diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
index d0098e7e2c..bcc5ddeaa6 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
@@ -81,6 +81,10 @@ public class SparkDedupTest implements Serializable {
lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("publication")))
.thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")));
+
+ lenient().when(isLookUpService.getResourceProfileByQuery(Mockito.contains("software")))
+ .thenReturn(IOUtils.toString(SparkDedupTest.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json")));
+
}
@Test
@@ -101,9 +105,11 @@ public class SparkDedupTest implements Serializable {
long orgs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel").count();
long pubs_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel").count();
+ long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
assertEquals(3288, orgs_simrel);
assertEquals(7260, pubs_simrel);
+ assertEquals(344, sw_simrel);
}
@Test
@@ -124,10 +130,11 @@ public class SparkDedupTest implements Serializable {
long orgs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").count();
long pubs_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel").count();
+ long sw_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel").count();
assertEquals(1244, orgs_mergerel);
assertEquals(1460, pubs_mergerel);
-
+ assertEquals(288, sw_mergerel);
}
@Test
@@ -148,9 +155,11 @@ public class SparkDedupTest implements Serializable {
long orgs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_deduprecord").count();
long pubs_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_deduprecord").count();
+ long sw_deduprecord = jsc.textFile(testOutputBasePath + "/" + testActionSetId + "/software_deduprecord").count();
assertEquals(82, orgs_deduprecord);
assertEquals(66, pubs_deduprecord);
+ assertEquals(51, sw_deduprecord);
}
@Test
@@ -171,6 +180,9 @@ public class SparkDedupTest implements Serializable {
long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
long publications = jsc.textFile(testDedupGraphBasePath + "/publication").count();
+ long projects = jsc.textFile(testDedupGraphBasePath + "/project").count();
+ long datasource = jsc.textFile(testDedupGraphBasePath + "/datasource").count();
+ long softwares = jsc.textFile(testDedupGraphBasePath + "/software").count();
long mergedOrgs = spark
.read().load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel").as(Encoders.bean(Relation.class))
@@ -188,6 +200,9 @@ public class SparkDedupTest implements Serializable {
assertEquals(897, publications);
assertEquals(835, organizations);
+ assertEquals(100, projects);
+ assertEquals(100, datasource);
+ assertEquals(200, softwares);
long deletedOrgs = jsc.textFile(testDedupGraphBasePath + "/organization")
.filter(this::isDeletedByInference).count();
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json
new file mode 100644
index 0000000000..5329005067
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json
@@ -0,0 +1,118 @@
+{
+ "wf" : {
+ "threshold" : "0.99",
+ "dedupRun" : "001",
+ "entityType" : "result",
+ "subEntityType" : "resulttype",
+ "subEntityValue" : "dataset",
+ "orderField" : "title",
+ "queueMaxSize" : "2000",
+ "groupMaxSize" : "100",
+ "maxChildren" : "100",
+ "slidingWindowSize" : "200",
+ "rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
+ "includeChildren" : "true"
+ },
+ "pace" : {
+ "clustering" : [
+ { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+ { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+ { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
+ ],
+ "decisionTree" : {
+ "start" : {
+ "fields": [
+ {
+ "field": "pid",
+ "comparator": "jsonListMatch",
+ "weight": 1.0,
+ "countIfUndefined": "false",
+ "params": {
+ "jpath_value": "$.value",
+ "jpath_classid": "$.qualifier.classid"
+ }
+ }
+ ],
+ "threshold": 0.5,
+ "aggregation": "AVG",
+ "positive": "MATCH",
+ "negative": "layer2",
+ "undefined": "layer2",
+ "ignoreUndefined": "true"
+ },
+ "layer2" : {
+ "fields": [
+ {
+ "field": "title",
+ "comparator": "titleVersionMatch",
+ "weight": 1.0,
+ "countIfUndefined": "false",
+ "params": {}
+ },
+ {
+ "field": "authors",
+ "comparator": "sizeMatch",
+ "weight": 1.0,
+ "countIfUndefined": "false",
+ "params": {}
+ }
+ ],
+ "threshold": 1.0,
+ "aggregation": "AND",
+ "positive": "layer3",
+ "negative": "NO_MATCH",
+ "undefined": "layer3",
+ "ignoreUndefined": "false"
+ },
+ "layer3" : {
+ "fields": [
+ {
