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dnet-hadoop
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merged changes from dnet-hadoop

This commit is contained in:
Antonis Lempesis 2024-01-29 21:51:47 +02:00
parent c548796463 f804c58bc7
commit bb10a22290
1300 changed files with 101933 additions and 40869 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

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.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
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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-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>

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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 +
'}';
}
}

94
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);
long currentSize = 0;
while (next && currentSize < bytesPerSplit) {
currentSize = writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, currentSize);
next = fileStatusListIterator.hasNext();
}
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;
}
}

271
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);
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);
}
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();
String body = getBody(conn);
try (Response response = httpClient.newCall(request).execute()) {
int responseCode = conn.getResponseCode();
conn.disconnect();
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
// Get response body
json = response.body().string();
ZenodoModel newSubmission = new Gson().fromJson(json, ZenodoModel.class);
ZenodoModel newSubmission = new Gson().fromJson(body, ZenodoModel.class);
this.bucket = newSubmission.getLinks().getBucket();
this.deposition_id = newSubmission.getId();
return response.code();
}
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");
try (Response response = httpClient.newCall(request).execute()) {
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
return response.code();
byte[] buf = new byte[8192];
int length;
try (OutputStream os = conn.getOutputStream()) {
while ((length = is.read(buf)) != -1) {
os.write(buf, 0, length);
}
}
int responseCode = conn.getResponseCode();
if (!checkOKStatus(responseCode)) {
throw new IOException("Unexpected code " + responseCode + getBody(conn));
}
return responseCode;
}
@NotNull
private String getBody(HttpURLConnection conn) throws IOException {
String body = "{}";
try (BufferedReader br = new BufferedReader(
new InputStreamReader(conn.getInputStream(), "utf-8"))) {
StringBuilder response = new StringBuilder();
String responseLine = null;
while ((responseLine = br.readLine()) != null) {
response.append(responseLine.trim());
}
body = response.toString();
}
return body;
}
/**
@ -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 (OutputStream os = conn.getOutputStream()) {
byte[] input = json.getBytes("utf-8");
os.write(input, 0, input.length);
try (Response response = httpClient.newCall(request).execute()) {
}
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
String body = getBody(conn);
ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
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 response.code();
}
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();
URL url = new URL(urlString + "/" + deposition_id);
HttpURLConnection conn = (HttpURLConnection) url.openConnection();
try (Response response = httpClient.newCall(request).execute()) {
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);
}
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
String body = getBody(conn);
ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
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 response.code();
return responseCode;
}
}
private void setDepositionId(String concept_rec_id, Integer page) throws IOException, MissingConceptDoiException {
private void setDepositionId(String concept_rec_id) 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)) {
@ -263,56 +308,58 @@ 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 inputUurl) throws IOException {
private String getBucket(String url) throws IOException {
OkHttpClient httpClient = new OkHttpClient.Builder()
.connectTimeout(600, TimeUnit.SECONDS)
.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");
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();
String body = getBody(conn);
try (Response response = httpClient.newCall(request).execute()) {
int responseCode = conn.getResponseCode();
if (!response.isSuccessful())
throw new IOException("Unexpected code " + response + response.body().string());
conn.disconnect();
if (!checkOKStatus(responseCode))
throw new IOException("Unexpected code " + responseCode + body);
// Get response body
ZenodoModel zenodoModel = new Gson().fromJson(response.body().string(), ZenodoModel.class);
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;
@ -94,23 +97,31 @@ 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);
@ -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
*

127
dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java
View File

@ -119,6 +119,131 @@ 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;
}
/**
* This method tries to figure out when two author are the same in the contest
* of ORCID enrichment
*
* @param left Author in the OAF entity
* @param right Author ORCID
* @return based on a heuristic on the names of the authors if they are the same.
*/
public static boolean checkORCIDSimilarity(final Author left, final Author right) {
final Person pl = parse(left);
final Person pr = parse(right);
// If one of them didn't have a surname we verify if they have the fullName not empty
// and verify if the normalized version is equal
if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) &&
pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) {
if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null
&& !pr.getFullname().isEmpty()) {
return pl
.getFullname()
.stream()
.anyMatch(
fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr))));
} else {
return false;
}
}
// The Authors have one surname in common
if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) {
// If one of them has only a surname and is the same we can say that they are the same author
if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) ||
(pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank)))
return true;
// The authors have the same initials of Name in common
if (pl
.getName()
.stream()
.anyMatch(
nl -> pr
.getName()
.stream()
.anyMatch(nr -> nr.equalsIgnoreCase(nl))))
return true;
}
// Sometimes we noticed that publication have author wrote in inverse order Surname, Name
// We verify if we have an exact match between name and surname
if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) &&
pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl))))
return true;
else
return false;
}
//
/**
* Method to enrich ORCID information in one list of authors based on another list
*
* @param baseAuthor the Author List in the OAF Entity
* @param orcidAuthor The list of ORCID Author intersected
* @return The Author List of the OAF Entity enriched with the orcid Author
*/
public static List<Author> enrichOrcid(List<Author> baseAuthor, List<Author> orcidAuthor) {
if (baseAuthor == null || baseAuthor.isEmpty())
return orcidAuthor;
if (orcidAuthor == null || orcidAuthor.isEmpty())
return baseAuthor;
if (baseAuthor.size() == 1 && orcidAuthor.size() > 10)
return baseAuthor;
final List<Author> oAuthor = new ArrayList<>();
oAuthor.addAll(orcidAuthor);
baseAuthor.forEach(ba -> {
Optional<Author> aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst();
if (aMatch.isPresent()) {
final Author sameAuthor = aMatch.get();
addPid(ba, sameAuthor.getPid());
oAuthor.remove(sameAuthor);
}
});
return baseAuthor;
}
private static void addPid(final Author a, final List<StructuredProperty> pids) {
if (a.getPid() == null) {
a.setPid(new ArrayList<>());
}
a.getPid().addAll(pids);
}
public static String pidToComparableString(StructuredProperty pid) {
final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
: "";
@ -171,7 +296,7 @@ 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
View File

@ -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.ReduceFunction;
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.OafMapperUtils;
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())
.reduceGroups((ReduceFunction<OafEntity>) OafMapperUtils::mergeEntities)
.map(
(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
t._2().getClass().getName(), t._2()),
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
View File

@ -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"));
}
});
}
}

14
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java Normal file
View File

@ -0,0 +1,14 @@
package eu.dnetlib.dhp.schema.oaf.utils;
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);
}
}

25
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/FundRefCleaningRule.java Normal file
View File

