From 0f364605ffa63941e622225eca3050a5b2e287e0 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 18 Feb 2020 11:48:19 +0100 Subject: [PATCH 1/4] removed stale tests, need to reimplemente them anyway --- .../dnetlib/dhp/graph/MappingUtilsTest.java | 66 ------------------- .../dhp/graph/XmlRecordFactoryTest.java | 55 ---------------- 2 files changed, 121 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java deleted file mode 100644 index a9d696bea..000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/MappingUtilsTest.java +++ /dev/null @@ -1,66 +0,0 @@ -package eu.dnetlib.dhp.graph; - -import eu.dnetlib.dhp.graph.model.EntityRelEntity; -import eu.dnetlib.dhp.graph.model.RelatedEntity; -import eu.dnetlib.dhp.graph.utils.GraphMappingUtils; -import org.codehaus.jackson.map.ObjectMapper; -import org.junit.Before; -import org.junit.Test; - -import java.io.IOException; -import java.io.InputStreamReader; - -public class MappingUtilsTest { - - private GraphMappingUtils utils; - - @Before - public void setUp() { - utils = new GraphMappingUtils(); - } - - @Test - public void testOafMappingDatasource() throws IOException { - - final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("datasource.json")); - final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class); - e.getSource().setType("datasource"); - - final EntityRelEntity out = utils.asRelatedEntity(e); - System.out.println(out); - - } - - //@Test - public void testOafMappingResult() throws IOException { - - final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("result.json")); - final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class); - - final EntityRelEntity out = utils.asRelatedEntity(e); - System.out.println(out); - - } - - @Test - public void testOafMappingSoftware() throws IOException { - - final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("software.json")); - final EntityRelEntity e = new ObjectMapper().readValue(in, EntityRelEntity.class); - - final EntityRelEntity out = utils.asRelatedEntity(e); - System.out.println(out); - - } - - - @Test - public void testParseRelatedEntity() throws IOException { - - final InputStreamReader in = new InputStreamReader(getClass().getResourceAsStream("related_entity.json")); - final RelatedEntity e = new ObjectMapper().readValue(in, RelatedEntity.class); - - System.out.println(e); - - } -} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java deleted file mode 100644 index 2a3c343ec..000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/graph/XmlRecordFactoryTest.java +++ /dev/null @@ -1,55 +0,0 @@ -package eu.dnetlib.dhp.graph; - -import eu.dnetlib.dhp.graph.utils.ContextMapper; -import org.apache.commons.io.FileUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; -import org.apache.spark.sql.SparkSession; -import org.junit.After; -import org.junit.Before; -import org.junit.Test; - -import java.io.File; -import java.io.IOException; -import java.nio.file.Files; -import java.nio.file.Path; - -public class XmlRecordFactoryTest { - - private static final Log log = LogFactory.getLog(XmlRecordFactoryTest.class); - - private Path testDir; - - @Before - public void setup() throws IOException { - testDir = Files.createTempDirectory(getClass().getSimpleName()); - log.info("created test directory " + testDir.toString()); - } - - @After - public void tearDown() throws IOException { - FileUtils.deleteDirectory(testDir.toFile()); - log.info("deleted test directory " + testDir.toString()); - } - - @Test - public void testXmlSerialization() throws Exception { - - final SparkSession spark = SparkSession - .builder() - .appName(SparkXmlRecordBuilderJob.class.getSimpleName()) - .master("local[*]") - .getOrCreate(); - - final String inputDir = testDir.toString() + "/3_joined_entities"; - FileUtils.forceMkdir(new File(inputDir)); - FileUtils.copyFile(new File("/Users/claudio/Downloads/joined_entities-part-00000"), new File(inputDir + "/joined_entities-part-00000")); - - final ContextMapper ctx = ContextMapper.fromIS("https://dev-openaire.d4science.org:443/is/services/isLookUp"); - - final GraphJoiner g = new GraphJoiner(spark, ctx, inputDir, testDir.toString()); - - g.asXML(); - } - -} From ed76521d9b0d5c761262997aa064d980bda46dd5 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Tue, 18 Feb 2020 11:50:39 +0100 Subject: [PATCH 2/4] removed stale test resources, will be re-added later on --- .../src/test/resources/eu/dnetlib/dhp/graph/datasource.json | 1 - .../test/resources/eu/dnetlib/dhp/graph/related_entity.json | 5 ----- .../src/test/resources/eu/dnetlib/dhp/graph/result.json | 1 - .../src/test/resources/eu/dnetlib/dhp/graph/software.json | 1 - 4 files changed, 8 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/software.json diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json deleted file mode 100644 index c26154c1e..000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/datasource.json +++ /dev/null @@ -1 +0,0 @@ -{"source":{"sourceId":"10|CRIS_UNS____::f66f1bd369679b5b077dcdf006089556","targetId":null,"deleted":false,"oaf":"{\"datasourcetype\":{\"classid\":\"crissystem\",\"classname\":\"CRIS System\",\"schemeid\":\"dnet:datasource_typologies\",\"schemename\":\"dnet:datasource_typologies\"},\"openairecompatibility\":{\"classid\":\"openaire-cris_1.1\",\"classname\":\"OpenAIRE CRIS v1.1\",\"schemeid\":\"dnet:datasourceCompatibilityLevel\",\"schemename\":\"dnet:datasourceCompatibilityLevel\"},\"officialname\":{\"value\":\"CRIS UNS (Current Research Information System University of Novi 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\ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json deleted file mode 100644 index 25c92baa3..000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/related_entity.json +++ /dev/null @@ -1,5 +0,0 @@ -{ - "id": "20|nih_________::6b8108b6d6399f7163a6a7ccdd0efc2d", - "type": "organization", - "legalname": "MCGILL UNIVERSITY" -} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json deleted file mode 100644 index 5d6c3f29b..000000000 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/graph/result.json +++ /dev/null @@ -1 +0,0 @@ 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inferred=false, deletedbyinference=false, trust=, inferenceprovenance=, provenanceaction={classid=, classname=, schemeid=, schemename=}}}"]}}]} \ No newline at end of file From e5d7cdf4226e552cd7757563083d218316d636ac Mon Sep 17 00:00:00 2001 From: "sandro.labruzzo" Date: Wed, 19 Feb 2020 10:13:36 +0100 Subject: [PATCH 3/4] fixed sql query --- .../dhp/migration/oozie_app/workflow.xml | 2 +- .../dhp/migration/sql/queryProjects.sql | 19 +++++++++---------- 2 files changed, 10 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml index 309a6d90f..59111b31d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/oozie_app/workflow.xml @@ -43,7 +43,7 @@ - + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql index 6cff18875..685b57ab6 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/migration/sql/queryProjects.sql @@ -28,15 +28,17 @@ SELECT p.summary AS summary, p.currency AS currency, p.totalcost AS totalcost, - p.fundedamount AS fundedamount, + p.fundedamount AS fundedamount, dc.id AS collectedfromid, dc.officialname AS collectedfromname, - ctc.code || '@@@' || ctc.name || '@@@' || cts.code || '@@@' || cts.name AS contracttype, - pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name AS provenanceaction, - array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, - array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects, - array_agg(DISTINCT fp.path) AS fundingtree + p.contracttype || '@@@' || p.contracttypename || '@@@' || p.contracttypescheme || '@@@' || p.contracttypescheme AS contracttype, + pac.code || '@@@' || pac.name || '@@@' || pas.code || '@@@' || pas.name AS provenanceaction, + array_agg(DISTINCT i.pid || '###' || i.issuertype) AS pid, + array_agg(DISTINCT s.name || '###' || sc.code || '@@@' || sc.name || '@@@' || ss.code || '@@@' || ss.name) AS subjects, + array_agg(DISTINCT fp.path) AS fundingtree + FROM projects p + LEFT OUTER JOIN class pac ON (pac.code = p.provenanceactionclass) LEFT OUTER JOIN scheme pas ON (pas.code = p.provenanceactionscheme) @@ -54,9 +56,6 @@ SELECT LEFT OUTER JOIN class sc ON (sc.code = s.semanticclass) LEFT OUTER JOIN scheme ss ON (ss.code = s.semanticscheme) - LEFT OUTER JOIN class ctc ON (ctc.code = p.contracttypeclass) - LEFT OUTER JOIN scheme cts ON (cts.code = p.contracttypescheme) - GROUP BY p.id, p.code, @@ -87,4 +86,4 @@ SELECT dc.id, dc.officialname, pac.code, pac.name, pas.code, pas.name, - ctc.code, ctc.name, cts.code, cts.name; \ No newline at end of file + p.contracttype , p.contracttypename, p.contracttypescheme; \ No newline at end of file From 33185fd0b7e923c36e0f0a451dd1412910f3dcbb Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Wed, 19 Feb 2020 16:56:38 +0100 Subject: [PATCH 4/4] ISLookupClientFactory moved in dhp-common --- dhp-common/pom.xml | 12 ++++++++++++ .../eu/dnetlib/dhp}/utils/ISLookupClientFactory.java | 2 +- dhp-workflows/dhp-graph-provision/pom.xml | 8 -------- .../eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java | 2 +- .../eu/dnetlib/dhp/graph/utils/ContextMapper.java | 1 + pom.xml | 7 +++++++ 6 files changed, 22 insertions(+), 10 deletions(-) rename {dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph => dhp-common/src/main/java/eu/dnetlib/dhp}/utils/ISLookupClientFactory.java (96%) diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 4416bd4ff..a9fb39ea0 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -46,6 +46,18 @@ net.sf.saxon Saxon-HE + + org.slf4j + jcl-over-slf4j + + + org.apache.cxf + cxf-rt-transports-http + + + eu.dnetlib + cnr-rmi-api + diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ISLookupClientFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java similarity index 96% rename from dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ISLookupClientFactory.java rename to dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java index d87f29452..c74cf3c11 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ISLookupClientFactory.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java @@ -1,4 +1,4 @@ -package eu.dnetlib.dhp.graph.utils; +package eu.dnetlib.dhp.utils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.apache.commons.logging.Log; diff --git a/dhp-workflows/dhp-graph-provision/pom.xml b/dhp-workflows/dhp-graph-provision/pom.xml index f74c9b666..ac4e01d21 100644 --- a/dhp-workflows/dhp-graph-provision/pom.xml +++ b/dhp-workflows/dhp-graph-provision/pom.xml @@ -66,14 +66,6 @@ zookeeper - - org.apache.cxf - cxf-rt-transports-http - - - eu.dnetlib - cnr-rmi-api - eu.dnetlib.dhp diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java index 2775d93b4..63ff8fb31 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/SparkXmlIndexingJob.java @@ -2,8 +2,8 @@ package eu.dnetlib.dhp.graph; import com.lucidworks.spark.util.SolrSupport; import eu.dnetlib.dhp.application.ArgumentApplicationParser; -import eu.dnetlib.dhp.graph.utils.ISLookupClientFactory; import eu.dnetlib.dhp.graph.utils.StreamingInputDocumentFactory; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpDocumentNotFoundException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java index 0c3a481d0..ad9e7dfad 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/graph/utils/ContextMapper.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.graph.utils; import com.google.common.base.Joiner; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; import org.dom4j.Document; diff --git a/pom.xml b/pom.xml index 7f5e1e3dc..faed1db35 100644 --- a/pom.xml +++ b/pom.xml @@ -129,6 +129,13 @@ provided + + org.slf4j + jcl-over-slf4j + 1.7.25 + provided + + org.apache.commons commons-lang3