate("May 8, 2009 5:57:51 PM"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, 1970"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, '70"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 1970"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 70"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 2006"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 MST 2006"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 02 15:04:05 -0700 2006"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Monday, 02-Jan-06 15:04:05 MST"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 MST"));
assertEquals("2017-07-11", GraphCleaningFunctions.cleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 -0700"));
assertEquals("2018-01-04", GraphCleaningFunctions.cleanDate("Thu, 4 Jan 2018 17:53:36 +0000"));
assertEquals("2015-08-10", GraphCleaningFunctions.cleanDate("Mon Aug 10 15:44:11 UTC+0100 2015"));
assertEquals(
"2015-07-03",
GraphCleaningFunctions.doCleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)").get());
assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 10:09am").get());
assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 at 10:09am PST-08").get());
assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012, 10:10:09").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7, 1970").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7th, 1970").get());
assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006, 19:17").get());
assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006 19:17").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 70").get());
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 1970").get());
assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("03 February 2013").get());
assertEquals("2013-07-01", GraphCleaningFunctions.doCleanDate("1 July 2013").get());
assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("2013-Feb-03").get());
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3/31/2014").get());
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03/31/2014").get());
assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08/21/71").get());
assertEquals("1971-01-08", GraphCleaningFunctions.doCleanDate("8/1/71").get());
assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/2014 22:05").get());
assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("04/08/2014 22:05").get());
assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/14 22:05").get());
assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("04/2/2014 03:00:51").get());
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00:00 AM").get());
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00:01 PM").get());
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00 PM").get());
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 1:00 PM").get());
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00 AM").get());
assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("4/02/2014 03:00:51").get());
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59").get());
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59.3186369").get());
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/3/31").get());
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/03/31").get());
assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/4/8 22:05").get());
assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/04/08 22:05").get());
assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/04/2 03:00:51").get());
assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/4/02 03:00:51").get());
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59").get());
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59.3186369").get());
assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014年04月08日").get());
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get());
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get());
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get());
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get());
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get());
assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43").get());
assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43:22").get());
assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 UTC").get());
assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 GMT").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 05:24:37 PM").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800 +08").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:44 +09:00").get());
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000 +0000 UTC").get());
assertEquals("2015-09-30", GraphCleaningFunctions.doCleanDate("2015-09-30 18:48:56.35272715 +0000 UTC").get());
assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 GMT").get());
assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 UTC").get());
GraphCleaningFunctions.cleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)"));
assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 10:09am"));
assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 at 10:09am PST-08"));
assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012, 10:10:09"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7, 1970"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7th, 1970"));
assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006, 19:17"));
assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006 19:17"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 70"));
assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 1970"));
assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("03 February 2013"));
assertEquals("2013-07-01", GraphCleaningFunctions.cleanDate("1 July 2013"));
assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("2013-Feb-03"));
assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3/31/2014"));
assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03/31/2014"));
assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08/21/71"));
assertEquals("1971-01-08", GraphCleaningFunctions.cleanDate("8/1/71"));
assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/2014 22:05"));
assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("04/08/2014 22:05"));
assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/14 22:05"));
assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("04/2/2014 03:00:51"));
assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00:00 AM"));
assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00:01 PM"));
assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00 PM"));
assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 1:00 PM"));
assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00 AM"));
assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("4/02/2014 03:00:51"));
assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59"));
assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59.3186369"));
assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/3/31"));
assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/03/31"));
assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/4/8 22:05"));
assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/04/08 22:05"));
assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/04/2 03:00:51"));
assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/4/02 03:00:51"));
assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59"));
assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59.3186369"));
assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014年04月08日"));
assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("2006-01-02T15:04:05+0000"));
assertEquals("2009-08-13", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09-07:00"));
assertEquals("2009-08-12", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.3186369"));
assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.123"));
assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43"));
assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43:22"));
assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 UTC"));
assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 GMT"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 05:24:37 PM"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800 +08"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:44 +09:00"));
assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000 +0000 UTC"));
assertEquals("2015-09-30", GraphCleaningFunctions.cleanDate("2015-09-30 18:48:56.35272715 +0000 UTC"));
assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 GMT"));
assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 UTC"));
assertEquals(
"2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001").get());
"2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001"));
assertEquals(
"2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001").get());
assertEquals("2017-07-19", GraphCleaningFunctions.doCleanDate("2017-07-19 03:21:51+00:00").get());
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26").get());
assertEquals("2014-04-01", GraphCleaningFunctions.doCleanDate("2014-04").get());
assertEquals("2014-01-01", GraphCleaningFunctions.doCleanDate("2014").get());
assertEquals("2014-05-11", GraphCleaningFunctions.doCleanDate("2014-05-11 08:20:13,787").get());
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3.31.2014").get());
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03.31.2014").get());
assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08.21.71").get());
assertEquals("2014-03-01", GraphCleaningFunctions.doCleanDate("2014.03").get());
assertEquals("2014-03-30", GraphCleaningFunctions.doCleanDate("2014.03.30").get());
assertEquals("2014-06-01", GraphCleaningFunctions.doCleanDate("20140601").get());
assertEquals("2014-07-22", GraphCleaningFunctions.doCleanDate("20140722105203").get());
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("1332151919").get());
assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367189").get());
assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222").get());
assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222333").get());
"2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001"));
assertEquals("2017-07-19", GraphCleaningFunctions.cleanDate("2017-07-19 03:21:51+00:00"));
assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26"));
assertEquals("2014-04-01", GraphCleaningFunctions.cleanDate("2014-04"));
assertEquals("2014-01-01", GraphCleaningFunctions.cleanDate("2014"));
assertEquals("2014-05-11", GraphCleaningFunctions.cleanDate("2014-05-11 08:20:13,787"));
assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3.31.2014"));
assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03.31.2014"));
assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08.21.71"));
assertEquals("2014-03-01", GraphCleaningFunctions.cleanDate("2014.03"));
assertEquals("2014-03-30", GraphCleaningFunctions.cleanDate("2014.03.30"));
assertEquals("2014-06-01", GraphCleaningFunctions.cleanDate("20140601"));
assertEquals("2014-07-22", GraphCleaningFunctions.cleanDate("20140722105203"));
assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("1332151919"));
assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367189"));
assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222"));
assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222333"));
}
@ -150,7 +149,7 @@ class OafMapperUtilsTest {
void testDate() {
final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
assertNotNull(date);
System.out.println(date);
assertEquals("1998-02-23", date);
}
@Test
@ -167,8 +166,8 @@ class OafMapperUtilsTest {
assertEquals(
ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
OafMapperUtils
.mergeResults(p1, d2)
MergeUtils
.mergeResult(p1, d2)
.getResulttype()
.getClassid());
@ -179,10 +178,26 @@ class OafMapperUtilsTest {
assertEquals(
ModelConstants.DATASET_RESULTTYPE_CLASSID,
OafMapperUtils
.mergeResults(p2, d1)
.getResulttype()
.getClassid());
((Result) MergeUtils
.merge(p2, d1))
.getResulttype()
.getClassid());
}
@Test
void testDelegatedAuthority() throws IOException {
Dataset d1 = read("dataset_2.json", Dataset.class);
Dataset d2 = read("dataset_delegated.json", Dataset.class);
assertEquals(1, d2.getCollectedfrom().size());
assertTrue(cfId(d2.getCollectedfrom()).contains(ModelConstants.ZENODO_OD_ID));
Result res = MergeUtils.mergeResult(d1, d2);
assertEquals(d2, res);
System.out.println(OBJECT_MAPPER.writeValueAsString(res));
}
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRuleTest.java Normal file
View File