@ -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 "";
}
}
}

632
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -1,6 +1,12 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
import java.net.MalformedURLException;
import java.net.URL;
import java.time.LocalDate;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
@ -16,6 +22,8 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
@ -23,6 +31,10 @@ import me.xuender.unidecode.Unidecode;
public class GraphCleaningFunctions extends CleaningFunctions {
public static final String DNET_PUBLISHERS = "dnet:publishers";
public static final String DNET_LICENSES = "dnet:licenses";
public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})";
public static final int ORCID_LEN = 19;
public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
@ -32,21 +44,200 @@ public class GraphCleaningFunctions extends CleaningFunctions {
public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST);
public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+";
private static final Set<String> INVALID_AUTHOR_NAMES = new HashSet<>();
private static final Set<String> INVALID_URLS = new HashSet<>();
private static final Set<String> INVALID_URL_HOSTS = new HashSet<>();
private static final HashSet<String> PEER_REVIEWED_TYPES = new HashSet<>();
static {
PEER_REVIEWED_TYPES.add("Article");
PEER_REVIEWED_TYPES.add("Part of book or chapter of book");
PEER_REVIEWED_TYPES.add("Book");
PEER_REVIEWED_TYPES.add("Doctoral thesis");
PEER_REVIEWED_TYPES.add("Master thesis");
PEER_REVIEWED_TYPES.add("Data Paper");
PEER_REVIEWED_TYPES.add("Thesis");
PEER_REVIEWED_TYPES.add("Bachelor thesis");
PEER_REVIEWED_TYPES.add("Conference object");
INVALID_AUTHOR_NAMES.add("(:null)");
INVALID_AUTHOR_NAMES.add("(:unap)");
INVALID_AUTHOR_NAMES.add("(:tba)");
INVALID_AUTHOR_NAMES.add("(:unas)");
INVALID_AUTHOR_NAMES.add("(:unav)");
INVALID_AUTHOR_NAMES.add("(:unkn)");
INVALID_AUTHOR_NAMES.add("(:unkn) unknown");
INVALID_AUTHOR_NAMES.add(":none");
INVALID_AUTHOR_NAMES.add(":null");
INVALID_AUTHOR_NAMES.add(":unas");
INVALID_AUTHOR_NAMES.add(":unav");
INVALID_AUTHOR_NAMES.add(":unkn");
INVALID_AUTHOR_NAMES.add("[autor desconocido]");
INVALID_AUTHOR_NAMES.add("[s. n.]");
INVALID_AUTHOR_NAMES.add("[s.n]");
INVALID_AUTHOR_NAMES.add("[unknown]");
INVALID_AUTHOR_NAMES.add("anonymous");
INVALID_AUTHOR_NAMES.add("n.n.");
INVALID_AUTHOR_NAMES.add("nn");
INVALID_AUTHOR_NAMES.add("no name supplied");
INVALID_AUTHOR_NAMES.add("none");
INVALID_AUTHOR_NAMES.add("none available");
INVALID_AUTHOR_NAMES.add("not available not available");
INVALID_AUTHOR_NAMES.add("null &na;");
INVALID_AUTHOR_NAMES.add("null anonymous");
INVALID_AUTHOR_NAMES.add("unbekannt");
INVALID_AUTHOR_NAMES.add("unknown");
INVALID_URL_HOSTS.add("creativecommons.org");
INVALID_URL_HOSTS.add("www.academia.edu");
INVALID_URL_HOSTS.add("academia.edu");
INVALID_URL_HOSTS.add("researchgate.net");
INVALID_URL_HOSTS.add("www.researchgate.net");
INVALID_URLS.add("http://repo.scoap3.org/api");
INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:");
INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf");
INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf");
INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/");
INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten");
}
public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
if (ModelSupport.isSubClass(value, Result.class)) {
final Result res = (Result) value;
if (shouldCleanContext(res, verifyParam)) {
res
.setContext(
res
.getContext()
.stream()
.filter(c -> !StringUtils.startsWith(c.getId().toLowerCase(), contextId))
.collect(Collectors.toList()));
}
return (T) res;
} else {
return value;
}
}
private static boolean shouldCleanContext(Result res, String verifyParam) {
boolean titleMatch = res
.getTitle()
.stream()
.filter(
t -> t
.getQualifier()
.getClassid()
.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()));
return titleMatch && Objects.nonNull(res.getContext());
}
public static <T extends Oaf> T cleanCountry(T value, String[] verifyParam, Set<String> hostedBy,
String collectedfrom, String country) {
if (ModelSupport.isSubClass(value, Result.class)) {
final Result res = (Result) value;
if (res.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
!res.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
return (T) res;
}
List<StructuredProperty> ids = getPidsAndAltIds(res).collect(Collectors.toList());
if (ids
.stream()
.anyMatch(
p -> p
.getQualifier()
.getClassid()
.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
res
.setCountry(
res
.getCountry()
.stream()
.filter(
c -> toTakeCountry(c, country))
.collect(Collectors.toList()));
}
return (T) res;
} else {
return value;
}
}
private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
final Stream<StructuredProperty> resultPids = Optional
.ofNullable(r.getPid())
.map(Collection::stream)
.orElse(Stream.empty());
final Stream<StructuredProperty> instancePids = Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.flatMap(
i -> Optional
.ofNullable(i.getPid())
.map(Collection::stream)
.orElse(Stream.empty())))
.orElse(Stream.empty());
final Stream<StructuredProperty> instanceAltIds = Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.flatMap(
i -> Optional
.ofNullable(i.getAlternateIdentifier())
.map(Collection::stream)
.orElse(Stream.empty())))
.orElse(Stream.empty());
return Stream
.concat(
Stream.concat(resultPids, instancePids),
instanceAltIds);
}
private static boolean pidInParam(String value, String[] verifyParam) {
for (String s : verifyParam)
if (value.startsWith(s))
return true;
return false;
}
private static boolean toTakeCountry(Country c, String country) {
// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
// inserted via propagation
if (!Optional.ofNullable(c.getDataInfo()).isPresent())
return true;
if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
return true;
return !(c
.getClassid()
.equalsIgnoreCase(country) &&
c.getDataInfo().getInferenceprovenance().equals("propagation"));
}
public static <T extends Oaf> T fixVocabularyNames(T value) {
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
// nothing to clean here
} else if (value instanceof Organization) {
Organization o = (Organization) value;
if (Objects.nonNull(o.getCountry())) {
fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE);
}
} else if (value instanceof Relation) {
// nothing to clean here
} else if (value instanceof Result) {
if (value instanceof OafEntity) {
OafEntity e = (OafEntity) value;
Optional
.ofNullable(e.getPid())
.ifPresent(pid -> pid.forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)));
if (value instanceof Result) {
Result r = (Result) value;
fixVocabName(r.getLanguage(), ModelConstants.DNET_LANGUAGES);
@ -60,6 +251,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
for (Instance i : r.getInstance()) {
fixVocabName(i.getAccessright(), ModelConstants.DNET_ACCESS_MODES);
fixVocabName(i.getRefereed(), ModelConstants.DNET_REVIEW_LEVELS);
Optional
.ofNullable(i.getPid())
.ifPresent(
pid -> pid.forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)));
}
}
if (Objects.nonNull(r.getAuthor())) {
@ -80,16 +276,46 @@ public class GraphCleaningFunctions extends CleaningFunctions {
} else if (value instanceof Software) {
}
} else if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
// nothing to clean here
} else if (value instanceof Organization) {
Organization o = (Organization) value;
if (Objects.nonNull(o.getCountry())) {
fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE);
}
}
} else if (value instanceof Relation) {
// nothing to clean here
}
return value;
}
public static <T extends Oaf> boolean filter(T value) {
if (!(value instanceof Relation) && (Boolean.TRUE
.equals(
Optional
.ofNullable(value)
.map(
o -> Optional
.ofNullable(o.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getInvisible())
.orElse(true))
.orElse(false))
.orElse(true)))) {
return true;
}
if (value instanceof Datasource) {
// nothing to evaluate here
} else if (value instanceof Project) {
// nothing to evaluate here
final Project p = (Project) value;
return Objects.nonNull(p.getCode()) && StringUtils.isNotBlank(p.getCode().getValue());
} else if (value instanceof Organization) {
// nothing to evaluate here
} else if (value instanceof Relation) {
@ -115,7 +341,21 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return true;
}
public static <T extends Oaf> T cleanup(T value) {
public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
if (Objects.isNull(value.getDataInfo())) {
final DataInfo d = new DataInfo();
d.setDeletedbyinference(false);
value.setDataInfo(d);
}
if (value instanceof OafEntity) {
OafEntity e = (OafEntity) value;
if (Objects.nonNull(e.getPid())) {
e.setPid(processPidCleaning(e.getPid()));
}
if (value instanceof Datasource) {
// nothing to clean here
} else if (value instanceof Project) {
@ -125,21 +365,20 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
o.setCountry(ModelConstants.UNKNOWN_COUNTRY);
}
} else if (value instanceof Relation) {
Relation r = (Relation) value;
Optional<String> validationDate = doCleanDate(r.getValidationDate());
if (validationDate.isPresent()) {
r.setValidationDate(validationDate.get());
r.setValidated(true);
} else {
r.setValidationDate(null);
r.setValidated(false);
}
} else if (value instanceof Result) {
Result r = (Result) value;
if (Objects.isNull(r.getContext())) {
r.setContext(new ArrayList<>());
}
if (Objects.nonNull(r.getFulltext())
&& (ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
r.setFulltext(null);
}
if (Objects.nonNull(r.getDateofacceptance())) {
Optional<String> date = cleanDateField(r.getDateofacceptance());
if (date.isPresent()) {
@ -164,8 +403,26 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
if (Objects.nonNull(r.getPublisher())) {
if (StringUtils.isBlank(r.getPublisher().getValue())) {
r.setPublisher(null);
} else {
r
.getPublisher()
.setValue(
r
.getPublisher()
.getValue()
.replaceAll(NAME_CLEANING_REGEX, " "));
if (vocs.vocabularyExists(DNET_PUBLISHERS)) {
vocs
.find(DNET_PUBLISHERS)
.map(voc -> voc.getTermBySynonym(r.getPublisher().getValue()))
.map(VocabularyTerm::getName)
.ifPresent(publisher -> r.getPublisher().setValue(publisher));
}
}
}
if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
r
@ -173,8 +430,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES));
}
if (Objects.nonNull(r.getSubject())) {
r
.setSubject(
List<Subject> subjects = Lists
.newArrayList(
r
.getSubject()
.stream()
@ -182,8 +439,26 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.filter(sp -> Objects.nonNull(sp.getQualifier()))
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
.map(s -> {
if ("dnet:result_subject".equals(s.getQualifier().getClassid())) {
s.getQualifier().setClassid(ModelConstants.DNET_SUBJECT_TYPOLOGIES);
s.getQualifier().setClassname(ModelConstants.DNET_SUBJECT_TYPOLOGIES);
}
