diff --git a/dump-schema/src/main/java/eu/dnetlib/dhp/eosc/model/EoscResult.java b/dump-schema/src/main/java/eu/dnetlib/dhp/eosc/model/EoscResult.java index caa98cc..65b568e 100644 --- a/dump-schema/src/main/java/eu/dnetlib/dhp/eosc/model/EoscResult.java +++ b/dump-schema/src/main/java/eu/dnetlib/dhp/eosc/model/EoscResult.java @@ -20,7 +20,7 @@ public class EoscResult extends CommunityResult { @JsonSchema(description = "The subject dumped by type associated to the result") private Map> subject; - @JsonSchema(description = "Te list of keywords associated to the result") + @JsonSchema(description = "The list of keywords associated to the result") private List keywords; @JsonSchema(description = "The list of organizations the result is affiliated to") diff --git a/dump-schema/src/main/resources/jsonschemas/eosc_result_schema.json b/dump-schema/src/main/resources/jsonschemas/eosc_result_schema.json index 886a173..11daa8b 100644 --- a/dump-schema/src/main/resources/jsonschemas/eosc_result_schema.json +++ b/dump-schema/src/main/resources/jsonschemas/eosc_result_schema.json @@ -268,26 +268,30 @@ "description": "Date when the embargo ends and this result turns Open Access" }, "eoscIF": { - "type": "object", - "properties": { - "code": { - "type": "string", - "description": "EOSC-IF local code. Later on it could be populated with a PID (e.g. DOI), but for the time being we stick to a more loose definition." + "description": "Describes a reference to the EOSC Interoperability Framework (IF) Guidelines", + "type": "array", + "items": { + "type": "object", + "properties": { + "code": { + "type": "string", + "description": "EOSC-IF local code. Later on it could be populated with a PID (e.g. DOI), but for the time being we stick to a more loose definition." + }, + "label": { + "type": "string", + "description": "EOSC-IF label" + }, + "semanticRelation": { + "type": "string", + "description": "EOSC-IF semantic relation (e.g. compliesWith)" + }, + "url": { + "type": "string", + "description": "EOSC-IF url to the guidelines" + } }, - "label": { - "type": "string", - "description": "EOSC-IF label" - }, - "semanticRelation": { - "type": "string", - "description": "EOSC-IF semantic relation (e.g. compliesWith)" - }, - "url": { - "type": "string", - "description": "EOSC-IF url to the guidelines" - } - }, - "description": "Describes a reference to the EOSC Interoperability Framework (IF) Guidelines" + "description": "Describes a reference to the EOSC Interoperability Framework (IF) Guidelines" + } }, "format": { "type": "array", @@ -310,6 +314,19 @@ "type": "string", "description": "The OpenAIRE identifiers for this result" }, + "indicator": { + "type": "object", + "properties": { + "usageCounts": { + "type": "object", + "properties": { + "downloads": {"type": "string"}, + "views": {"type": "string"} + } + } + }, + "description": "The indicators for this result" + }, "instance": { "description": "Each instance is one specific materialisation or version of the result. For example, you can have one result with three instance: one is the pre-print, one is the post-print, one is te published version", "type": "array", @@ -423,11 +440,11 @@ } }, "keywords": { - "description": "Te list of keywords associated to the result", + "description": "The list of keywords associated to the result", "type": "array", "items": { "type": "string", - "description": "Te list of keywords associated to the result" + "description": "The list of keywords associated to the result" } }, "language": { diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 9ca571d..03d3151 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -250,10 +250,16 @@ public class ResultMapper implements Serializable { if (Optional.ofNullable(input.getEoscifguidelines()).isPresent()) { ((EoscResult) out) - .setEoscIF(input.getEoscifguidelines() - .stream() - .map(eig -> EoscInteroperabilityFramework.newInstance(eig.getCode(), eig.getLabel(), eig.getUrl(), eig.getSemanticRelation())) - .collect(Collectors.toList())); + .setEoscIF( + input + .getEoscifguidelines() + .stream() + .map( + eig -> EoscInteroperabilityFramework + .newInstance( + eig.getCode(), eig.getLabel(), eig.getUrl(), + eig.getSemanticRelation())) + .collect(Collectors.toList())); } } diff --git a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java index 2df780f..9ca1f2f 100644 --- a/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java +++ b/dump/src/main/java/eu/dnetlib/dhp/oa/graph/dump/eosc/ExtendEoscResultWithOrganizationStep2.java @@ -131,8 +131,16 @@ public class ExtendEoscResultWithOrganizationStep2 implements Serializable { } EoscResult ret = first._1(); List affiliation = new ArrayList<>(); + Set alreadyInsertedAffiliations = new HashSet<>(); affiliation.add(first._2().getAffiliation()); - it.forEachRemaining(res -> affiliation.add(res._2().getAffiliation())); + alreadyInsertedAffiliations.add(first._2().getAffiliation().getId()); + it.forEachRemaining(res -> { + if (!alreadyInsertedAffiliations.contains(res._2().getAffiliation().getId())) { + affiliation.add(res._2().getAffiliation()); + alreadyInsertedAffiliations.add(res._2().getAffiliation().getId()); + } + + }); ret.setAffiliation(affiliation); return ret; }, Encoders.bean(EoscResult.class)) diff --git a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 77bf857..a35f109 100644 --- a/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dump/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -921,15 +921,104 @@ public class DumpJobTest { Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); - Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getCode().equals("EOSC::Twitter Data"))).count()); - Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getLabel().equals("EOSC::Twitter Data"))).count()); - Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getUrl().equals(""))).count()); - Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getSemanticRelation().equals("compliesWith"))).count()); + Assertions + .assertEquals( + 1, + tmp + .filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getCode().equals("EOSC::Twitter Data"))) + .count()); + Assertions + .assertEquals( + 1, + tmp + .filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getLabel().equals("EOSC::Twitter Data"))) + .count()); + Assertions + .assertEquals(1, tmp.filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getUrl().equals(""))).count()); + Assertions + .assertEquals( + 1, + tmp + .filter(d -> d.getEoscIF().stream().anyMatch(c -> c.getSemanticRelation().equals("compliesWith"))) + .count()); System.out.println(OBJECT_MAPPER.writeValueAsString(verificationDataset.first())); } + + @Test + public void testEOSCDumpZenodoReview() throws Exception { + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/zenodo7353841") + .getPath(), workingDir.toString() + "/orp", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(), OtherResearchProduct.class, + EoscResult.class, Constants.DUMPTYPE.EOSC.getType()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/orp") + .map(item -> OBJECT_MAPPER.readValue(item, EoscResult.class)); + + System.out.println(OBJECT_MAPPER.writeValueAsString(tmp.first())); + + dump + .run( + false, getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/zenodo7351393") + .getPath(), workingDir.toString() + "/soft", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(), Software.class, + EoscResult.class, Constants.DUMPTYPE.EOSC.getType()); + + + JavaRDD tmp2 = sc + .textFile(workingDir.toString() + "/soft") + .map(item -> OBJECT_MAPPER.readValue(item, EoscResult.class)); + + System.out.println(OBJECT_MAPPER.writeValueAsString(tmp2.first())); + + dump + .run( + false, getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/zenodo7351221") + .getPath(), workingDir.toString() + "/soft2", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(), Software.class, + EoscResult.class, Constants.DUMPTYPE.EOSC.getType()); + + + JavaRDD tmp3 = sc + .textFile(workingDir.toString() + "/soft2") + .map(item -> OBJECT_MAPPER.readValue(item, EoscResult.class)); + + System.out.println(OBJECT_MAPPER.writeValueAsString(tmp3.first())); + + + dump + .run( + false, getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/rohub") + .getPath(), workingDir.toString() + "/orp2", getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(), OtherResearchProduct.class, + EoscResult.class, Constants.DUMPTYPE.EOSC.getType()); + + + JavaRDD tmp4 = sc + .textFile(workingDir.toString() + "/orp2") + .map(item -> OBJECT_MAPPER.readValue(item, EoscResult.class)); + + System.out.println(OBJECT_MAPPER.writeValueAsString(tmp4.first())); + + } + @Test public void testArticlePCA() { final String sourcePath = getClass() diff --git a/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/rohub b/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/rohub new file mode 100644 index 0000000..9729c60 --- /dev/null +++ b/dump/src/test/resources/eu/dnetlib/dhp/oa/graph/dump/eosc/input/review202211/rohub @@ -0,0 +1 @@ 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title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[{"value":"2022-11-23","qualifier":{"classid":"Issued","classname":"Issued","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"description":[{"value":"