+ "field": "title",
+ "comparator": "levensteinTitle",
+ "weight": 1.0,
+ "countIfUndefined": "true"
+ }
+ ],
+ "threshold": 0.99,
+ "aggregation": "AVG",
+ "positive": "MATCH",
+ "negative": "NO_MATCH",
+ "undefined": "NO_MATCH",
+ "ignoreUndefined": "true"
+ }
+ },
+ "model" : [
+ {
+ "name" : "doi",
+ "type" : "String",
+ "path" : "$.pid[@.qualifier.classid = 'doi'].value"
+ },
+ {
+ "name" : "pid",
+ "type" : "JSON",
+ "path" : "$.pid",
+ "overrideMatch" : "true"
+ },
+ {
+ "name" : "title",
+ "type" : "String",
+ "path" : "$.title[@.qualifier.classid = 'main title'].value",
+ "length" : 250,
+ "size" : 5
+ },
+ {
+ "name" : "authors",
+ "type" : "String",
+ "path" : "$.author[*].fullname",
+ "size" : 200
+ },
+ {
+ "name" : "resulttype",
+ "type" : "String",
+ "path" : "$.resulttype.classid"
+ }
+ ],
+ "blacklists" : {},
+ "synonyms" : {}
+ }
+}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json
new file mode 100644
index 0000000000..76e656743f
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json
@@ -0,0 +1,118 @@
+{
+ "wf" : {
+ "threshold" : "0.99",
+ "dedupRun" : "001",
+ "entityType" : "result",
+ "subEntityType" : "resulttype",
+ "subEntityValue" : "otherresearchproduct",
+ "orderField" : "title",
+ "queueMaxSize" : "2000",
+ "groupMaxSize" : "100",
+ "maxChildren" : "100",
+ "slidingWindowSize" : "200",
+ "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
+ "includeChildren" : "true"
+ },
+ "pace" : {
+ "clustering" : [
+ { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+ { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+ { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
+ ],
+ "decisionTree" : {
+ "start" : {
+ "fields": [
+ {
+ "field": "pid",
+ "comparator": "jsonListMatch",
+ "weight": 1.0,
+ "countIfUndefined": "false",
+ "params": {
+ "jpath_value": "$.value",
+ "jpath_classid": "$.qualifier.classid"
+ }
+ }
+ ],
+ "threshold": 0.5,
+ "aggregation": "AVG",
+ "positive": "MATCH",
+ "negative": "layer2",
+ "undefined": "layer2",
+ "ignoreUndefined": "true"
+ },
+ "layer2" : {
+ "fields": [
+ {
+ "field": "title",
+ "comparator": "titleVersionMatch",
+ "weight": 1.0,
+ "countIfUndefined": "false",
+ "params": {}
+ },
+ {
+ "field": "authors",
+ "comparator": "sizeMatch",
+ "weight": 1.0,
+ "countIfUndefined": "false",
+ "params": {}
+ }
+ ],
+ "threshold": 1.0,
+ "aggregation": "AND",
+ "positive": "layer3",
+ "negative": "NO_MATCH",
+ "undefined": "layer3",
+ "ignoreUndefined": "false"
+ },
+ "layer3" : {
+ "fields": [
+ {
+ "field": "title",
+ "comparator": "levensteinTitle",
+ "weight": 1.0,
+ "countIfUndefined": "true"
+ }
+ ],
+ "threshold": 0.99,
+ "aggregation": "AVG",
+ "positive": "MATCH",
+ "negative": "NO_MATCH",
+ "undefined": "NO_MATCH",
+ "ignoreUndefined": "true"
+ }
+ },
+ "model" : [
+ {
+ "name" : "doi",
+ "type" : "String",
+ "path" : "$.pid[@.qualifier.classid = 'doi'}].value"
+ },
+ {
+ "name" : "pid",
+ "type" : "JSON",
+ "path" : "$.pid",
+ "overrideMatch" : "true"
+ },
+ {
+ "name" : "title",
+ "type" : "String",
+ "path" : "$.title[@.qualifier.classid = 'main title'].value",
+ "length" : 250,
+ "size" : 5
+ },
+ {
+ "name" : "authors",
+ "type" : "String",
+ "path" : "$.author[*].fullname",
+ "size" : 200
+ },
+ {
+ "name" : "resulttype",
+ "type" : "String",
+ "path" : "$.resulttype.classid"
+ }
+ ],
+ "blacklists" : {},
+ "synonyms" : {}
+ }
+}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json
new file mode 100644
index 0000000000..815dd7a572
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json
@@ -0,0 +1,92 @@
+ {
+ "wf" : {
+ "threshold" : "0.99",
+ "dedupRun" : "001",
+ "entityType" : "result",
+ "subEntityType" : "resulttype",
+ "subEntityValue" : "software",
+ "orderField" : "title",
+ "queueMaxSize" : "2000",
+ "groupMaxSize" : "100",
+ "maxChildren" : "100",
+ "slidingWindowSize" : "200",
+ "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
+ "includeChildren" : "true"
+ },
+ "pace" : {
+ "clustering" : [
+ { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+ { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+ { "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
+ ],
+ "decisionTree": {
+ "start": {
+ "fields": [
+ {
+ "field": "doi",
+ "comparator": "exactMatch",
+ "weight": 1,
+ "countIfUndefined": "false",
+ "params": {}
+ },
+ {
+ "field": "url",
+ "comparator": "exactMatch",
+ "weight": 1,
+ "countIfUndefined": "false",
+ "params": {}
+ }