return s;
})
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
.collect(
Collectors
.toMap(
s -> Optional
.ofNullable(s.getQualifier())
.map(q -> q.getClassid() + s.getValue())
.orElse(s.getValue()),
Function.identity(),
(s1, s2) -> Collections
.min(Lists.newArrayList(s1, s2), new SubjectProvenanceComparator())))
.values());
r.setSubject(subjects);
}
if (Objects.nonNull(r.getTitle())) {
r
@ -212,6 +487,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getFormat())) {
r
.setFormat(
r
.getFormat()
.stream()
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getDescription())) {
r
.setDescription(
@ -223,9 +507,6 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getPid())) {
r.setPid(processPidCleaning(r.getPid()));
}
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
r
.setResourcetype(
@ -234,6 +515,40 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.nonNull(r.getInstance())) {
for (Instance i : r.getInstance()) {
if (!vocs
.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
if (r instanceof Publication) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0038", "Other literature type",
ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Dataset) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof Software) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
} else if (r instanceof OtherResearchProduct) {
i
.setInstancetype(
OafMapperUtils
.qualifier(
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
ModelConstants.DNET_PUBLICATION_RESOURCE));
}
}
if (Objects.nonNull(i.getPid())) {
i.setPid(processPidCleaning(i.getPid()));
}
@ -252,7 +567,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
});
});
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
if (Objects.isNull(i.getAccessright())
|| StringUtils.isBlank(i.getAccessright().getClassid())) {
i
.setAccessright(
accessRight(
@ -262,9 +578,46 @@ public class GraphCleaningFunctions extends CleaningFunctions {
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
}
if (Objects.isNull(i.getRefereed())) {
if (Objects.isNull(i.getRefereed()) || StringUtils.isBlank(i.getRefereed().getClassid())) {
i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
}
if (Objects.nonNull(i.getLicense()) && Objects.nonNull(i.getLicense().getValue())) {
vocs
.find(DNET_LICENSES)
.map(voc -> voc.getTermBySynonym(i.getLicense().getValue()))
.map(VocabularyTerm::getId)
.ifPresent(license -> i.getLicense().setValue(license));
}
// from the script from Dimitris
if ("0000".equals(i.getRefereed().getClassid())) {
final boolean isFromCrossref = Optional
.ofNullable(i.getCollectedfrom())
.map(KeyValue::getKey)
.map(id -> id.equals(ModelConstants.CROSSREF_ID))
.orElse(false);
final boolean hasDoi = Optional
.ofNullable(i.getPid())
.map(
pid -> pid
.stream()
.anyMatch(
p -> PidType.doi.toString().equals(p.getQualifier().getClassid())))
.orElse(false);
final boolean isPeerReviewedType = PEER_REVIEWED_TYPES
.contains(i.getInstancetype().getClassname());
final boolean noOtherLitType = r
.getInstance()
.stream()
.noneMatch(ii -> "Other literature type".equals(ii.getInstancetype().getClassname()));
if (isFromCrossref && hasDoi && isPeerReviewedType && noOtherLitType) {
i.setRefereed(qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS));
} else {
i.setRefereed(qualifier("0002", "nonPeerReviewed", ModelConstants.DNET_REVIEW_LEVELS));
}
}
if (Objects.nonNull(i.getDateofacceptance())) {
Optional<String> date = cleanDateField(i.getDateofacceptance());
if (date.isPresent()) {
@ -273,9 +626,24 @@ public class GraphCleaningFunctions extends CleaningFunctions {
i.setDateofacceptance(null);
}
}
if (StringUtils.isNotBlank(i.getFulltext()) &&
(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
i.setFulltext(null);
}
if (Objects.nonNull(i.getUrl())) {
i
.setUrl(
i
.getUrl()
.stream()
.filter(GraphCleaningFunctions::urlFilter)
.collect(Collectors.toList()));
}
}
if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
}
if (Objects.isNull(r.getBestaccessright())
|| StringUtils.isBlank(r.getBestaccessright().getClassid())) {
Qualifier bestaccessrights = OafMapperUtils.createBestAccessRights(r.getInstance());
if (Objects.isNull(bestaccessrights)) {
r
@ -294,8 +662,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.getAuthor()
.stream()
.filter(Objects::nonNull)
.filter(a -> StringUtils.isNotBlank(a.getFullname()))
.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
.filter(GraphCleaningFunctions::isValidAuthorName)
.map(GraphCleaningFunctions::cleanupAuthor)
.collect(Collectors.toList()));
boolean nullRank = r
@ -321,23 +689,20 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(Objects::nonNull)
.filter(p -> Objects.nonNull(p.getQualifier()))
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.filter(
p -> StringUtils
.contains(StringUtils.lowerCase(p.getQualifier().getClassid()), ORCID))
.map(p -> {
// hack to distinguish orcid from orcid_pending
String pidProvenance = Optional
.ofNullable(p.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
String pidProvenance = getProvenance(p.getDataInfo());
if (p
.getQualifier()
.getClassid()
.toLowerCase()
.contains(ModelConstants.ORCID)) {
if (pidProvenance
.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY) ||
pidProvenance.equals("ORCID_ENRICHMENT")) {
p.getQualifier().setClassid(ModelConstants.ORCID);
} else {
p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
@ -378,11 +743,54 @@ public class GraphCleaningFunctions extends CleaningFunctions {
} else if (value instanceof Software) {
}
}
} else if (value instanceof Relation) {
Relation r = (Relation) value;
Optional<String> validationDate = doCleanDate(r.getValidationDate());
if (validationDate.isPresent()) {
r.setValidationDate(validationDate.get());
r.setValidated(true);
} else {
r.setValidationDate(null);
r.setValidated(false);
}
}
return value;
}
private static Author cleanupAuthor(Author author) {
if (StringUtils.isNotBlank(author.getFullname())) {
author
.setFullname(
author
.getFullname()
.replaceAll(NAME_CLEANING_REGEX, " ")
.replace("\"", "\\\""));
}
if (StringUtils.isNotBlank(author.getName())) {
author
.setName(
author
.getName()
.replaceAll(NAME_CLEANING_REGEX, " ")
.replace("\"", "\\\""));
}
if (StringUtils.isNotBlank(author.getSurname())) {
author
.setSurname(
author
.getSurname()
.replaceAll(NAME_CLEANING_REGEX, " ")
.replace("\"", "\\\""));
}
return author;
}
private static Optional<String> cleanDateField(Field<String> dateofacceptance) {
return Optional
.ofNullable(dateofacceptance)
@ -416,14 +824,32 @@ public class GraphCleaningFunctions extends CleaningFunctions {
// HELPERS
private static boolean isValidAuthorName(Author a) {
return !Stream
return StringUtils.isNotBlank(a.getFullname()) &&
StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) &&
!INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) &&
!Stream
.of(a.getFullname(), a.getName(), a.getSurname())
.filter(s -> s != null && !s.isEmpty())
.filter(StringUtils::isNotBlank)
.collect(Collectors.joining(""))
.toLowerCase()
.matches(INVALID_AUTHOR_REGEX);
}
private static boolean urlFilter(String u) {
try {
final URL url = new URL(u);
if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) {
return false;
}
if (INVALID_URL_HOSTS.contains(url.getHost())) {
return false;
}
return !INVALID_URLS.contains(url.toString());
} catch (MalformedURLException ex) {
return false;
}
}
private static List<StructuredProperty> processPidCleaning(List<StructuredProperty> pids) {
return pids
.stream()
@ -432,7 +858,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(sp -> !PID_BLACKLIST.contains(sp.getValue().trim().toLowerCase()))
.filter(sp -> Objects.nonNull(sp.getQualifier()))
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
.map(CleaningFunctions::normalizePidValue)
.map(PidCleaner::normalizePidValue)
.filter(CleaningFunctions::pidFilter)
.collect(Collectors.toList());
}
@ -461,9 +887,115 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return s;
}
protected static Subject cleanValue(Subject s) {
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
return s;
}
protected static Field<String> cleanValue(Field<String> s) {
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
return s;
}
public static OafEntity applyCoarVocabularies(OafEntity entity, VocabularyGroup vocs) {
if (entity instanceof Result) {
final Result result = (Result) entity;
Optional
.ofNullable(result.getInstance())
.ifPresent(
instances -> instances
.forEach(
instance -> {
if (Objects.isNull(instance.getInstanceTypeMapping())) {
List<InstanceTypeMapping> mapping = Lists.newArrayList();
mapping
.add(
OafMapperUtils
.instanceTypeMapping(
instance.getInstancetype().getClassname(),
OPENAIRE_COAR_RESOURCE_TYPES_3_1));
instance.setInstanceTypeMapping(mapping);
}
Optional<InstanceTypeMapping> optionalItm = instance
.getInstanceTypeMapping()
.stream()
.filter(GraphCleaningFunctions::originalResourceType)
.findFirst();
if (optionalItm.isPresent()) {
InstanceTypeMapping coarItm = optionalItm.get();
Optional
.ofNullable(
vocs
.lookupTermBySynonym(
OPENAIRE_COAR_RESOURCE_TYPES_3_1, coarItm.getOriginalType()))
.ifPresent(type -> {
coarItm.setTypeCode(type.getClassid());
coarItm.setTypeLabel(type.getClassname());
});
final List<InstanceTypeMapping> mappings = Lists.newArrayList();
if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) {
Optional
.ofNullable(
vocs
.lookupTermBySynonym(
OPENAIRE_USER_RESOURCE_TYPES, coarItm.getTypeCode()))
.ifPresent(
type -> mappings
.add(
OafMapperUtils
.instanceTypeMapping(coarItm.getTypeCode(), type)));
}
if (!mappings.isEmpty()) {
instance.getInstanceTypeMapping().addAll(mappings);
}
}
}));
result.setMetaResourceType(getMetaResourceType(result.getInstance(), vocs));
}
return entity;
}
private static boolean originalResourceType(InstanceTypeMapping itm) {
return StringUtils.isNotBlank(itm.getOriginalType()) &&
OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()) &&
StringUtils.isBlank(itm.getTypeCode()) &&
StringUtils.isBlank(itm.getTypeLabel());
}
private static Qualifier getMetaResourceType(final List<Instance> instances, final VocabularyGroup vocs) {
return Optional
.ofNullable(instances)
.map(ii -> {
if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) {
Optional<InstanceTypeMapping> itm = ii
.stream()
.filter(Objects::nonNull)
.flatMap(
i -> Optional
.ofNullable(i.getInstanceTypeMapping())
.map(Collection::stream)
.orElse(Stream.empty()))
.filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()))
.findFirst();
if (!itm.isPresent() || Objects.isNull(itm.get().getTypeCode())) {
return null;
} else {
final String typeCode = itm.get().getTypeCode();
return Optional
.ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode))
.orElseThrow(
() -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " +
OPENAIRE_META_RESOURCE_TYPE));
}
} else {
throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available");
}
})
.orElse(null);
}
}

