From 9b3a9b2381b2b901122cbd92abcfe80501a466a2 Mon Sep 17 00:00:00 2001 From: miconis Date: Mon, 30 Sep 2024 16:02:01 +0200 Subject: [PATCH] bug fix and test implementation --- .../dhp/oa/dedup/jpath/JsonPathTest.java | 15 + .../oa/dedup/local/DedupLocalTestUtils.java | 26 +- .../oa/dedup/local/SparkDedupLocalTest.java | 31 +- .../dhp/oa/dedup/jpath/dataset_example1.json | 1 + .../oa/dedup/jpath/dedup_conf_dataset.json | 496 ++++++++++++++++++ 5 files changed, 543 insertions(+), 26 deletions(-) create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/dataset_example1.json create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/dedup_conf_dataset.json diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java index 18c9ce18d..4c3850033 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java @@ -54,4 +54,19 @@ class JsonPathTest { Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier"))); } + @Test + void testJPath2() throws IOException { + + DedupConfig conf = DedupConfig + .load(IOUtils.toString(getClass().getResourceAsStream("dedup_conf_dataset.json"))); + + final String dat = IOUtils.toString(getClass().getResourceAsStream("dataset_example1.json")); + + Row row = SparkModel.apply(conf).rowFromJson(dat); + + System.out.println("row = " + row); + Assertions.assertNotNull(row); + Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier"))); + + } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/DedupLocalTestUtils.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/DedupLocalTestUtils.java index 806b1cf38..e584142a9 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/DedupLocalTestUtils.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/DedupLocalTestUtils.java @@ -18,8 +18,10 @@ import org.apache.spark.sql.Row; import org.spark_project.guava.hash.Hashing; import scala.collection.JavaConverters; import scala.collection.convert.Wrappers; +import scala.collection.mutable.ArrayBuffer; import java.io.*; +import java.util.ArrayList; import java.util.List; import java.util.stream.Collectors; @@ -33,17 +35,16 @@ public abstract class DedupLocalTestUtils { if(value.getClass() == String.class){ ret.append("").append(fieldName).append("").append(value).append(""); } - else { - List strings = IteratorUtils.toList(JavaConverters.asJavaIteratorConverter(((Wrappers.JListWrapper) value).iterator()).asJava()); - - if(value.toString().contains("value")) { - List values = strings.stream().map(DedupLocalTestUtils::takeValue).collect(Collectors.toList()); - ret.append("").append(fieldName).append("[").append(String.join(";", values)).append("]"); - } - else { - ret.append("").append(fieldName).append("[").append(String.join(";", strings)).append("]"); - } - + else if(value.getClass() == Wrappers.JListWrapper.class) { + List values = IteratorUtils.toList(JavaConverters.asJavaIteratorConverter(((Wrappers.JListWrapper) value).iterator()).asJava()) + .stream() + .map(DedupLocalTestUtils::takeValue) + .collect(Collectors.toList()); + ret.append("").append(fieldName).append("[").append(String.join(";", values)).append("]"); + } + else if(value.getClass() == ArrayBuffer.class){ + List values = new ArrayList<>(IteratorUtils.toList(JavaConverters.asJavaIteratorConverter(((ArrayBuffer) value).iterator()).asJava())); + ret.append("").append(fieldName).append("[").append(String.join(";", values)).append("]"); } } @@ -122,10 +123,9 @@ public abstract class DedupLocalTestUtils { return rootNode.get("value").toString().replaceAll("\"", ""); } catch (Exception e) { - return ""; + return json; } - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/SparkDedupLocalTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/SparkDedupLocalTest.java index 36460fc08..f362878f7 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/SparkDedupLocalTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/local/SparkDedupLocalTest.java @@ -29,6 +29,7 @@ import org.mockito.junit.jupiter.MockitoExtension; import scala.Tuple2; import scala.Tuple3; import scala.collection.JavaConversions; +import scala.collection.mutable.WrappedArray; import java.awt.