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@khituras
khituras committed Apr 10, 2022
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6 changes: 3 additions & 3 deletions ...pi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java
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Expand Up @@ -135,23 +135,23 @@ public IFieldValue generateFieldValue(FeatureStructure fs) throws FieldGeneratio
document.addField("argumentcoveredtext", createRawFieldValueForAnnotations(argPair, "/:coveredText()"));
document.addField("argumentprefnames", createRawFieldValueForAnnotations(argPair, "/ref/resourceEntryList/entryId", geneFb.egid2prefNameReplaceFilter));
document.addField("argumenthomoprefnames", createRawFieldValueForAnnotations(argPair, "/ref/resourceEntryList/entryId", geneFb.egid2homoPrefNameReplaceFilter));
document.addField("argumentmatchtypes", Stream.of(argPair).map(ArgumentMention.class::cast).map(ArgumentMention::getRef).map(ConceptMention.class::cast).map(cm -> cm.getResourceEntryList(0).getConfidence().contains("9999") ? "exact" : "fuzzy").toArray());
document.addField("argumentmatchtypes", Stream.of(argPair).map(ArgumentMention.class::cast).map(ArgumentMention::getRef).map(ConceptMention.class::cast).map(cm -> cm.getResourceEntryList(0).getConfidence() == null || cm.getResourceEntryList(0).getConfidence().contains("9999") ? "exact" : "fuzzy").toArray());
document.addField("argument1", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList/entryId", geneFb.gene2tid2atidAddonFilter));
document.addField("argument1geneid", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList/entryId", null));
document.addField("argument1conceptid", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList/entryId", geneFb.eg2tidReplaceFilter));
document.addField("argument1tophomoid", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList/entryId", geneFb.eg2tophomoFilter));
document.addField("argument1coveredtext", createRawFieldValueForAnnotation(argPair[0], "/:coveredText()", null));
document.addField("argument1prefname", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList/entryId", geneFb.egid2prefNameReplaceFilter));
document.addField("argument1homoprefname", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList/entryId", geneFb.egid2homoPrefNameReplaceFilter));
document.addField("argument1matchtype", Stream.of(argPair).map(ArgumentMention.class::cast).map(ArgumentMention::getRef).map(ConceptMention.class::cast).map(cm -> cm.getResourceEntryList(0).getConfidence().contains("9999") ? "exact" : "fuzzy").toArray());
document.addField("argument1matchtype", Stream.of(argPair).map(ArgumentMention.class::cast).map(ArgumentMention::getRef).map(ConceptMention.class::cast).map(cm -> cm.getResourceEntryList(0).getConfidence() == null || cm.getResourceEntryList(0).getConfidence().contains("9999") ? "exact" : "fuzzy").toArray());
document.addField("argument2", createRawFieldValueForAnnotation(argPair[1], "/ref/resourceEntryList/entryId", geneFb.gene2tid2atidAddonFilter));
document.addField("argument2geneid", createRawFieldValueForAnnotation(argPair[1], "/ref/resourceEntryList/entryId", null));
document.addField("argument2conceptid", createRawFieldValueForAnnotation(argPair[1], "/ref/resourceEntryList/entryId", geneFb.eg2tidReplaceFilter));
document.addField("argument2tophomoid", createRawFieldValueForAnnotation(argPair[1], "/ref/resourceEntryList/entryId", geneFb.eg2tophomoFilter));
document.addField("argument2coveredtext", createRawFieldValueForAnnotation(argPair[1], "/:coveredText()", null));
document.addField("argument2prefname", createRawFieldValueForAnnotation(argPair[1], "/ref/resourceEntryList/entryId", geneFb.egid2prefNameReplaceFilter));
document.addField("argument2homoprefname", createRawFieldValueForAnnotation(argPair[1], "/ref/resourceEntryList/entryId", geneFb.egid2homoPrefNameReplaceFilter));
document.addField("argument2matchtype", Stream.of(argPair).map(ArgumentMention.class::cast).map(ArgumentMention::getRef).map(ConceptMention.class::cast).map(cm -> cm.getResourceEntryList(0).getConfidence().contains("9999") ? "exact" : "fuzzy").toArray());
document.addField("argument2matchtype", Stream.of(argPair).map(ArgumentMention.class::cast).map(ArgumentMention::getRef).map(ConceptMention.class::cast).map(cm -> cm.getResourceEntryList(0).getConfidence() == null || cm.getResourceEntryList(0).getConfidence().contains("9999") ? "exact" : "fuzzy").toArray());
document.addField("maineventtype", createRawFieldValueForAnnotation(rel.getRootRelation(), "/specificType", null));
document.addField("alleventtypes", Stream.of(rel.getRelations().toArray()).map(EventMention.class::cast).map(EventMention::getSpecificType).collect(Collectors.toSet()).toArray());
document.addField("ARGUMENT_FS", argPair);