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

@ -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
View File

@ -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 "";
}
}
}

169
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;
@ -47,6 +49,17 @@ public class OafMapperUtils {
}
public static Result mergeResults(Result left, Result right) {
final boolean leftFromDelegatedAuthority = isFromDelegatedAuthority(left);
final boolean rightFromDelegatedAuthority = isFromDelegatedAuthority(right);
if (leftFromDelegatedAuthority && !rightFromDelegatedAuthority) {
return left;
}
if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
return right;
}
if (new ResultTypeComparator().compare(left, right) < 0) {
left.mergeFrom(right);
return left;
@ -56,6 +69,18 @@ public class OafMapperUtils {
}
}
private static boolean isFromDelegatedAuthority(Result r) {
return Optional
.ofNullable(r.getInstance())
.map(
instance -> instance
.stream()
.filter(i -> Objects.nonNull(i.getCollectedfrom()))
.map(i -> i.getCollectedfrom().getKey())
.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
.orElse(false);
}
public static KeyValue keyValue(final String k, final String v) {
final KeyValue kv = new KeyValue();
kv.setKey(k);
@ -95,6 +120,17 @@ 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 +140,30 @@ 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 +211,17 @@ 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 +233,20 @@ 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 +451,88 @@ 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("");
}
}

21
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRule.java Normal file
View File

@ -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 "";
}
}
}

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;
}
}
}

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

@ -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
View File

@ -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 "";
}
}

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
View File

@ -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
View File

@ -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
View File

@ -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
}
]

73
dhp-common/src/main/scala/eu/dnetlib/dhp/application/SparkScalaApplication.scala Normal file
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@ -0,0 +1,73 @@
package eu.dnetlib.dhp.application
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()
}
}

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
View File

@ -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;
}
}

18
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRuleTest.java Normal file
View File

@ -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
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 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"));
}
}

201
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"));
}
@ -185,6 +184,22 @@ class OafMapperUtilsTest {
.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 = OafMapperUtils.mergeResults(d1, d2);
assertEquals(d2, res);
System.out.println(OBJECT_MAPPER.writeValueAsString(res));
}
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
}

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRuleTest.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 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
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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 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
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@ -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
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@ -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"));
}
}

114
dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java Normal file
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@ -0,0 +1,114 @@
package eu.dnetlib.oa.merge;
import static org.junit.jupiter.api.Assertions.*;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.util.List;
import java.util.Objects;
import org.junit.jupiter.api.Test;
import org.junit.platform.commons.util.StringUtils;
import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.oa.merge.AuthorMerger;
import eu.dnetlib.dhp.schema.oaf.Author;
public class AuthorMergerTest {
@Test
public void testEnrcichAuthor() throws Exception {
final ObjectMapper mapper = new ObjectMapper();
BufferedReader pr = new BufferedReader(new InputStreamReader(
Objects
.requireNonNull(
AuthorMergerTest.class
.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json"))));
BufferedReader or = new BufferedReader(new InputStreamReader(
Objects
.requireNonNull(
AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json"))));
TypeReference<List<Author>> aclass = new TypeReference<List<Author>>() {
};
String pubLine;
int i = 0;
while ((pubLine = pr.readLine()) != null) {
final String pubId = pubLine;
final String MatchPidOrcid = or.readLine();
final String pubOrcid = or.readLine();
final String data = pr.readLine();
if (StringUtils.isNotBlank(data)) {
List<Author> publicationAuthors = mapper.readValue(data, aclass);
List<Author> orcidAuthors = mapper.readValue(or.readLine(), aclass);
System.out.printf("OAF ID = %s \n", pubId);
System.out.printf("ORCID Intersected ID = %s \n", pubOrcid);
System.out.printf("OAF Author Size = %d \n", publicationAuthors.size());
System.out.printf("Oricd Author Size = %d \n", orcidAuthors.size());
System.out.printf("Oricd Matched PID = %s \n", MatchPidOrcid);
long originalAuthorWithPiD = publicationAuthors
.stream()
.filter(
a -> a.getPid() != null && a
.getPid()
.stream()
.anyMatch(
p -> p.getQualifier() != null
&& p.getQualifier().getClassid().toLowerCase().contains("orcid")))
.count();
long start = System.currentTimeMillis();
// final List<Author> enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors);
final List<Author> enrichedList = AuthorMerger.enrichOrcid(publicationAuthors, orcidAuthors);
long enrichedAuthorWithPid = enrichedList
.stream()
.filter(
a -> a.getPid() != null && a
.getPid()
.stream()
.anyMatch(
p -> p.getQualifier() != null
&& p.getQualifier().getClassid().toLowerCase().contains("orcid")))
.count();
long totalTime = (System.currentTimeMillis() - start) / 1000;
System.out
.printf(
"Enriched authors in %d seconds from %d pid to %d pid \n", totalTime, originalAuthorWithPiD,
enrichedAuthorWithPid);
System.out.println("=================");
}
}
}
@Test
public void checkSimilarityTest() {
final Author left = new Author();
left.setName("Anand");
left.setSurname("Rachna");
left.setFullname("Anand, Rachna");
System.out.println(AuthorMerger.normalizeFullName(left.getFullname()));
final Author right = new Author();
right.setName("Rachna");
right.setSurname("Anand");
right.setFullname("Rachna, Anand");
// System.out.println(AuthorMerger.normalize(right.getFullname()));
boolean same = AuthorMerger.checkORCIDSimilarity(left, right);
assertTrue(same);
}
}

3
dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json Normal file
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2
dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json Normal file
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File diff suppressed because one or more lines are too long

3
dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/publications_with_authors.json
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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": [
{
"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|opendoar____::358aee4cc897452c00244351e4d91f69",
"value": "Zenodo"
},
"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"
}
}
]
}

110
dhp-pace-core/pom.xml Normal file
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@ -0,0 +1,110 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
<modelVersion>4.0.0</modelVersion>
<parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp</artifactId>
<version>1.2.5-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
<groupId>eu.dnetlib.dhp</groupId>
<artifactId>dhp-pace-core</artifactId>
<version>1.2.5-SNAPSHOT</version>
<packaging>jar</packaging>
<build>
<plugins>
<plugin>
<groupId>net.alchim31.maven</groupId>
<artifactId>scala-maven-plugin</artifactId>
<version>${net.alchim31.maven.version}</version>
<executions>
<execution>
<id>scala-compile-first</id>
<phase>initialize</phase>
<goals>
<goal>add-source</goal>
<goal>compile</goal>
</goals>
</execution>
<execution>
<id>scala-test-compile</id>
<phase>process-test-resources</phase>
<goals>
<goal>testCompile</goal>
</goals>
</execution>
</executions>
<configuration>
<failOnMultipleScalaVersions>true</failOnMultipleScalaVersions>
<scalaCompatVersion>${scala.binary.version}</scalaCompatVersion>
<scalaVersion>${scala.version}</scalaVersion>
</configuration>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>edu.cmu</groupId>
<artifactId>secondstring</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
<dependency>
<groupId>com.google.code.gson</groupId>
<artifactId>gson</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>org.antlr</groupId>
<artifactId>stringtemplate</artifactId>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
</dependency>
<dependency>
<groupId>org.reflections</groupId>
<artifactId>reflections</artifactId>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
<artifactId>jackson-databind</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-math3</artifactId>
</dependency>
<dependency>
<groupId>com.jayway.jsonpath</groupId>
<artifactId>json-path</artifactId>
</dependency>
<dependency>
<groupId>com.ibm.icu</groupId>
<artifactId>icu4j</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.binary.version}</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_${scala.binary.version}</artifactId>
</dependency>
</dependencies>
</project>