*; import java.io.File; @@ -48,15 +49,18 @@ public class SparkDedupLocalTest extends DedupLocalTestUtils { static DedupConfig config; static JavaSparkContext context; - final String entitiesPath = Paths - .get(Objects.requireNonNull(SparkDedupLocalTest.class.getResource("/eu/dnetlib/dhp/dedup/entities/publication")).toURI()) - .toFile() - .getAbsolutePath(); +// final String entitiesPath = Paths +// .get(Objects.requireNonNull(SparkDedupLocalTest.class.getResource("/eu/dnetlib/dhp/dedup/entities/publication")).toURI()) +// .toFile() +// .getAbsolutePath(); - final String dedupConfPath = Paths - .get(Objects.requireNonNull(SparkDedupLocalTest.class.getResource("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")).toURI()) - .toFile() - .getAbsolutePath(); +// final String dedupConfPath = Paths +// .get(Objects.requireNonNull(SparkDedupLocalTest.class.getResource("/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json")).toURI()) +// .toFile() +// .getAbsolutePath(); + + final String entitiesPath = "/Users/miconis/Desktop/pub_to_fix1.json"; + final String dedupConfPath = "/Users/miconis/Desktop/pub.conf.json"; final static int MAX_ACCEPTANCE_DATE = 20; @@ -254,8 +258,8 @@ public class SparkDedupLocalTest extends DedupLocalTestUtils { @Disabled public void matchTest() { - String json1 = "{\"author\":[{\"fullname\":\"Lubarsky, R.\",\"name\":\"R.\",\"pid\":[],\"rank\":1,\"surname\":\"Lubarsky\"},{\"fullname\":\"Plunkett, O. A.\",\"name\":\"O. A.\",\"pid\":[],\"rank\":2,\"surname\":\"Plunkett\"}],\"bestaccessright\":{\"classid\":\"OPEN\",\"classname\":\"Open Access\",\"schemeid\":\"dnet:access_modes\",\"schemename\":\"dnet:access_modes\"},\"collectedfrom\":[{\"key\":\"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357\",\"value\":\"PubMed Central\"},{\"key\":\"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c\",\"value\":\"Europe PubMed Central\"}],\"context\":[],\"contributor\":[],\"country\":[],\"coverage\":[],\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"dateofacceptance\":{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"value\":\"1955-08-01\"},\"dateofcollection\":\"2020-08-03T18:38:58Z\",\"dateoftransformation\":\"\",\"description\":[],\"eoscifguidelines\":[],\"externalReference\":[],\"extraInfo\":[],\"format\":[],\"fulltext\":[],\"id\":\"50|pmid________::df91c1110a2cad1c2e91ca9ef3f1793b\",\"instance\":[{\"accessright\":{\"classid\":\"OPEN\",\"classname\":\"Open Access\",\"schemeid\":\"dnet:access_modes\",\"schemename\":\"dnet:access_modes\"},\"alternateIdentifier\":[],\"collectedfrom\":{\"key\":\"10|opendoar____::eda80a3d5b344bc40f3bc04f65b7a357\",\"value\":\"PubMed Central\"},\"dateofacceptance\":{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"value\":\"1955-08-01\"},\"distributionlocation\":\"\",\"hostedby\":{\"key\":\"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c\",\"value\":\"Europe PubMed Central\"},\"instancetype\":{\"classid\":\"0038\",\"classname\":\"Other literature type\",\"schemeid\":\"dnet:publication_resource\",\"schemename\":\"dnet:publication_resource\"},\"pid\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmc\",\"classname\":\"PubMed Central ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"PMC357660\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmid\",\"classname\":\"PubMed ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"13251984\"}],\"refereed\":{\"classid\":\"0000\",\"classname\":\"UNKNOWN\",\"schemeid\":\"dnet:review_levels\",\"schemename\":\"dnet:review_levels\"},\"url\":[\"https://europepmc.org/articles/PMC357660/\"]},{\"accessright\":{\"classid\":\"UNKNOWN\",\"classname\":\"not available\",\"schemeid\":\"dnet:access_modes\",\"schemename\":\"dnet:access_modes\"},\"alternateIdentifier\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"doi\",\"classname\":\"Digital Object Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"10.1128/jb.70.2.182-186.1955\"}],\"collectedfrom\":{\"key\":\"10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c\",\"value\":\"Europe