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dnet-hadoop
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Merge branch 'beta' into preserve_openorg_parent_child_relations

This commit is contained in:
Claudio Atzori 2021-11-19 11:35:46 +01:00
parent f4538f3c4c fc03c99805
commit e5a2c596b2
18 changed files with 194 additions and 11 deletions
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5
dhp-build/dhp-code-style/pom.xml
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@ -22,6 +22,10 @@
<id>dnet45-releases</id> <id>dnet45-releases</id>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url> <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
</repository> </repository>
<site>
<id>DHPSite</id>
<url>file://${dhp.site.stage.path}/site/dhp-build/dhp-code-style</url>
</site>
</distributionManagement> </distributionManagement>
<build> <build>
@ -43,6 +47,7 @@
<properties> <properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<dhp.site.stage.path>/tmp/dhp-site</dhp.site.stage.path>
</properties> </properties>
</project> </project>

11
dhp-build/pom.xml
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@ -10,6 +10,9 @@
<packaging>pom</packaging> <packaging>pom</packaging>
<description>This module is a container for the build tools used in dnet-hadoop</description> <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> <modules>
<module>dhp-code-style</module> <module>dhp-code-style</module>
@ -17,4 +20,12 @@
<module>dhp-build-properties-maven-plugin</module> <module>dhp-build-properties-maven-plugin</module>
</modules> </modules>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>file://${dhp.site.stage.path}/site/dhp-build</url>
</site>
</distributionManagement>
</project> </project>

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

7
dhp-common/pom.xml
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@ -13,6 +13,13 @@
<artifactId>dhp-common</artifactId> <artifactId>dhp-common</artifactId>
<packaging>jar</packaging> <packaging>jar</packaging>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>file://${dhp.site.stage.path}/site/dhp-common</url>
</site>
</distributionManagement>
<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description> <description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
<dependencies> <dependencies>

15
dhp-workflows/dhp-aggregation/src/site/markdown/index.md
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@ -1,9 +1,20 @@
##DHP-Aggregation ##DHP-Aggregation
This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records. This module defines a set of oozie workflows for
Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure 1. the **collection** and **transformation** of metadata records.
2. the **integration** of new external information in the result
### Collection and Transformation
The workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
of each MDStore. of each MDStore.
It defines [mappings](mappings.md) for transformation of different datasource (See mapping section). It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).
### Integration of external information in the result
The workflows create new entity in the OpenAIRE format (OAF) which aim is to enrich the result already contained in the graph.
See integration section for more insight

36
dhp-workflows/dhp-aggregation/src/site/markdown/integration.md Normal file
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@ -0,0 +1,36 @@
DHP Aggregation - Integration method
=====================================
The integration method can be applied every time new information, which is not aggregated from the repositories
nor computed directly by OpenAIRE, should be added to the results of the graph.
The information integrated so far is:
1. Article impact measures
1. [Bip!Finder](https://dl.acm.org/doi/10.1145/3357384.3357850) scores
2. Result Subjects
1. Integration of Fields od Science and Techonology ([FOS](https://www.qnrf.org/en-us/FOS)) classification in
results subjects.
The method always consists in the creation of a new entity in the OpenAIRE format (OAF entity) containing only the id
and the element in the OAF model that should be used to map the information we want to integrate.
The id is set by using a particular encoding of the given PID
*unresolved:[pid]:[pidtype]*
where
1. *unresolved* is a constant value
2. *pid* is the persistent id value, e.g. 10.5281/zenodo.4707307
3. *pidtype* is the persistent id type, e.g. doi
Such entities are matched against those available in the graph using the result.instance.pid values.
This mechanism can be used to integrate enrichments produced as associated by a given PID.
If a match will be found with one of the results already in the graph that said result will be enriched with the information
present in the new OAF.
All the objects for which a match is not found are discarded.