59
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/AbstractClusteringFunction.java Normal file
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@ -0,0 +1,59 @@
package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.pace.common.AbstractPaceFunctions;
import eu.dnetlib.pace.config.Config;
public abstract class AbstractClusteringFunction extends AbstractPaceFunctions implements ClusteringFunction {
protected Map<String, Object> params;
public AbstractClusteringFunction(final Map<String, Object> params) {
this.params = params;
}
protected abstract Collection<String> doApply(Config conf, String s);
@Override
public Collection<String> apply(Config conf, List<String> fields) {
return fields
.stream()
.filter(f -> !f.isEmpty())
.map(s -> normalize(s))
.map(s -> filterAllStopWords(s))
.map(s -> doApply(conf, s))
.map(c -> filterBlacklisted(c, ngramBlacklist))
.flatMap(c -> c.stream())
.filter(StringUtils::isNotBlank)
.collect(Collectors.toCollection(HashSet::new));
}
public Map<String, Object> getParams() {
return params;
}
protected Integer param(String name) {
Object val = params.get(name);
if (val == null)
return null;
if (val instanceof Number) {
return ((Number) val).intValue();
}
return Integer.parseInt(val.toString());
}
protected int paramOrDefault(String name, int i) {
Integer res = param(name);
if (res == null)
res = i;
return res;
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/Acronyms.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.Map;
import java.util.Set;
import java.util.StringTokenizer;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("acronyms")
public class Acronyms extends AbstractClusteringFunction {
public Acronyms(Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return extractAcronyms(s, param("max"), param("minLen"), param("maxLen"));
}
private Set<String> extractAcronyms(final String s, int maxAcronyms, int minLen, int maxLen) {
final Set<String> acronyms = Sets.newLinkedHashSet();
for (int i = 0; i < maxAcronyms; i++) {
final StringTokenizer st = new StringTokenizer(s);
final StringBuilder sb = new StringBuilder();
while (st.hasMoreTokens()) {
final String token = st.nextToken();
if (sb.length() > maxLen) {
break;
}
if (token.length() > 1 && i < token.length()) {
sb.append(token.charAt(i));
}
}
String acronym = sb.toString();
if (acronym.length() > minLen) {
acronyms.add(acronym);
}
}
return acronyms;
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/ClusteringClass.java Normal file
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package eu.dnetlib.pace.clustering;
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
@Retention(RetentionPolicy.RUNTIME)
@Target(ElementType.TYPE)
public @interface ClusteringClass {
public String value();
}

16
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/ClusteringFunction.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import eu.dnetlib.pace.config.Config;
public interface ClusteringFunction {
public Collection<String> apply(Config config, List<String> fields);
public Map<String, Object> getParams();
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/ImmutableFieldValue.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("immutablefieldvalue")
public class ImmutableFieldValue extends AbstractClusteringFunction {
public ImmutableFieldValue(final Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(final Config conf, final String s) {
final List<String> res = Lists.newArrayList();
res.add(s);
return res;
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/JSONListClustering.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.jayway.jsonpath.Configuration;
import com.jayway.jsonpath.DocumentContext;
import com.jayway.jsonpath.JsonPath;
import com.jayway.jsonpath.Option;
import eu.dnetlib.pace.common.AbstractPaceFunctions;
import eu.dnetlib.pace.config.Config;
import eu.dnetlib.pace.util.MapDocumentUtil;
@ClusteringClass("jsonlistclustering")
public class JSONListClustering extends AbstractPaceFunctions implements ClusteringFunction {
private Map<String, Object> params;
public JSONListClustering(Map<String, Object> params) {
this.params = params;
}
@Override
public Map<String, Object> getParams() {
return params;
}
@Override
public Collection<String> apply(Config conf, List<String> fields) {
return fields
.stream()
.filter(f -> !f.isEmpty())
.map(s -> doApply(conf, s))
.filter(StringUtils::isNotBlank)
.collect(Collectors.toCollection(HashSet::new));
}
private String doApply(Config conf, String json) {
StringBuilder st = new StringBuilder(); // to build the string used for comparisons basing on the jpath into
// parameters
final DocumentContext documentContext = JsonPath
.using(Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS))
.parse(json);
// for each path in the param list
for (String key : params.keySet().stream().filter(k -> k.contains("jpath")).collect(Collectors.toList())) {
String path = params.get(key).toString();
String value = MapDocumentUtil.getJPathString(path, documentContext);
if (value == null || value.isEmpty())
value = "";
st.append(value);
st.append(" ");
}
st.setLength(st.length() - 1);
if (StringUtils.isBlank(st)) {
return "1";
}
return st.toString();
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("keywordsclustering")
public class KeywordsClustering extends AbstractClusteringFunction {
public KeywordsClustering(Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(final Config conf, String s) {
// takes city codes and keywords codes without duplicates
Set<String> keywords = getKeywords(s, conf.translationMap(), paramOrDefault("windowSize", 4));
Set<String> cities = getCities(s, paramOrDefault("windowSize", 4));
// list of combination to return as result
final Collection<String> combinations = new LinkedHashSet<String>();
for (String keyword : keywordsToCodes(keywords, conf.translationMap())) {
for (String city : citiesToCodes(cities)) {
combinations.add(keyword + "-" + city);
if (combinations.size() >= paramOrDefault("max", 2)) {
return combinations;
}
}
}
return combinations;
}
@Override
public Collection<String> apply(final Config conf, List<String> fields) {
return fields
.stream()
.filter(f -> !f.isEmpty())
.map(KeywordsClustering::cleanup)
.map(KeywordsClustering::normalize)
.map(s -> filterAllStopWords(s))
.map(s -> doApply(conf, s))
.map(c -> filterBlacklisted(c, ngramBlacklist))
.flatMap(c -> c.stream())
.filter(StringUtils::isNotBlank)
.collect(Collectors.toCollection(HashSet::new));
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/LastNameFirstInitial.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.config.Config;
import eu.dnetlib.pace.model.Person;
@ClusteringClass("lnfi")
public class LastNameFirstInitial extends AbstractClusteringFunction {
private boolean DEFAULT_AGGRESSIVE = true;
public LastNameFirstInitial(final Map<String, Object> params) {
super(params);
}
@Override
public Collection<String> apply(Config conf, List<String> fields) {
return fields
.stream()
.filter(f -> !f.isEmpty())
.map(LastNameFirstInitial::normalize)
.map(s -> doApply(conf, s))
.map(c -> filterBlacklisted(c, ngramBlacklist))
.flatMap(c -> c.stream())
.filter(StringUtils::isNotBlank)
.collect(Collectors.toCollection(HashSet::new));
}
public static String normalize(final String s) {
return fixAliases(transliterate(nfd(unicodeNormalization(s))))
// 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();
}
@Override
protected Collection<String> doApply(final Config conf, final String s) {
final List<String> res = Lists.newArrayList();
final boolean aggressive = (Boolean) (getParams().containsKey("aggressive") ? getParams().get("aggressive")
: DEFAULT_AGGRESSIVE);
Person p = new Person(s, aggressive);
if (p.isAccurate()) {
String lastName = p.getNormalisedSurname().toLowerCase();
String firstInitial = p.getNormalisedFirstName().toLowerCase().substring(0, 1);
res.add(firstInitial.concat(lastName));
} else { // is not accurate, meaning it has no defined name and surname
List<String> fullname = Arrays.asList(p.getNormalisedFullname().split(" "));
if (fullname.size() == 1) {
res.add(p.getNormalisedFullname().toLowerCase());
} else if (fullname.size() == 2) {
res.add(fullname.get(0).substring(0, 1).concat(fullname.get(1)).toLowerCase());
res.add(fullname.get(1).substring(0, 1).concat(fullname.get(0)).toLowerCase());
} else {
res.add(fullname.get(0).substring(0, 1).concat(fullname.get(fullname.size() - 1)).toLowerCase());
res.add(fullname.get(fullname.size() - 1).substring(0, 1).concat(fullname.get(0)).toLowerCase());
}
}
return res;
}
}

38
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/LowercaseClustering.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("lowercase")
public class LowercaseClustering extends AbstractClusteringFunction {
public LowercaseClustering(final Map<String, Object> params) {
super(params);
}
@Override
public Collection<String> apply(Config conf, List<String> fields) {
Collection<String> c = Sets.newLinkedHashSet();
for (String f : fields) {
c.addAll(doApply(conf, f));
}
return c;
}
@Override
protected Collection<String> doApply(final Config conf, final String s) {
if (StringUtils.isBlank(s)) {
return Lists.newArrayList();
}
return Lists.newArrayList(s.toLowerCase().trim());
}
}

24
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NGramUtils.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.pace.common.AbstractPaceFunctions;
public class NGramUtils extends AbstractPaceFunctions {
static private final NGramUtils NGRAMUTILS = new NGramUtils();
private static final int SIZE = 100;
private static final Set<String> stopwords = AbstractPaceFunctions
.loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
public static String cleanupForOrdering(String s) {
return (NGRAMUTILS.filterStopWords(NGRAMUTILS.normalize(s), stopwords) + StringUtils.repeat(" ", SIZE))
.substring(0, SIZE)
.replaceAll(" ", "");
}
}

41
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NgramPairs.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("ngrampairs")
public class NgramPairs extends Ngrams {
public NgramPairs(Map<String, Object> params) {
super(params, false);
}
public NgramPairs(Map<String, Object> params, boolean sorted) {
super(params, sorted);
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return ngramPairs(Lists.newArrayList(getNgrams(s, param("ngramLen"), param("max") * 2, 1, 2)), param("max"));
}
protected Collection<String> ngramPairs(final List<String> ngrams, int maxNgrams) {
Collection<String> res = Lists.newArrayList();
int j = 0;
for (int i = 0; i < ngrams.size() && res.size() < maxNgrams; i++) {
if (++j >= ngrams.size()) {
break;
}
res.add(ngrams.get(i) + ngrams.get(j));
// System.out.println("-- " + concatNgrams);
}
return res;
}
}