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2 changes: 1 addition & 1 deletion gepi/gepi-indexing/gepi-indexing-pubmed/aeDescriptions.json
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2 changes: 1 addition & 1 deletion gepi/gepi-indexing/gepi-indexing-pubmed/ccDescriptions.json
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[{"uri":"file:/Users/faessler/Coding/git/gepi/gepi/gepi-indexing/gepi-indexing-pubmed/./desc/JCoRe%20Database%20Checkpoint%20Writer.xml","location":"de.julielab.jcore.ae.checkpoint.desc.jcore-db-checkpoint-consumer","category":"consumer","uimaDescPath":"JCoRe Database Checkpoint Writer.xml","metaDescription":{"description":"This is a JeDIS component. It can be used to set the 'last component' column in a subset table. This help to keep track of the pipeline status.","group":"general","module":{"type":"GitHubRepository","name":"jcore-base","version":"v2.6","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["consumer","ae"],"pear":false,"name":"JCoRe Database Checkpoint AE","base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-db-checkpoint-ae","version":"2.6.0-SNAPSHOT","classifier":null,"file":"/Users/faessler/.m2/repository/de/julielab/jcore-db-checkpoint-ae/2.6.0-SNAPSHOT/jcore-db-checkpoint-ae-2.6.0-SNAPSHOT.jar","packaging":"jar"}},"name":"JCoRe Database Checkpoint Writer","active":true},{"uri":"file:/Users/faessler/Coding/git/gepi/gepi/gepi-indexing/gepi-indexing-pubmed/./desc/JCoRe%20Neo4j%20Relations%20Consumer.xml","location":"de.julielab.jcore.consumer.neo4jrelations.desc.jcore-neo4j-relations-consumer","category":"consumer","uimaDescPath":"JCoRe Neo4j Relations Consumer.xml","metaDescription":{"description":"Writes EventMentions to Neo4j.","group":"general","module":{"type":"GitHubRepository","name":"jcore-base","version":"v2.6","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["consumer"],"pear":false,"name":"JCoRe Neo4j Relations Consumer","base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-neo4j-relations-consumer","version":"2.6.0-SNAPSHOT","classifier":null,"file":"/Users/faessler/.m2/repository/de/julielab/jcore-neo4j-relations-consumer/2.6.0-SNAPSHOT/jcore-neo4j-relations-consumer-2.6.0-20210618.074226-31.jar","packaging":"jar"}},"name":"JCoRe Neo4j Relations Consumer","active":true},{"uri":"file:/Users/faessler/Coding/git/gepi/gepi/gepi-indexing/gepi-indexing-pubmed/./desc/JCore%20ElasticSearch%20Consumer.xml","location":"de.julielab.jcore.consumer.es.desc.jcore-elasticsearch-consumer","category":"consumer","uimaDescPath":"JCore ElasticSearch Consumer.xml","metaDescription":{"description":"This component converts CAS annotations into a JSON format that originates from Solr's preanalyzed field type. At the JulieLab, there is an ElasticSearch plugin making this format accessible also by ElasticSearch. Configuration happens right in Java code. Note that the component is also able to generate perfectly valid ElasticSearch default JSON which does not require the plugin. Then, however, the preanalyzed data format cannot be used because this is the format that required the ElasticSearch plugin.","group":"general","module":{"type":"GitHubRepository","name":"jcore-base","version":"v2.6","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["consumer"],"pear":false,"name":"JCoRe ElasticSearch Consumer","base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-elasticsearch-consumer","version":"2.6.0-SNAPSHOT","classifier":null,"file":"/Users/faessler/.m2/repository/de/julielab/jcore-elasticsearch-consumer/2.6.0-SNAPSHOT/jcore-elasticsearch-consumer-2.6.0-SNAPSHOT.jar","packaging":"jar"}},"name":"JCore ElasticSearch Consumer","active":true}]
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2 changes: 1 addition & 1 deletion gepi/gepi-indexing/gepi-indexing-pubmed/cmDescriptions.json
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[{"uri":null,"location":"de.julielab.jcore.reader.xmi.desc.jcore-xmi-db-multiplier","category":"multiplier","uimaDescPath":"JCoRe Abstract Database Multiplier.xml","metaDescription":{"description":"Reads CAS XMI data from a relational database (Postgres). Thus, the stored CASes may then be processed further.","group":"general","module":{"type":"GitHubRepository","name":"jcore-base","version":"v2.6","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["multiplier","reader"],"pear":false,"name":"JCoRe XMI Database Reader","base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-xmi-db-reader","version":"2.6.0-SNAPSHOT","classifier":null,"file":"/Users/faessler/.m2/repository/de/julielab/jcore-xmi-db-reader/2.6.0-SNAPSHOT/jcore-xmi-db-reader-2.6.0-SNAPSHOT.jar","packaging":"jar"}},"name":"JCoRe Abstract Database Multiplier","active":true}]
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