PubMed Central\"},\"dateofacceptance\":{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"value\":\"1955-08-01\"},\"hostedby\":{\"dataInfo\":{\"deletedbyinference\":false,\"invisible\":false},\"key\":\"10|openaire____::55045bd2a65019fd8e6741a755395c8c\",\"value\":\"Unknown Repository\"},\"instancetype\":{\"classid\":\"0001\",\"classname\":\"Article\",\"schemeid\":\"dnet:publication_resource\",\"schemename\":\"dnet:publication_resource\"},\"pid\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmid\",\"classname\":\"PubMed ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"13251984\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmc\",\"classname\":\"PubMed Central ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"PMC357660\"}],\"refereed\":{\"classid\":\"0000\",\"classname\":\"UNKNOWN\",\"schemeid\":\"dnet:review_levels\",\"schemename\":\"dnet:review_levels\"},\"url\":[\"https://pubmed.ncbi.nlm.nih.gov/13251984\"]}],\"language\":{\"classid\":\"eng\",\"classname\":\"English\",\"schemeid\":\"dnet:languages\",\"schemename\":\"dnet:languages\"},\"lastupdatetimestamp\":1688084171694,\"measures\":[],\"oaiprovenance\":{\"originDescription\":{\"altered\":true,\"baseURL\":\"https://www.ncbi.nlm.nih.gov/pmc/oai/oai.cgi\",\"datestamp\":\"2004-03-04\",\"harvestDate\":\"2018-07-12T21:51:08.484Z\",\"identifier\":\"oai:pubmedcentral.nih.gov:357660\",\"metadataNamespace\":\"http://www.openarchives.org/OAI/2.0/oai_dc/\"}},\"originalId\":[\"oai:pubmedcentral.nih.gov:357660\",\"50|od_______267::273c0e0c3c9813aba26a0f6c22ba3217\",\"od_______267::273c0e0c3c9813aba26a0f6c22ba3217\",\"13251984\",\"PMC357660\"],\"pid\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmc\",\"classname\":\"PubMed Central ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"PMC357660\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmid\",\"classname\":\"PubMed ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"13251984\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmid\",\"classname\":\"PubMed ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"13251984\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmc\",\"classname\":\"PubMed Central ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"PMC357660\"}],\"relevantdate\":[],\"resourcetype\":{\"classid\":\"UNKNOWN\",\"classname\":\"UNKNOWN\",\"schemeid\":\"dnet:dataCite_resource\",\"schemename\":\"dnet:dataCite_resource\"},\"resulttype\":{\"classid\":\"publication\",\"classname\":\"publication\",\"schemeid\":\"dnet:result_typologies\",\"schemename\":\"dnet:result_typologies\"},\"source\":[],\"subject\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"keyword\",\"classname\":\"keyword\",\"schemeid\":\"dnet:subject_classification_typologies\",\"schemename\":\"dnet:subject_classification_typologies\"},\"value\":\"Coccidioides\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"keyword\",\"classname\":\"keyword\",\"schemeid\":\"dnet:subject_classification_typologies\",\"schemename\":\"dnet:subject_classification_typologies\"},\"value\":\"Articles\"},{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"keyword\",\"classname\":\"keyword\",\"schemeid\":\"dnet:subject_classification_typologies\",\"schemename\":\"dnet:subject_classification_typologies\"},\"value\":\"In Vitro Techniques\"}],\"title\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"main title\",\"classname\":\"main title\",\"schemeid\":\"dnet:dataCite_title\",\"schemename\":\"dnet:dataCite_title\"},\"value\":\"IN VITRO PRODUCTION OF THE SPHERULE PHASE OF COCCIDIOIDES IMMITIS1\"}]}"; - String json2 = "{\"author\":[{\"affiliation\":[{\"value\":\"University of California, Los Angeles\"}],\"fullname\":\"R. Lubarsky\",\"pid\":[{\"qualifier\":{\"classid\":\"URL\",\"classname\":\"URL\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"https://academic.microsoft.com/#/detail/2656212943\"}],\"rank\":1},{\"affiliation\":[{\"value\":\"University of California, Los