52
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/Ngrams.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.*;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("ngrams")
public class Ngrams extends AbstractClusteringFunction {
private final boolean sorted;
public Ngrams(Map<String, Object> params) {
this(params, false);
}
public Ngrams(Map<String, Object> params, boolean sorted) {
super(params);
this.sorted = sorted;
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return getNgrams(s, param("ngramLen"), param("max"), param("maxPerToken"), param("minNgramLen"));
}
protected Collection<String> getNgrams(String s, int ngramLen, int max, int maxPerToken, int minNgramLen) {
final Collection<String> ngrams = sorted ? new TreeSet<>() : new LinkedHashSet<String>();
final StringTokenizer st = new StringTokenizer(s);
while (st.hasMoreTokens()) {
final String token = st.nextToken();
if (!token.isEmpty()) {
for (int i = 0; i < maxPerToken && ngramLen + i <= token.length(); i++) {
String ngram = token.substring(i, Math.min(ngramLen + i, token.length())).trim();
if (ngram.length() >= minNgramLen) {
ngrams.add(ngram);
if (ngrams.size() >= max) {
return ngrams;
}
}
}
}
}
// System.out.println(ngrams + " n: " + ngrams.size());
return ngrams;
}
}

113
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NumAuthorsTitleSuffixPrefixChain.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.*;
import java.util.stream.Collectors;
import java.util.stream.StreamSupport;
import com.google.common.base.Splitter;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("numAuthorsTitleSuffixPrefixChain")
public class NumAuthorsTitleSuffixPrefixChain extends AbstractClusteringFunction {
public NumAuthorsTitleSuffixPrefixChain(Map<String, Object> params) {
super(params);
}
@Override
public Collection<String> apply(Config conf, List<String> fields) {
try {
int num_authors = Math.min(Integer.parseInt(fields.get(0)), 21); // SIZE threshold is 20, +1
if (num_authors > 0) {
return super.apply(conf, fields.subList(1, fields.size()))
.stream()
.map(s -> num_authors + "-" + s)
.collect(Collectors.toList());
}
} catch (NumberFormatException e) {
// missing or null authors array
}
return Collections.emptyList();
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return suffixPrefixChain(cleanup(s), param("mod"));
}
private Collection<String> suffixPrefixChain(String s, int mod) {
// create the list of words from the string (remove short words)
List<String> wordsList = Arrays
.stream(s.split(" "))
.filter(si -> si.length() > 3)
.collect(Collectors.toList());
final int words = wordsList.size();
final int letters = s.length();
// create the prefix: number of words + number of letters/mod
String prefix = words / mod + "-";
return doSuffixPrefixChain(wordsList, prefix);
}
private Collection<String> doSuffixPrefixChain(List<String> wordsList, String prefix) {
Set<String> set = Sets.newLinkedHashSet();
switch (wordsList.size()) {
case 0:
break;
case 1:
set.add(wordsList.get(0));
break;
case 2:
set
.add(
prefix +
suffix(wordsList.get(0), 3) +
prefix(wordsList.get(1), 3));
set
.add(
prefix +
prefix(wordsList.get(0), 3) +
suffix(wordsList.get(1), 3));
break;
default:
set
.add(
prefix +
suffix(wordsList.get(0), 3) +
prefix(wordsList.get(1), 3) +
suffix(wordsList.get(2), 3));
set
.add(
prefix +
prefix(wordsList.get(0), 3) +
suffix(wordsList.get(1), 3) +
prefix(wordsList.get(2), 3));
break;
}
return set;
}
private String suffix(String s, int len) {
return s.substring(s.length() - len);
}
private String prefix(String s, int len) {
return s.substring(0, len);
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/PersonClustering.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.common.AbstractPaceFunctions;
import eu.dnetlib.pace.config.Config;
import eu.dnetlib.pace.model.Person;
@ClusteringClass("personClustering")
public class PersonClustering extends AbstractPaceFunctions implements ClusteringFunction {
private Map<String, Object> params;
private static final int MAX_TOKENS = 5;
public PersonClustering(final Map<String, Object> params) {
this.params = params;
}
@Override
public Collection<String> apply(final Config conf, final List<String> fields) {
final Set<String> hashes = Sets.newHashSet();
for (final String f : fields) {
final Person person = new Person(f, false);
if (StringUtils.isNotBlank(person.getNormalisedFirstName())
&& StringUtils.isNotBlank(person.getNormalisedSurname())) {
hashes.add(firstLC(person.getNormalisedFirstName()) + person.getNormalisedSurname().toLowerCase());
} else {
for (final String token1 : tokens(f, MAX_TOKENS)) {
for (final String token2 : tokens(f, MAX_TOKENS)) {
if (!token1.equals(token2)) {
hashes.add(firstLC(token1) + token2);
}
}
}
}
}
return hashes;
}
// @Override
// public Collection<String> apply(final List<Field> fields) {
// final Set<String> hashes = Sets.newHashSet();
//
// for (final Field f : fields) {
//
// final GTAuthor gta = GTAuthor.fromOafJson(f.stringValue());
//
// final Author a = gta.getAuthor();
//
// if (StringUtils.isNotBlank(a.getFirstname()) && StringUtils.isNotBlank(a.getSecondnames())) {
// hashes.add(firstLC(a.getFirstname()) + a.getSecondnames().toLowerCase());
// } else {
// for (final String token1 : tokens(f.stringValue(), MAX_TOKENS)) {
// for (final String token2 : tokens(f.stringValue(), MAX_TOKENS)) {
// if (!token1.equals(token2)) {
// hashes.add(firstLC(token1) + token2);
// }
// }
// }
// }
// }
//
// return hashes;
// }
@Override
public Map<String, Object> getParams() {
return params;
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/PersonHash.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.config.Config;
import eu.dnetlib.pace.model.Person;
@ClusteringClass("personHash")
public class PersonHash extends AbstractClusteringFunction {
private boolean DEFAULT_AGGRESSIVE = false;
public PersonHash(final Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(final Config conf, final String s) {
final List<String> res = Lists.newArrayList();
final boolean aggressive = (Boolean) (getParams().containsKey("aggressive") ? getParams().get("aggressive")
: DEFAULT_AGGRESSIVE);
res.add(new Person(s, aggressive).hash());
return res;
}
}

20
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/RandomClusteringFunction.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.Map;
import eu.dnetlib.pace.config.Config;
public class RandomClusteringFunction extends AbstractClusteringFunction {
public RandomClusteringFunction(Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(final Config conf, String s) {
return null;
}
}

34
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/SortedNgramPairs.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("sortedngrampairs")
public class SortedNgramPairs extends NgramPairs {
public SortedNgramPairs(Map<String, Object> params) {
super(params, false);
}
@Override
protected Collection<String> doApply(Config conf, String s) {
final List<String> tokens = Lists.newArrayList(Splitter.on(" ").omitEmptyStrings().trimResults().split(s));
Collections.sort(tokens);
return ngramPairs(
Lists.newArrayList(getNgrams(Joiner.on(" ").join(tokens), param("ngramLen"), param("max") * 2, 1, 2)),
param("max"));
}
}

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dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/SpaceTrimmingFieldValue.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import com.google.common.collect.Lists;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("spacetrimmingfieldvalue")
public class SpaceTrimmingFieldValue extends AbstractClusteringFunction {
public SpaceTrimmingFieldValue(final Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(final Config conf, final String s) {
final List<String> res = Lists.newArrayList();
res
.add(
StringUtils.isBlank(s) ? RandomStringUtils.random(param("randomLength"))
: s.toLowerCase().replaceAll("\\s+", ""));
return res;
}
}

42
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/SuffixPrefix.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.Map;
import java.util.Set;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("suffixprefix")
public class SuffixPrefix extends AbstractClusteringFunction {
public SuffixPrefix(Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return suffixPrefix(s, param("len"), param("max"));
}
private Collection<String> suffixPrefix(String s, int len, int max) {
final Set<String> bigrams = Sets.newLinkedHashSet();
int i = 0;
while (++i < s.length() && bigrams.size() < max) {
int j = s.indexOf(" ", i);
int offset = j + len + 1 < s.length() ? j + len + 1 : s.length();
if (j - len > 0) {
String bigram = s.substring(j - len, offset).replaceAll(" ", "").trim();
if (bigram.length() >= 4) {
bigrams.add(bigram);
}
}
}
return bigrams;
}
}

52
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/UrlClustering.java Normal file
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package eu.dnetlib.pace.clustering;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import eu.dnetlib.pace.common.AbstractPaceFunctions;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("urlclustering")
public class UrlClustering extends AbstractPaceFunctions implements ClusteringFunction {
protected Map<String, Object> params;
public UrlClustering(final Map<String, Object> params) {
this.params = params;
}
@Override
public Map<String, Object> getParams() {
return params;
}
@Override
public Collection<String> apply(final Config conf, List<String> fields) {
try {
return fields
.stream()
.filter(f -> !f.isEmpty())
.map(this::asUrl)
.map(URL::getHost)
.collect(Collectors.toCollection(HashSet::new));
} catch (IllegalStateException e) {
return new HashSet<>();
}
}
private URL asUrl(String value) {
try {
return new URL(value);
} catch (MalformedURLException e) {
// should not happen as checked by pace typing
throw new IllegalStateException("invalid URL: " + value);
}
}
}