+ ],
+ "threshold": 1,
+ "aggregation": "OR",
+ "positive": "MATCH",
+ "negative": "layer2",
+ "undefined": "layer2",
+ "ignoreUndefined": "false"
+ },
+ "layer2": {
+ "fields": [
+ {
+ "field": "title",
+ "comparator": "levensteinTitleIgnoreVersion",
+ "weight": 1,
+ "countIfUndefined": "false",
+ "params": {}
+ }
+ ],
+ "threshold": 0.99,
+ "aggregation": "AVG",
+ "positive": "MATCH",
+ "negative": "NO_MATCH",
+ "undefined": "NO_MATCH",
+ "ignoreUndefined": "false"
+ }
+ },
+ "model" : [
+ {
+ "name" : "doi",
+ "type" : "String",
+ "path" : "$.pid[?(@.qualifier.classid == 'doi')].value"
+ },
+ {
+ "name" : "title",
+ "type" : "String",
+ "path" : "$.title[?(@.qualifier.classid == 'main title')].value",
+ "length" : 250,
+ "size" : 5
+ },
+ {
+ "name" : "url",
+ "type" : "String",
+ "path" : "$.instance.url"
+ },
+ {
+ "name" : "resulttype",
+ "type" : "String",
+ "path" : "$.resulttype.classid"
+ }
+ ],
+ "blacklists" : {},
+ "synonyms": {}
+ }
+ }
\ No newline at end of file
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource
index e69de29bb2..f54cbf0716 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/datasource
@@ -0,0 +1,100 @@
+{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk:entityregistry', "classname": "sysimport:crosswalk:entityregistry', "schemename": "dnet:provenance_actions', "schemeid": "dnet:provenance_actions'}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9'}, "datauploadtype": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "accessinfopackage": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://dspace-cris.4science.cloud/oai/openairecris'}], "pid": [], "websiteurl": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "https://www.4science.it'}, "dateofvalidation": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "logourl": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "collectedfrom": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "", "key": ""}], "qualitymanagementkind": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "id": "10|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556', "odnumberofitems": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "lastupdatetimestamp": 0, "odnumberofitemsdate": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "serviceprovider": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": false}, "namespaceprefix": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "4ScienceCRIS'}, "contactemail": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "subjects": [], "databaseaccessrestriction": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "latitude": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": "0.0'}, "dateofcollection": "2019-11-04', "releasestartdate": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "dateoftransformation": "", "description": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "journal": {"issnPrinted": "", "conferencedate": "", "conferenceplace": "", "name": "", "edition": "", "vol": "", "sp": "", "iss": "", "dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "issnOnline": "", "ep": "", "issnLinking": ""}, "citationguidelineurl": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "releaseenddate": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "datauploadrestriction": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "certificates": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "", "classname": "", "schemename": "", "schemeid": ""}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": ""}, "value": ""}, "missionstatementurl": {"dataInfo": {"deletedbyinference": false, 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diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/project b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/project
index e69de29bb2..e04415c428 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/project
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/project
@@ -0,0 +1,100 @@
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diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software
index e69de29bb2..06b0d3276e 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/entities/software
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\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************
\\n\\n
\\n--- Overview ---
\\nThis software numerically solves the equation of motion for a network of long (entangled) polymer chains.