@ -0,0 +1,19 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class PICCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("887624982", PICCleaningRule.clean("887624982"));
assertEquals("", PICCleaningRule.clean("887 624982"));
assertEquals("887624982", PICCleaningRule.clean(" 887624982 "));
assertEquals("887624982", PICCleaningRule.clean(" 887624982x "));
assertEquals("887624982", PICCleaningRule.clean(" 88762498200 "));
}
}

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PmcCleaningRuleTest.java Normal file
View File

@ -0,0 +1,19 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class PmcCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("PMC1234", PmcCleaningRule.clean("PMC1234"));
assertEquals("PMC1234", PmcCleaningRule.clean(" PMC1234"));
assertEquals("PMC12345678", PmcCleaningRule.clean("PMC12345678"));
assertEquals("PMC12345678", PmcCleaningRule.clean("PMC123456789"));
assertEquals("PMC12345678", PmcCleaningRule.clean("PMC 12345678"));
}
}

24
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PmidCleaningRuleTest.java Normal file
View File

@ -0,0 +1,24 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class PmidCleaningRuleTest {
@Test
void testCleaning() {
// leading zeros are removed
assertEquals("1234", PmidCleaningRule.clean("01234"));
// tolerant to spaces in the middle
assertEquals("1234567", PmidCleaningRule.clean("0123 4567"));
// stop parsing at first not numerical char
assertEquals("123", PmidCleaningRule.clean("0123x4567"));
// invalid id leading to empty result
assertEquals("", PmidCleaningRule.clean("abc"));
// valid id with zeroes in the number
assertEquals("20794075", PmidCleaningRule.clean("20794075"));
}
}

17
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/RorCleaningRuleTest.java Normal file
View File

@ -0,0 +1,17 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class RorCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("https://ror.org/05rpz9w55", RorCleaningRule.clean("https://ror.org/05rpz9w55"));
assertEquals("https://ror.org/05rpz9w55", RorCleaningRule.clean("05rpz9w55"));
assertEquals("", RorCleaningRule.clean("05rpz9w_55"));
}
}

3
dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json
View File

File diff suppressed because one or more lines are too long

141
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/dataset_2.json
View File

@ -1 +1,140 @@
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3", "value" : "Repository B"} ]}
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
"resuttype": {"classid": "dataset"},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2011.03.013"
},
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
],
"collectedfrom": [
{
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3",
"value": "Repository B"
}
],
"instance": [
{
"refereed": {
"classid": "0000",
"classname": "UNKNOWN",
"schemeid": "dnet:review_levels",
"schemename": "dnet:review_levels"
},
"hostedby": {
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"accessright": {
"classid": "OPEN",
"classname": "Open Access",
"schemeid": "dnet:access_modes",
"schemename": "dnet:access_modes"
},
"processingchargecurrency": {
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"value": "EUR"
},
"pid": [
{
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"qualifier": {
"classid": "doi",
"classname": "Digital Object Identifier",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "10.1371/journal.pone.0085605"
}
],
"distributionlocation": "",
"url": ["https://doi.org/10.1371/journal.pone.0085605"],
"alternateIdentifier": [
{
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"qualifier": {
"classid": "pmid",
"classname": "PubMed ID",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": "24454899.0"
}
],
"collectedfrom": {
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3",
"value": "Repository B"
},
"processingchargeamount": {
"dataInfo": {
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "Harvested",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"deletedbyinference": false,
"inferred": false,
"inferenceprovenance": "",
"invisible": true,
"trust": "0.9"
},
"value": "1022.02"
},
"instancetype": {
"classid": "0004",
"classname": "Conference object",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
}
}
]
}

140
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/dataset_delegated.json Normal file
View File

@ -0,0 +1,140 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g",
"resuttype": {"classid": "dataset"},
"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2011.03.013"
},
{
"qualifier": {"classid": "urn"},
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
"qualifier": {"classid": "scp-number"},
"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
],
"collectedfrom": [
{
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
}
],
"instance": [
{
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"value": "Europe PubMed Central"
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"pid": [
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"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
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{
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37
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi4.json Normal file
View File

@ -0,0 +1,37 @@
{
"id": "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66",
"instance": [
{
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"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
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"pid": [
{
"qualifier": {"classid": "doi"},
"value": "10.1016/j.cmet.2010.03.013"
},
{
"qualifier": {"classid": "handle"},
"value": "11012/83840"
}
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},
{
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"value": "Digital library of Brno University of Technology"
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{
"qualifier": {"classid": "handle"},
"value": "11012/83840"
}
]
}
]
}

37
dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi5.json Normal file
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@ -0,0 +1,37 @@
{
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
"instance": [
{
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"value": "Zenodo"
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"pid": [
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"qualifier": {"classid": "doi"},
"value": "10.5281/zenodo.5121485"
}
]
},
{
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"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
},
{
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"value": "79953761260"
},
{
"qualifier": {"classid": "pmc"},
"value": "21459329"
}
]
}
]
}

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