91
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/WordsStatsSuffixPrefixChain.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.*;
import java.util.stream.Collectors;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("wordsStatsSuffixPrefixChain")
public class WordsStatsSuffixPrefixChain extends AbstractClusteringFunction {
public WordsStatsSuffixPrefixChain(Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return suffixPrefixChain(s, param("mod"));
}
private Collection<String> suffixPrefixChain(String s, int mod) {
// create the list of words from the string (remove short words)
List<String> wordsList = Arrays
.stream(s.split(" "))
.filter(si -> si.length() > 3)
.collect(Collectors.toList());
final int words = wordsList.size();
final int letters = s.length();
// create the prefix: number of words + number of letters/mod
String prefix = words + "-" + letters / mod + "-";
return doSuffixPrefixChain(wordsList, prefix);
}
private Collection<String> doSuffixPrefixChain(List<String> wordsList, String prefix) {
Set<String> set = Sets.newLinkedHashSet();
switch (wordsList.size()) {
case 0:
case 1:
break;
case 2:
set
.add(
prefix +
suffix(wordsList.get(0), 3) +
prefix(wordsList.get(1), 3));
set
.add(
prefix +
prefix(wordsList.get(0), 3) +
suffix(wordsList.get(1), 3));
break;
default:
set
.add(
prefix +
suffix(wordsList.get(0), 3) +
prefix(wordsList.get(1), 3) +
suffix(wordsList.get(2), 3));
set
.add(
prefix +
prefix(wordsList.get(0), 3) +
suffix(wordsList.get(1), 3) +
prefix(wordsList.get(2), 3));
break;
}
return set;
}
private String suffix(String s, int len) {
return s.substring(s.length() - len);
}
private String prefix(String s, int len) {
return s.substring(0, len);
}
}

59
dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/WordsSuffixPrefix.java Normal file
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package eu.dnetlib.pace.clustering;
import java.util.Collection;
import java.util.Map;
import java.util.Set;
import com.google.common.collect.Sets;
import eu.dnetlib.pace.config.Config;
@ClusteringClass("wordssuffixprefix")
public class WordsSuffixPrefix extends AbstractClusteringFunction {
public WordsSuffixPrefix(Map<String, Object> params) {
super(params);
}
@Override
protected Collection<String> doApply(Config conf, String s) {
return suffixPrefix(s, param("len"), param("max"));
}
private Collection<String> suffixPrefix(String s, int len, int max) {
final int words = s.split(" ").length;
// adjust the token length according to the number of words
switch (words) {
case 1:
return Sets.newLinkedHashSet();
case 2:
return doSuffixPrefix(s, len + 2, max, words);
case 3:
return doSuffixPrefix(s, len + 1, max, words);
default:
return doSuffixPrefix(s, len, max, words);
}
}
private Collection<String> doSuffixPrefix(String s, int len, int max, int words) {
final Set<String> bigrams = Sets.newLinkedHashSet();
int i = 0;
while (++i < s.length() && bigrams.size() < max) {
int j = s.indexOf(" ", i);
int offset = j + len + 1 < s.length() ? j + len + 1 : s.length();
if (j - len > 0) {
String bigram = s.substring(j - len, offset).replaceAll(" ", "").trim();
if (bigram.length() >= 4) {
bigrams.add(words + bigram);
}
}
}
return bigrams;
}
}

359
dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java Normal file
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package eu.dnetlib.pace.common;
import java.io.IOException;
import java.io.StringWriter;
import java.nio.charset.StandardCharsets;
import java.text.Normalizer;
import java.util.*;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.Iterables;
import com.google.common.collect.Sets;
import com.ibm.icu.text.Transliterator;
import eu.dnetlib.pace.clustering.NGramUtils;
/**
* Set of common functions for the framework
*
* @author claudio
*/
public class AbstractPaceFunctions {
// city map to be used when translating the city names into codes
private static Map<String, String> cityMap = AbstractPaceFunctions
.loadMapFromClasspath("/eu/dnetlib/pace/config/city_map.csv");
// list of stopwords in different languages
protected static Set<String> stopwords_gr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_gr.txt");
protected static Set<String> stopwords_en = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
protected static Set<String> stopwords_de = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_de.txt");
protected static Set<String> stopwords_es = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_es.txt");
protected static Set<String> stopwords_fr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_fr.txt");
protected static Set<String> stopwords_it = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_it.txt");
protected static Set<String> stopwords_pt = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_pt.txt");
// transliterator
protected static Transliterator transliterator = Transliterator.getInstance("Any-Eng");
// blacklist of ngrams: to avoid generic keys
protected static Set<String> ngramBlacklist = loadFromClasspath("/eu/dnetlib/pace/config/ngram_blacklist.txt");
// html regex for normalization
public static final Pattern HTML_REGEX = Pattern.compile("<[^>]*>");
private static final String alpha = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789 ";
private static final String aliases_from = "⁰¹²³⁴⁵⁶⁷⁸⁹⁺⁻⁼⁽⁾ⁿ₀₁₂₃₄₅₆₇₈₉₊₋₌₍₎àáâäæãåāèéêëēėęəîïíīįìôöòóœøōõûüùúūßśšłžźżçćčñń";
private static final String aliases_to = "0123456789+-=()n0123456789+-=()aaaaaaaaeeeeeeeeiiiiiioooooooouuuuussslzzzcccnn";
// doi prefix for normalization
public static final Pattern DOI_PREFIX = Pattern.compile("(https?:\\/\\/dx\\.doi\\.org\\/)|(doi:)");
private static Pattern numberPattern = Pattern.compile("-?\\d+(\\.\\d+)?");
private static Pattern hexUnicodePattern = Pattern.compile("\\\\u(\\p{XDigit}{4})");
private static Pattern romanNumberPattern = Pattern
.compile("^M{0,4}(CM|CD|D?C{0,3})(XC|XL|L?X{0,3})(IX|IV|V?I{0,3})$");
protected static String concat(final List<String> l) {
return Joiner.on(" ").skipNulls().join(l);
}
public static String cleanup(final String s) {
final String s1 = HTML_REGEX.matcher(s).replaceAll("");
final String s2 = unicodeNormalization(s1.toLowerCase());
final String s3 = nfd(s2);
final String s4 = fixXML(s3);
final String s5 = s4.replaceAll("([0-9]+)", " $1 ");
final String s6 = transliterate(s5);
final String s7 = fixAliases(s6);
final String s8 = s7.replaceAll("[^\\p{ASCII}]", "");
final String s9 = s8.replaceAll("[\\p{Punct}]", " ");
final String s10 = s9.replaceAll("\\n", " ");
final String s11 = s10.replaceAll("(?m)\\s+", " ");
final String s12 = s11.trim();
return s12;
}
protected static String fixXML(final String a) {
return a
.replaceAll("&ndash;", " ")
.replaceAll("&amp;", " ")
.replaceAll("&quot;", " ")
.replaceAll("&minus;", " ");
}
protected static boolean checkNumbers(final String a, final String b) {
final String numbersA = getNumbers(a);
final String numbersB = getNumbers(b);
final String romansA = getRomans(a);
final String romansB = getRomans(b);
return !numbersA.equals(numbersB) || !romansA.equals(romansB);
}
protected static String getRomans(final String s) {
final StringBuilder sb = new StringBuilder();
for (final String t : s.split(" ")) {
sb.append(isRoman(t) ? t : "");
}
return sb.toString();
}
protected static boolean isRoman(final String s) {
Matcher m = romanNumberPattern.matcher(s);
return m.matches() && m.hitEnd();
}
protected static String getNumbers(final String s) {
final StringBuilder sb = new StringBuilder();
for (final String t : s.split(" ")) {
sb.append(isNumber(t) ? t : "");
}
return sb.toString();
}
public static boolean isNumber(String strNum) {
if (strNum == null) {
return false;
}
return numberPattern.matcher(strNum).matches();
}
protected static String fixAliases(final String s) {
final StringBuilder sb = new StringBuilder();
s.chars().forEach(ch -> {
final int i = StringUtils.indexOf(aliases_from, ch);
sb.append(i >= 0 ? aliases_to.charAt(i) : (char) ch);
});
return sb.toString();
}
protected static String transliterate(final String s) {
try {
return transliterator.transliterate(s);
} catch (Exception e) {
return s;
}
}
protected static String removeSymbols(final String s) {
final StringBuilder sb = new StringBuilder();
s.chars().forEach(ch -> {
sb.append(StringUtils.contains(alpha, ch) ? (char) ch : ' ');
});
return sb.toString().replaceAll("\\s+", " ");
}
protected static boolean notNull(final String s) {
return s != null;
}
public static String normalize(final String s) {
return fixAliases(transliterate(nfd(unicodeNormalization(s))))
.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();
}
public static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD);
}
public static String utf8(final String s) {
byte[] bytes = s.getBytes(StandardCharsets.UTF_8);
return new String(bytes, StandardCharsets.UTF_8);
}
public static String unicodeNormalization(final String s) {
Matcher m = hexUnicodePattern.matcher(s);
StringBuffer buf = new StringBuffer(s.length());
while (m.find()) {
String ch = String.valueOf((char) Integer.parseInt(m.group(1), 16));
m.appendReplacement(buf, Matcher.quoteReplacement(ch));
}
m.appendTail(buf);
return buf.toString();
}
protected static String filterStopWords(final String s, final Set<String> stopwords) {
final StringTokenizer st = new StringTokenizer(s);
final StringBuilder sb = new StringBuilder();
while (st.hasMoreTokens()) {
final String token = st.nextToken();
if (!stopwords.contains(token)) {
sb.append(token);
sb.append(" ");
}
}
return sb.toString().trim();
}
public static String filterAllStopWords(String s) {
s = filterStopWords(s, stopwords_en);
s = filterStopWords(s, stopwords_de);
s = filterStopWords(s, stopwords_it);
s = filterStopWords(s, stopwords_fr);
s = filterStopWords(s, stopwords_pt);
s = filterStopWords(s, stopwords_es);
s = filterStopWords(s, stopwords_gr);
return s;
}
protected static Collection<String> filterBlacklisted(final Collection<String> set,
final Set<String> ngramBlacklist) {
final Set<String> newset = Sets.newLinkedHashSet();
for (final String s : set) {
if (!ngramBlacklist.contains(s)) {
newset.add(s);
}
}
return newset;
}
public static Set<String> loadFromClasspath(final String classpath) {
Transliterator transliterator = Transliterator.getInstance("Any-Eng");
final Set<String> h = Sets.newHashSet();
try {
for (final String s : IOUtils
.readLines(NGramUtils.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
h.add(fixAliases(transliterator.transliterate(s))); // transliteration of the stopwords
}
} catch (final Throwable e) {
return Sets.newHashSet();
}
return h;
}
public static Map<String, String> loadMapFromClasspath(final String classpath) {
Transliterator transliterator = Transliterator.getInstance("Any-Eng");
final Map<String, String> m = new HashMap<>();
try {
for (final String s : IOUtils
.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
// string is like this: code;word1;word2;word3
String[] line = s.split(";");
String value = line[0];
for (int i = 1; i < line.length; i++) {
m.put(fixAliases(transliterator.transliterate(line[i].toLowerCase())), value);
}
}
} catch (final Throwable e) {
return new HashMap<>();
}
return m;
}
public static String removeKeywords(String s, Set<String> keywords) {
s = " " + s + " ";
for (String k : keywords) {
s = s.replaceAll(k.toLowerCase(), "");
}
return s.trim();
}
public static double commonElementsPercentage(Set<String> s1, Set<String> s2) {
double longer = Math.max(s1.size(), s2.size());
return (double) s1.stream().filter(s2::contains).count() / longer;
}
// convert the set of keywords to codes
public static Set<String> toCodes(Set<String> keywords, Map<String, String> translationMap) {
return keywords.stream().map(s -> translationMap.get(s)).collect(Collectors.toSet());
}
public static Set<String> keywordsToCodes(Set<String> keywords, Map<String, String> translationMap) {
return toCodes(keywords, translationMap);
}
public static Set<String> citiesToCodes(Set<String> keywords) {
return toCodes(keywords, cityMap);
}
protected static String firstLC(final String s) {
return StringUtils.substring(s, 0, 1).toLowerCase();
}
protected static Iterable<String> tokens(final String s, final int maxTokens) {
return Iterables.limit(Splitter.on(" ").omitEmptyStrings().trimResults().split(s), maxTokens);
}
public static String normalizePid(String pid) {
return DOI_PREFIX.matcher(pid.toLowerCase()).replaceAll("");
}
// get the list of keywords into the input string
public static Set<String> getKeywords(String s1, Map<String, String> translationMap, int windowSize) {
String s = s1;
List<String> tokens = Arrays.asList(s.toLowerCase().split(" "));
Set<String> codes = new HashSet<>();
if (tokens.size() < windowSize)
windowSize = tokens.size();
int length = windowSize;
while (length != 0) {
for (int i = 0; i <= tokens.size() - length; i++) {
String candidate = concat(tokens.subList(i, i + length));
if (translationMap.containsKey(candidate)) {
codes.add(candidate);
s = s.replace(candidate, "").trim();
}
}
tokens = Arrays.asList(s.split(" "));
length -= 1;
}
return codes;
}
public static Set<String> getCities(String s1, int windowSize) {
return getKeywords(s1, cityMap, windowSize);
}
public static <T> String readFromClasspath(final String filename, final Class<T> clazz) {
final StringWriter sw = new StringWriter();
try {
IOUtils.copy(clazz.getResourceAsStream(filename), sw, StandardCharsets.UTF_8);
return sw.toString();
} catch (final IOException e) {
throw new RuntimeException("cannot load resource from classpath: " + filename);
}
}
}