10
dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md
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@ -4,13 +4,13 @@ This section describes the mapping implemented for [MEDLINE/PubMed](https://pubm
Collection Collection
--------- ---------
The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with
the following [shcema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html) the following [schema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html)
Parsing Parsing
------- -------
The resposible class of parsing is [PMParser](./scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates The resposible class of parsing is [PMParser](/dnet-hadoop/scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates
an intermediate mapping of PubMed Article defined [here](/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html) an intermediate mapping of PubMed Article defined [here](/dnet-hadoop/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
Mapping Mapping
@ -50,6 +50,10 @@ The table below describes the mapping from the XML Native to the OAF mapping
|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist | |//Author/FullName| author.Forename| Concatenation of forname + lastName if exist |
|FOR ALL AUTHOR | author.rank| sequential number starting from 1| |FOR ALL AUTHOR | author.rank| sequential number starting from 1|
#TODO
Missing item mapped

4
dhp-workflows/dhp-aggregation/src/site/site.xml
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@ -20,7 +20,9 @@
<item name="Pubmed" href="pubmed.html"/> <item name="Pubmed" href="pubmed.html"/>
<item name="Datacite" href="datacite.html"/> <item name="Datacite" href="datacite.html"/>
</item> </item>
<item name="Release Notes" href="release-notes.html" /> <item name="Integration" href="integration.html" collapse="true">
</item>
<item name="General Information" href="about.html"/> <item name="General Information" href="about.html"/>
<item name="JavaDoc" href="apidocs/" /> <item name="JavaDoc" href="apidocs/" />

2
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java
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@ -19,7 +19,7 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate;
import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
class UpdateMatcherTest { public class UpdateMatcherTest {
UpdateMatcher<String> matcher = new EnrichMissingPublicationDate(); UpdateMatcher<String> matcher = new EnrichMissingPublicationDate();

2
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java
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@ -11,7 +11,7 @@ import org.junit.jupiter.api.Test;
import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.broker.objects.OaBrokerMainEntity;
class EnrichMissingPublicationDateTest { public class EnrichMissingPublicationDateTest {
final EnrichMissingPublicationDate matcher = new EnrichMissingPublicationDate(); final EnrichMissingPublicationDate matcher = new EnrichMissingPublicationDate();

2
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java
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@ -8,7 +8,7 @@ import java.util.Arrays;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
class SubscriptionUtilsTest { public class SubscriptionUtilsTest {
@Test @Test
void testVerifyListSimilar() { void testVerifyListSimilar() {

2
dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java
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@ -9,7 +9,7 @@ import eu.dnetlib.broker.objects.OaBrokerAuthor;
import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.broker.objects.OaBrokerMainEntity;
import eu.dnetlib.broker.objects.OaBrokerTypedValue; import eu.dnetlib.broker.objects.OaBrokerTypedValue;
class TrustUtilsTest { public class TrustUtilsTest {
private static final double THRESHOLD = 0.95; private static final double THRESHOLD = 0.95;

1
dhp-workflows/dhp-enrichment/src/site/markdown/about.md Normal file
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@ -0,0 +1 @@
#DHP Enrichment

26
dhp-workflows/dhp-enrichment/src/site/site.xml Normal file
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@ -0,0 +1,26 @@
<?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 name="Documentation">
<item name="Link1 Collapsable" href="about.html" collapse="true">
<item name="item1" href="pubmed.html"/>
<item name="item2" href="datacite.html"/>
</item>
</menu>
<menu ref="reports"/>
</body>
</project>

7
dhp-workflows/pom.xml
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@ -15,6 +15,13 @@
<description>This module is the container for the oozie workflow definitions in dnet-hadoop project</description> <description>This module is the container for the oozie workflow definitions in dnet-hadoop project</description>
<distributionManagement>
<site>
<id>DHPSite</id>
<url>file://${dhp.site.stage.path}/site/dhp-workflows</url>
</site>
</distributionManagement>
<modules> <modules>
<module>dhp-workflow-profiles</module> <module>dhp-workflow-profiles</module>
<module>dhp-aggregation</module> <module>dhp-aggregation</module>

25
dhp-workflows/src/site/site.xml Normal file
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@ -0,0 +1,25 @@
<?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 name="APIDocs">
<item name="JavaDoc" href="apidocs/" />
<item name="ScalaDoc" href="scaladocs/" />
</menu>
<menu ref="modules" />
<menu ref="reports"/>
</body>
</project>

5
pom.xml
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@ -719,6 +719,10 @@
<id>dnet45-releases</id> <id>dnet45-releases</id>
<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url> <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
</repository> </repository>
<site>
<id>DHPSite</id>
<url>file://${dhp.site.stage.path}/site/</url>
</site>
</distributionManagement> </distributionManagement>
<reporting> <reporting>
<plugins> <plugins>
@ -734,6 +738,7 @@
</reporting> </reporting>
<properties> <properties>
<dhp.site.stage.path>/tmp/dhp-site</dhp.site.stage.path>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding> <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding> <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version> <maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>

21
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>