diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 77aa2aedb..7a6a32e0e 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -22,6 +22,10 @@ dnet45-releases https://maven.d4science.org/nexus/content/repositories/dnet45-releases + + DHPSite + file://${dhp.site.stage.path}/site/dhp-build/dhp-code-style + @@ -43,6 +47,7 @@ UTF-8 + /tmp/dhp-site \ No newline at end of file diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 12b999b9c..fed689a06 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -10,6 +10,9 @@ pom This module is a container for the build tools used in dnet-hadoop + + true + dhp-code-style @@ -17,4 +20,12 @@ dhp-build-properties-maven-plugin + + + + DHPSite + file://${dhp.site.stage.path}/site/dhp-build + + + diff --git a/dhp-build/src/site/site.xml b/dhp-build/src/site/site.xml new file mode 100644 index 000000000..2d9d769a2 --- /dev/null +++ b/dhp-build/src/site/site.xml @@ -0,0 +1,22 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index c057123b1..686b89f6b 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -13,6 +13,13 @@ dhp-common jar + + + DHPSite + file://${dhp.site.stage.path}/site/dhp-common + + + This module contains common utilities meant to be used across the dnet-hadoop submodules diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/index.md b/dhp-workflows/dhp-aggregation/src/site/markdown/index.md index c0c756082..240617f91 100644 --- a/dhp-workflows/dhp-aggregation/src/site/markdown/index.md +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/index.md @@ -1,9 +1,20 @@ ##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 of each MDStore. -It defines [mappings](mappings.md) for transformation of different datasource (See mapping section). \ No newline at end of file +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 diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md b/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md new file mode 100644 index 000000000..baf232e40 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md @@ -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. + + diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md b/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md index f6327a51b..c1813394b 100644 --- a/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md @@ -4,13 +4,13 @@ This section describes the mapping implemented for [MEDLINE/PubMed](https://pubm Collection --------- 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 ------- -The resposible class of parsing is [PMParser](./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) +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](/dnet-hadoop/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html) 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 | |FOR ALL AUTHOR | author.rank| sequential number starting from 1| +#TODO + +Missing item mapped + diff --git a/dhp-workflows/dhp-aggregation/src/site/site.xml b/dhp-workflows/dhp-aggregation/src/site/site.xml index da5da0f1e..75fc5032e 100644 --- a/dhp-workflows/dhp-aggregation/src/site/site.xml +++ b/dhp-workflows/dhp-aggregation/src/site/site.xml @@ -20,7 +20,9 @@ - + + + diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java index 45bfc785f..52e9917bb 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java @@ -19,7 +19,7 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; @ExtendWith(MockitoExtension.class) -class UpdateMatcherTest { +public class UpdateMatcherTest { UpdateMatcher matcher = new EnrichMissingPublicationDate(); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java index 550ded9f4..5af81a31a 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java @@ -11,7 +11,7 @@ import org.junit.jupiter.api.Test; import eu.dnetlib.broker.objects.OaBrokerMainEntity; -class EnrichMissingPublicationDateTest { +public class EnrichMissingPublicationDateTest { final EnrichMissingPublicationDate matcher = new EnrichMissingPublicationDate(); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java index b532aa9f7..d93390e4a 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java @@ -8,7 +8,7 @@ import java.util.Arrays; import org.junit.jupiter.api.Test; -class SubscriptionUtilsTest { +public class SubscriptionUtilsTest { @Test void testVerifyListSimilar() { diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java index a8bc03e31..117bdeef4 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java @@ -9,7 +9,7 @@ import eu.dnetlib.broker.objects.OaBrokerAuthor; import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.broker.objects.OaBrokerTypedValue; -class TrustUtilsTest { +public class TrustUtilsTest { private static final double THRESHOLD = 0.95; diff --git a/dhp-workflows/dhp-enrichment/src/site/markdown/about.md b/dhp-workflows/dhp-enrichment/src/site/markdown/about.md new file mode 100644 index 000000000..c220c63b2 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/site/markdown/about.md @@ -0,0 +1 @@ +#DHP Enrichment \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/site/site.xml b/dhp-workflows/dhp-enrichment/src/site/site.xml new file mode 100644 index 000000000..dad0cd996 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/site/site.xml @@ -0,0 +1,26 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 22ee77619..89ba2bf70 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -15,6 +15,13 @@ This module is the container for the oozie workflow definitions in dnet-hadoop project + + + DHPSite + file://${dhp.site.stage.path}/site/dhp-workflows + + + dhp-workflow-profiles dhp-aggregation diff --git a/dhp-workflows/src/site/site.xml b/dhp-workflows/src/site/site.xml new file mode 100644 index 000000000..6b742db6a --- /dev/null +++ b/dhp-workflows/src/site/site.xml @@ -0,0 +1,25 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/pom.xml b/pom.xml index 71c55d1f0..f7e3c6226 100644 --- a/pom.xml +++ b/pom.xml @@ -719,6 +719,10 @@ dnet45-releases https://maven.d4science.org/nexus/content/repositories/dnet45-releases + + DHPSite + file://${dhp.site.stage.path}/site/ + @@ -734,6 +738,7 @@ + /tmp/dhp-site UTF-8 UTF-8 3.6.0 diff --git a/src/site/site.xml b/src/site/site.xml new file mode 100644 index 000000000..634a2c154 --- /dev/null +++ b/src/site/site.xml @@ -0,0 +1,21 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + \ No newline at end of file