53
dhp-pace-core/src/main/java/eu/dnetlib/pace/config/Config.java Normal file
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package eu.dnetlib.pace.config;
import java.util.List;
import java.util.Map;
import java.util.function.Predicate;
import eu.dnetlib.pace.model.ClusteringDef;
import eu.dnetlib.pace.model.FieldDef;
import eu.dnetlib.pace.tree.support.TreeNodeDef;
/**
* Interface for PACE configuration bean.
*
* @author claudio
*/
public interface Config {
/**
* Field configuration definitions.
*
* @return the list of definitions
*/
public List<FieldDef> model();
/**
* Decision Tree definition
*
* @return the map representing the decision tree
*/
public Map<String, TreeNodeDef> decisionTree();
/**
* Clusterings.
*
* @return the list
*/
public List<ClusteringDef> clusterings();
/**
* Blacklists.
*
* @return the map
*/
public Map<String, Predicate<String>> blacklists();
/**
* Translation map.
*
* @return the map
* */
public Map<String, String> translationMap();
}

178
dhp-pace-core/src/main/java/eu/dnetlib/pace/config/DedupConfig.java Normal file
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package eu.dnetlib.pace.config;
import java.io.IOException;
import java.io.Serializable;
import java.nio.charset.StandardCharsets;
import java.util.AbstractMap;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.function.Predicate;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
import java.util.stream.Collectors;
import org.antlr.stringtemplate.StringTemplate;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Maps;
import eu.dnetlib.pace.model.ClusteringDef;
import eu.dnetlib.pace.model.FieldDef;
import eu.dnetlib.pace.tree.support.TreeNodeDef;
import eu.dnetlib.pace.util.PaceException;
public class DedupConfig implements Config, Serializable {
private static String CONFIG_TEMPLATE = "dedupConfig.st";
private PaceConfig pace;
private WfConfig wf;
@JsonIgnore
private Map<String, Predicate<String>> blacklists;
private static Map<String, String> defaults = Maps.newHashMap();
static {
defaults.put("dedupRun", "001");
defaults.put("entityType", "result");
defaults.put("subEntityType", "resulttype");
defaults.put("subEntityValue", "publication");
defaults.put("orderField", "title");
defaults.put("queueMaxSize", "2000");
defaults.put("groupMaxSize", "10");
defaults.put("slidingWindowSize", "200");
defaults.put("rootBuilder", "result");
defaults.put("includeChildren", "true");
defaults.put("maxIterations", "20");
defaults.put("idPath", "$.id");
}
public DedupConfig() {
}
public static DedupConfig load(final String json) {
final DedupConfig config;
try {
config = new ObjectMapper().readValue(json, DedupConfig.class);
config.getPace().initModel();
config.getPace().initTranslationMap();
config.blacklists = config
.getPace()
.getBlacklists()
.entrySet()
.stream()
.map(
e -> new AbstractMap.SimpleEntry<String, List<Pattern>>(e.getKey(),
e
.getValue()
.stream()
.filter(s -> !StringUtils.isBlank(s))
.map(Pattern::compile)
.collect(Collectors.toList())))
.collect(
Collectors
.toMap(
e -> e.getKey(),
e -> (Predicate<String> & Serializable) s -> e
.getValue()
.stream()
.filter(p -> p.matcher(s).matches())
.findFirst()
.isPresent()))
;
return config;
} catch (IOException | PatternSyntaxException e) {
throw new PaceException("Error in parsing configuration json", e);
}
}
public static DedupConfig loadDefault() throws IOException {
return loadDefault(new HashMap<String, String>());
}
public static DedupConfig loadDefault(final Map<String, String> params) throws IOException {
final StringTemplate template = new StringTemplate(new DedupConfig().readFromClasspath(CONFIG_TEMPLATE));
for (final Entry<String, String> e : defaults.entrySet()) {
template.setAttribute(e.getKey(), e.getValue());
}
for (final Entry<String, String> e : params.entrySet()) {
if (template.getAttribute(e.getKey()) != null) {
template.getAttributes().computeIfPresent(e.getKey(), (o, o2) -> e.getValue());
} else {
template.setAttribute(e.getKey(), e.getValue());
}
}
final String json = template.toString();
return load(json);
}
private String readFromClasspath(final String resource) throws IOException {
return IOUtils.toString(getClass().getResource(resource), StandardCharsets.UTF_8);
}
public PaceConfig getPace() {
return pace;
}
public void setPace(final PaceConfig pace) {
this.pace = pace;
}
public WfConfig getWf() {
return wf;
}
public void setWf(final WfConfig wf) {
this.wf = wf;
}
@Override
public String toString() {
try {
return new ObjectMapper().writeValueAsString(this);
} catch (IOException e) {
throw new PaceException("unable to serialise configuration", e);
}
}
@Override
public Map<String, TreeNodeDef> decisionTree() {
return getPace().getDecisionTree();
}
@Override
public List<FieldDef> model() {
return getPace().getModel();
}
@Override
public List<ClusteringDef> clusterings() {
return getPace().getClustering();
}
@Override
public Map<String, Predicate<String>> blacklists() {
return blacklists;
}
@Override
public Map<String, String> translationMap() {
return getPace().translationMap();
}
}

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