Angeles\"}],\"fullname\":\"O. A. Plunkett\",\"pid\":[{\"qualifier\":{\"classid\":\"URL\",\"classname\":\"URL\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"https://academic.microsoft.com/#/detail/2722962550\"}],\"rank\":2}],\"bestaccessright\":{\"classid\":\"OPEN\",\"classname\":\"Open Access\",\"schemeid\":\"dnet:access_modes\",\"schemename\":\"dnet:access_modes\"},\"collectedfrom\":[{\"key\":\"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2\",\"value\":\"Crossref\"},{\"key\":\"10|openaire____::8ac8380272269217cb09a928c8caa993\",\"value\":\"UnpayWall\"},{\"key\":\"10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a\",\"value\":\"Microsoft Academic Graph\"}],\"context\":[],\"contributor\":[],\"country\":[],\"coverage\":[],\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"dateofacceptance\":{\"value\":\"1955-08-01\"},\"dateofcollection\":\"2023-05-26T02:11:42Z\",\"description\":[],\"eoscifguidelines\":[],\"externalReference\":[],\"extraInfo\":[],\"format\":[],\"fulltext\":[],\"id\":\"50|doi_________::ffffdeb480a1d91049a54768e60930f2\",\"instance\":[{\"accessright\":{\"classid\":\"CLOSED\",\"classname\":\"Closed 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As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using classical histological criteria and quantitative cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of D\\\\u00fcsseldorf. The results of the cytoarchitectonic analysis were then mapped to the reference space, where each voxel was assigned the probability to belong to Area 5Ci (SPL). The probability map of Area 5Ci (SPL) is provided in NifTi format for each hemisphere in the reference space. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and updated probability estimates for new brain structures may in some cases lead to measurable but negligible deviations of existing probability maps, as compared to earlier released datasets. 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B.\", \"pid\": [], \"rank\": 3, \"affiliation\": [], \"fullname\": \"Eickhoff, S. B.\"}, {\"surname\": \"Amunts\", \"name\": \"K.\", \"pid\": [], \"rank\": 4, \"affiliation\": [], \"fullname\": \"Amunts, K.\"}, {\"surname\": \"Schleicher\", \"name\": \"A.\", \"pid\": [], \"rank\": 5, \"affiliation\": [], \"fullname\": \"Schleicher, A.\"}, {\"surname\": \"Hoemke\", \"name\": \"L.\", \"pid\": [], \"rank\": 6, \"affiliation\": [], \"fullname\": \"Hoemke, L.\"}, {\"surname\": \"Mohlberg\", \"name\": \"H.\", \"pid\": [], \"rank\": 7, \"affiliation\": [], \"fullname\": \"Mohlberg, H.\"}, {\"surname\": \"Zilles\", \"name\": \"K.\", \"pid\": [], \"rank\": 8, \"affiliation\": [], \"fullname\": \"Zilles, K.\"}], \"description\": [{\"value\": \"This dataset contains the distinct probabilistic cytoarchitectonic map of Area 5Ci (SPL) in the individual, single subject template of the MNI Colin 27 reference space. As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using classical histological criteria and quantitative cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of D\\\\u00fcsseldorf. The results of the cytoarchitectonic analysis were then mapped to the reference space, where each voxel was assigned the probability to belong to Area 5Ci (SPL). The probability map of Area 5Ci (SPL) is provided in NifTi format for each hemisphere in the reference space. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and updated probability estimates for new brain structures may in some cases lead to measurable but negligible deviations of existing probability maps, as compared to earlier released datasets. Other available data versions of Area 5Ci (SPL): Scheperjans et al. (2019) [Data set, v8.4] [DOI: 10.25493/SQVP-GK1](https://doi.org/10.25493%2FSQVP-GK1) The most probable delineation of Area 5Ci (SPL) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. (2020) [Data set, v2.2] [DOI: 10.25493/TAKY-64D](https://doi.org/10.25493%2FTAKY-64D)\"}], \"instance\": [{\"refereed\": {\"classid\": \"0002\", \"classname\": \"nonPeerReviewed\", \"schemename\": \"dnet:review_levels\", \"schemeid\": \"dnet:review_levels\"}, \"hostedby\": {\"value\": \"EBRAINS\", \"key\": \"10|fairsharing_::2ef3e50fd7c1091dda165f25be7f64fd\"}, \"license\": {\"value\": \"CC