\\n\\nThe physics and math were originally described in this publication: (attached here)
\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. "Simulation of entangled polymer solutions." The Journal of Chemical Physics 145.12 (2016): 124113.
\\n\\nThe extension for shear flow is described in this article: (also attached)
\\nAiridas Korolkovas, Philipp Gutfreund, and Maximilian Wolff. "Dynamical structure of entangled polymers simulated under shear flow." (in preparation)
\\n\\n
\\n--- System requirements ---
\\nThe code runs in Matlab, and was tested for the Matlab 2016a version. There is both a CPU and a GPU option (about 10-50x faster).
\\nTo run the GPU code effectively, a CUDA-enabled Nvidia card is required. Quadro M5000 model was tested to give acceptable performance.
\\n\\n
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\\n************* by Airidas Korolkovas *************\\n\\n
\\n--- Overview ---
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\\n--------------------------------------------------
\\n************* by Airidas Korolkovas *************
\\n\\n
\\n--- Overview ---
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\\nAiridas Korolkovas, Philipp Gutfreund, and Jean-Louis Barrat. \"Simulation of entangled polymer solutions.\" The Journal of Chemical Physics 145.12 (2016): 124113.
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\\n\\n\\n\\t- ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)
\\n\\t- ENH: Created interface for BrainSuite Cortical Surface Extraction command line tools (https://github.com/nipy/nipype/pull/1305)
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\\n\\t- ENH: Provides a Nipype wrapper for antsJointFusion (https://github.com/nipy/nipype/pull/1351)
\\n\\t- ENH: Added support for PETPVC (https://github.com/nipy/nipype/pull/1335)
\\n\\t- ENH: Merge S3DataSink into DataSink, added AWS documentation (https://github.com/nipy/nipype/pull/1316)
\\n\\t- TST: Cache APT in CircleCI (https://github.com/nipy/nipype/pull/1333)
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\\n\\t- FIX: Use released Prov python library (https://github.com/nipy/nipype/pull/1279)
\\n\\t- ENH: Support for Python 3 (https://github.com/nipy/nipype/pull/1221)
\\n\\t- FIX: VTK version check missing when using tvtk (https://github.com/nipy/nipype/pull/1219)
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\\n\\t- API: Default model level for the bedpostx workflow has been set to "2" following FSL 5.0.9 lead
\\n\\t- ENH: New interfaces for interacting with AWS S3: S3DataSink and S3DataGrabber (https://github.com/nipy/nipype/pull/1201)
\\n\\t- ENH: Interfaces for MINC tools (https://github.com/nipy/nipype/pull/1304)
\\n\\t- FIX: Use realpath to determine hard link source (https://github.com/nipy/nipype/pull/1388)
\\n\\t- FIX: Correct linking/copying fallback behavior (https://github.com/nipy/nipype/pull/1391)
\\n\\t- ENH: Nipype workflow and interfaces for FreeSurfer's recon-all (https://github.com/nipy/nipype/pull/1326)
\\n\\t- FIX: Permit relative path for concatenated_file input to Concatenate() (https://github.com/nipy/nipype/pull/1411)
\\n\\t- ENH: Makes ReconAll workflow backwards compatible with FreeSurfer 5.3.0 (https://github.com/nipy/nipype/pull/1434)
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This software package was developed for use with MATLAB 2016a running on Windows. Users can execute the main script immediately, provided all attached files are located in the same directory and that directory is included in the MATLAB path. One must then enter \"main_simulate_C\" in the MATLAB command line.
Updated Zenodo badge to point to v2.0 of the tutorial.
\\n\\nAdded updated citations and DOI (for PSA paper in PLOS Computational Biology):
\\n\\nSeyler SL, Kumar A, Thorpe MF, Beckstein O (2015) Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways. PLoS Comput Biol. doi: 10.1371/journal.pcbi.1004568 (also: arXiv:1505.04807 [q-bio.QM])
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diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml
index 9a4871223c..42d3f0b698 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/profiles/mock_orchestrator.xml
@@ -14,6 +14,7 @@
+
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