From 003a58fbe09a09f665f8734093f9523fccb5f337 Mon Sep 17 00:00:00 2001 From: khituras Date: Sun, 10 Apr 2022 14:57:25 +0200 Subject: [PATCH] Minor changes. --- .../julielab/gepi/indexing/RelationFieldValueGenerator.java | 6 +++--- gepi/gepi-indexing/gepi-indexing-pubmed/aeDescriptions.json | 2 +- gepi/gepi-indexing/gepi-indexing-pubmed/ccDescriptions.json | 2 +- gepi/gepi-indexing/gepi-indexing-pubmed/cmDescriptions.json | 2 +- gepi/gepi-indexing/gepi-indexing-pubmed/crDescriptions.json | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/gepi/gepi-indexing/gepi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java b/gepi/gepi-indexing/gepi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java index 5e5eac11..ebe54ecd 100644 --- a/gepi/gepi-indexing/gepi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java +++ b/gepi/gepi-indexing/gepi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java @@ -135,7 +135,7 @@ 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)); @@ -143,7 +143,7 @@ public IFieldValue generateFieldValue(FeatureStructure fs) throws FieldGeneratio 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)); @@ -151,7 +151,7 @@ public IFieldValue generateFieldValue(FeatureStructure fs) throws FieldGeneratio 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); diff --git a/gepi/gepi-indexing/gepi-indexing-pubmed/aeDescriptions.json b/gepi/gepi-indexing/gepi-indexing-pubmed/aeDescriptions.json index 2082b619..f803d561 100644 --- a/gepi/gepi-indexing/gepi-indexing-pubmed/aeDescriptions.json +++ b/gepi/gepi-indexing/gepi-indexing-pubmed/aeDescriptions.json @@ -1 +1 @@ -[{"uri":null,"location":"de.julielab.jcore.ae.likelihooddetection.desc.jcore-likelihood-detection-ae","category":"ae","uimaDescPath":null,"metaDescription":{"description":"Analysis Engine to detect epistemic modal expressions and assign the appropriate likelihood category.","group":"general","module":{"type":"GitHubRepository","name":"jcore-base","version":"v2.6","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["ae"],"pear":false,"name":"JCoRe Likelihood Detection AE","base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-likelihood-detection-ae","version":"2.6.0-SNAPSHOT","classifier":null,"file":"/Users/faessler/.m2/repository/de/julielab/jcore-likelihood-detection-ae/2.6.0-SNAPSHOT/jcore-likelihood-detection-ae-2.6.0-20210618.074215-31.jar","packaging":"jar"}},"name":"JCoRe Likelihood Detection AE","active":true},{"uri":null,"location":"de.julielab.jcore.ae.likelihoodassignment.desc.jcore-likelihood-assignment-ae","category":"ae","uimaDescPath":null,"metaDescription":{"description":"Analysis Engine to assign likelihood indicators to their corresponding entities and events.","group":"general","module":{"type":"GitHubRepository","name":"jcore-base","version":"v2.6","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["ae"],"pear":false,"name":"JCoRe Likelihood Assignment AE","base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-likelihood-assignment-ae","version":"2.6.0-SNAPSHOT","classifier":null,"file":"/Users/faessler/.m2/repository/de/julielab/jcore-likelihood-assignment-ae/2.6.0-SNAPSHOT/jcore-likelihood-assignment-ae-2.6.0-20210618.074150-31.jar","packaging":"jar"}},"name":"JCoRe Likelihood Assignment AE","active":true},{"uri":null,"location":"de.julielab.jcore.ae.eventflattener.desc.jcore-event-flattener-ae","category":"ae","uimaDescPath":null,"metaDescription":{"description":"This component reads de.julielab.jcore.types.EventMention annotations and converts event structures into de.julielab.jcore.types.ext.FlattenedRelation annotation. 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