A Knowledge graph representation of compounds and associated biological entities in the BY-COVID and EOSC Future project.

\n\n

Current status

\n\n
    \n
  • Number of Nodes: 35952
    • \n
  • Number of Edges: 279462
    • \n
  • Human Proteins: 1347
    • \n
  • Assay: 15835
    • \n
  • Chemical/Compound: 4096
    • \n
  • Mechanism of Action: 739
    • \n
  • Pathway: 1513
    • \n
  • Disease: 1585
    • \n
  • SideEffect: 7420
    • \n
  • Biological Process: 2085
    • \n
  • Molecular Function: 1332
    • \n
\n\n

Please check the BY_COVID_update_August.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in 'data\\export' folder.

\n\n

 

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The Monkeypox KG is built using viral and human proteins reported in different resources. Additionally, the KG represents chemicals tested against Monkeypox and their targets, associated biological processes, molecular functions, diseases and side effects.

\n\n

KG status

\n\n

Version 1 stats:

\n\n
    \n
  • Number of Nodes: 8235
    • \n
  • Number of Edges: 40422
    • \n
\n\n

Version 2 stats (2nd September) :

\n\n
    \n
  • Number of Nodes: 9129
    • \n
  • Number of Edges: 44568
    • \n
\n\n

Please check the graph.ipynb for understanding step wise process of KG generation and KG statistics. The KG has been exported to formats such as graphml, sif and so on for visualizations in other platforms. For example, the graphml file can be imported to Cytoscape directly. These files are located in 'data\\export' folder.

\n\n

 

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The attached .yaml file is used as input to the Dashboard State of the Environment, which is a science project of the ENVRI-FAIR science cluster within EOSC-FUTURE. The contents of the file enable the visualization of Ocean indicators on the dashboard. It is possible to download the attached file and change the contents to include indicators from different domains such as atmosphere or biodiversity. 

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