BY NC SA\"}, \"url\": [\"https://dx.doi.org/10.25493/bq0h-znc\"], \"pid\": [{\"dataInfo\": {\"invisible\": false, \"trust\": \"0.9\", \"deletedbyinference\": false, \"inferred\": false, \"provenanceaction\": {\"classid\": \"sysimport:actionset\", \"classname\": \"Harvested\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}}, \"qualifier\": {\"classid\": \"doi\", \"classname\": \"Digital Object Identifier\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"10.25493/bq0h-znc\"}], \"instanceTypeMapping\": [{\"originalType\": \"Dataset\", \"typeLabel\": \"dataset\", \"vocabularyName\": \"openaire::coar_resource_types_3_1\", \"typeCode\": \"http://purl.org/coar/resource_type/c_ddb1\"}], \"dateofacceptance\": {\"value\": \"2018-05-22\"}, \"collectedfrom\": {\"value\": \"Datacite\", \"key\": \"10|openaire____::9e3be59865b2c1c335d32dae2fe7b254\"}, \"accessright\": {\"classid\": \"UNKNOWN\", \"classname\": \"not available\", \"schemename\": \"dnet:access_modes\", \"schemeid\": \"dnet:access_modes\"}, \"instancetype\": {\"classid\": \"0021\", \"classname\": \"Dataset\", \"schemename\": \"dnet:publication_resource\", \"schemeid\": \"dnet:publication_resource\"}}], \"dateofcollection\": \"2021-07-20T01:01:03+0000\", \"metaResourceType\": {\"classid\": \"Research Data\", \"classname\": \"Research Data\", \"schemename\": \"openaire::meta_resource_types\", \"schemeid\": \"openaire::meta_resource_types\"}, \"dateoftransformation\": \"2021-07-20T01:01:03+0000\", \"dateofacceptance\": {\"value\": \"2018-05-22\"}, \"publisher\": {\"value\": \"Human Brain Project Neuroinformatics Platform\"}, \"language\": {\"classid\": \"und\", \"classname\": \"Undetermined\", \"schemename\": \"dnet:languages\", \"schemeid\": \"dnet:languages\"}, \"resulttype\": {\"classid\": \"dataset\", \"classname\": \"dataset\", \"schemename\": \"dnet:result_typologies\", \"schemeid\": \"dnet:result_typologies\"}, \"title\": [{\"qualifier\": {\"classid\": \"main title\", \"classname\": \"main title\", \"schemename\": \"dnet:dataCite_title\", \"schemeid\": \"dnet:dataCite_title\"}, \"value\": \"Probabilistic cytoarchitectonic map of Area 5Ci (SPL) (v8.2)\"}], \"originalId\": [\"50|datacite____::7f98d6c254b0d743c4634412ed94817b\", \"10.25493/bq0h-znc\"], \"context\": []}"; Row a = model.rowFromJson(json1); Row b = model.rowFromJson(json2); @@ -270,8 +274,8 @@ public class SparkDedupLocalTest extends DedupLocalTestUtils { @Disabled public void blockingTest() { - String json1 = "{\"author\":[{\"affiliation\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"value\":\"CSC - IT Centre for Science\"}],\"fullname\":\"Minna Lappalainen\",\"name\":\"\",\"pid\":[],\"rank\":1,\"surname\":\"\"}],\"bestaccessright\":{\"classid\":\"OPEN\",\"classname\":\"Open Access\",\"schemeid\":\"dnet:access_modes\",\"schemename\":\"dnet:access_modes\"},\"collectedfrom\":[{\"key\":\"10|opendoar____::358aee4cc897452c00244351e4d91f69\",\"value\":\"ZENODO\"}],\"context\":[{\"dataInfo\":[{\"deletedbyinference\":false,\"inferenceprovenance\":\"bulktagging\",\"inferred\":true,\"invisible\":false,\"provenanceaction\":{\"classid\":\"community:datasource\",\"classname\":\"Inferred by OpenAIRE\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.8\"}],\"id\":\"eosc\"}],\"contributor\":[],\"country\":[],\"coverage\":[],\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"dateofacceptance\":{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"value\":\"2023-02-21\"},\"dateofcollection\":\"2023-09-05T02:17:42+0000\",\"dateoftransformation\":\"2023-09-05T10:28:52.475Z\",\"description\":[{\"dataInfo\":{\"deletedbyinference\":false,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"value\":\"

This presentation gives an introduction to LUMI's new model for business.

It was delivered at the Special Interest Group on Marketing and Communications on February 21, 2023.

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As part of the Julich-Brain cytoarchitectonic atlas, the area was identified using classical histological criteria and quantitative cytoarchitectonic analysis on cell-body-stained histological sections of 10 human postmortem brains obtained from the body donor program of the University of D\\\\u00fcsseldorf. The results of the cytoarchitectonic analysis were then mapped to the reference space, where each voxel was assigned the probability to belong to Area 5Ci (SPL). The probability map of Area 5Ci (SPL) is provided in NifTi format for each hemisphere in the reference space. The Julich-Brain atlas relies on a modular, flexible and adaptive framework containing workflows to create the probabilistic brain maps for these structures. Note that methodological improvements and updated probability estimates for new brain structures may in some cases lead to measurable but negligible deviations of existing probability maps, as compared to earlier released datasets. Other available data versions of Area 5Ci (SPL): Scheperjans et al. (2019) [Data set, v8.4] [DOI: 10.25493/SQVP-GK1](https://doi.org/10.25493%2FSQVP-GK1) The most probable delineation of Area 5Ci (SPL) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. 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Row a = model.rowFromJson(json1); Row b = model.rowFromJson(json2); @@ -283,7 +287,8 @@ public class SparkDedupLocalTest extends DedupLocalTestUtils { .transform(deduper.generateClustersWithCollect()); for (Row r: rowsDS.toJavaRDD().collect()) { - System.out.println("block = " + r); + System.out.println("block key = " + r.get(0)); + System.out.println("block size = " + r.get(1)); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/dataset_example1.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/dataset_example1.json new file mode 100644 index 000000000..c129755f3 --- /dev/null +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/dataset_example1.json @@ -0,0 +1 @@ +{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": true, "inferred": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "resourcetype": {"classid": "UNKNOWN", "classname": "UNKNOWN", "schemename": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource"}, "pid": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.25493/cg41-q6u"}], "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "issued", "classname": "issued", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2018-05-22"}, {"qualifier": {"classid": "available", "classname": "available", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2018-03-31"}], "collectedfrom": [{"value": "Datacite", "key": "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254"}], "id": "50|doi_________::098cabeb288616a6a4ae7e950f2a372e", "subject": [{"qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Neuroscience"}], "embargoenddate": {"value": "2018-03-31"}, "author": [{"surname": "Scheperjans", "name": "F.", "pid": [], "rank": 1, "affiliation": [], "fullname": "Scheperjans, F."}, {"surname": "Hermann", "name": "K.", "pid": [], "rank": 2, "affiliation": [], "fullname": "Hermann, K."}, {"surname": "Eickhoff", "name": "S. B.", "pid": [], "rank": 3, "affiliation": [], "fullname": "Eickhoff, S. B."}, {"surname": "Amunts", "name": "K.", "pid": [], "rank": 4, "affiliation": [], "fullname": "Amunts, K."}, {"surname": "Schleicher", "name": "A.", "pid": [], "rank": 5, "affiliation": [], "fullname": "Schleicher, A."}, {"surname": "Hoemke", "name": "L.", "pid": [], "rank": 6, "affiliation": [], "fullname": "Hoemke, L."}, {"surname": "Mohlberg", "name": "H.", "pid": [], "rank": 7, "affiliation": [], "fullname": "Mohlberg, H."}, {"surname": "Zilles", "name": "K.", "pid": [], "rank": 8, "affiliation": [], "fullname": "Zilles, K."}], "description": [{"value": "This dataset contains the distinct probabilistic cytoarchitectonic map of Area 5M (SPL) in the individual, single subject template of the MNI Colin 27 reference space. 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Other available data versions of Area 5M (SPL): Scheperjans et al. (2019) [Data set, v8.4] [DOI: 10.25493/Y12F-YMU](https://doi.org/10.25493%2FY12F-YMU) The most probable delineation of Area 5M (SPL) derived from the calculation of a maximum probability map of all currently released Julich-Brain brain structures can be found here: Amunts et al. (2019) [Data set, v1.13] [DOI: 10.25493/Q3ZS-NV6](https://doi.org/10.25493%2FQ3ZS-NV6) Amunts et al. (2019) [Data set, v1.18] [DOI: 10.25493/8EGG-ZAR](https://doi.org/10.25493%2F8EGG-ZAR) Amunts et al. 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