Maintenance message, add source (PM or PMC) to mapping file.

JULIELab · Sep 5, 2024 · 68e2aab · 68e2aab
1 parent 9e7ab40
commit 68e2aab
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Showing 22 changed files with 223 additions and 121 deletions.
diff --git a/gepi/gepi-indexing/gepi-indexing-base/pom.xml b/gepi/gepi-indexing/gepi-indexing-base/pom.xml
@@ -25,7 +25,7 @@
  <dependency>
  <groupId>de.julielab</groupId>
  <artifactId>jcore-descriptor-creator</artifactId>
- <version>2.6.0-SNAPSHOT</version>
+ <version>2.6.1</version>
  <scope>provided</scope>
  </dependency>
  </dependencies>

diff --git a/...pi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java b/...pi-indexing-base/src/main/java/de/julielab/gepi/indexing/RelationFieldValueGenerator.java
@@ -184,7 +184,7 @@ else if (j > i)
  String arg2EntryIdPath = "/ref/resourceEntryList[" + l + "]/entryId";
  document.addField("argument1", createRawFieldValueForParallelAnnotations(new FeatureStructure[]{argPair[0], argPair[0], argPair[0], argPair[0], argPair[0]}, new String[]{arg1EntryIdPath, arg1EntryIdPath, arg1EntryIdPath, arg1EntryIdPath, arg1EntryIdPath}, new Filter[]{geneFb.orgid2tid2atidAddonFilter, geneFb.eg2famplexFilter, geneFb.eg2hgncFilter, geneFb.eg2gohypertidFilter, geneFb.orgid2equalnameatidReplaceFilter}, new UniqueFilter()));
 // document.addField("argument1geneid", createRawFieldValueForAnnotation(argPair[0], arg1EntryIdPath, null));
-// document.addField("argument1taxid", createRawFieldValueForAnnotation(argPair[0], arg1EntryIdPath, geneFb.egid2taxidReplaceFilter));
+ document.addField("argument1taxid", createRawFieldValueForAnnotation(argPair[0], arg1EntryIdPath, geneFb.egid2taxidReplaceFilter));
 // document.addField("argument1conceptid", createRawFieldValueForAnnotation(argPair[0], arg1EntryIdPath, geneFb.eg2tidReplaceFilter));
 // document.addField("argument1tophomoid", createRawFieldValueForAnnotation(argPair[0], arg1EntryIdPath, geneFb.eg2tophomoFilter));
 // document.addField("argument1famplexid", createRawFieldValueForAnnotation(argPair[0], arg1EntryIdPath, geneFb.eg2famplexFilter));
@@ -202,7 +202,7 @@ else if (j > i)
 // document.addField("argument1genemappingsource", createRawFieldValueForAnnotation(argPair[0], "/ref/resourceEntryList[" + k + "]/componentId", geneComponentIdProcessingfilter));
  document.addField("argument2", createRawFieldValueForParallelAnnotations(new FeatureStructure[]{argPair[1], argPair[1], argPair[1], argPair[1], argPair[1]}, new String[]{arg2EntryIdPath, arg2EntryIdPath, arg2EntryIdPath, arg2EntryIdPath, arg2EntryIdPath}, new Filter[]{geneFb.orgid2tid2atidAddonFilter, geneFb.eg2famplexFilter, geneFb.eg2hgncFilter, geneFb.eg2gohypertidFilter, geneFb.orgid2equalnameatidReplaceFilter}, new UniqueFilter()));
 // document.addField("argument2geneid", createRawFieldValueForAnnotation(argPair[1], arg2EntryIdPath, null));
-// document.addField("argument2taxid", createRawFieldValueForAnnotation(argPair[1], arg2EntryIdPath, geneFb.egid2taxidReplaceFilter));
+ document.addField("argument2taxid", createRawFieldValueForAnnotation(argPair[1], arg2EntryIdPath, geneFb.egid2taxidReplaceFilter));
 // document.addField("argument2conceptid", createRawFieldValueForAnnotation(argPair[1], arg2EntryIdPath, geneFb.eg2tidReplaceFilter));
 // document.addField("argument2tophomoid", createRawFieldValueForAnnotation(argPair[1], arg2EntryIdPath, geneFb.eg2tophomoFilter));
 // document.addField("argument2famplexid", createRawFieldValueForAnnotation(argPair[1], arg2EntryIdPath, geneFb.eg2famplexFilter));

diff --git a/gepi/gepi-indexing/gepi-indexing-base/src/main/resources/elasticSearchMapping.json b/gepi/gepi-indexing/gepi-indexing-base/src/main/resources/elasticSearchMapping.json
@@ -27,6 +27,10 @@
  "enabled": false
  },
  "properties": {
+ "source": {
+ "type": "text",
+ "store": true
+ },
  "pmid": {
  "type": "keyword",
  "store": true
@@ -103,6 +107,9 @@
  "type": "keyword",
  "store": true
  },
+ "argument1taxid": {
+ "type": "keyword"
+ },
  "argument1coveredtext": {
  "type": "text",
  "store": true,
@@ -160,6 +167,9 @@
  "type": "keyword",
  "store": true
  },
+ "argument2taxid": {
+ "type": "keyword"
+ },
  "argument2coveredtext": {
  "type": "text",
  "store": true,
@@ -314,16 +324,8 @@
  "headings": {
  "type": "text",
  "norms": false,
- "store": true,
- "copy_to": ["paragraph.headingscompletion", "paragraph.headingskw"]
- },
- "headingskw": {
- "type": "keyword",
  "store": true
  },
- "headingscompletion": {
- "type": "completion"
- },
  "textscope": {
  "type": "keyword",
  "store": true

diff --git a/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCore ElasticSearch Consumer.xml b/gepi/gepi-indexing/gepi-indexing-pmc/descAll/JCore ElasticSearch Consumer.xml
@@ -29,6 +29,34 @@
 
  </configurationParameter>
 
+ <configurationParameter>
+
+ <name>docIdTransformBeforeDeletionRegex</name>
+
+ <description>Optional regular expression to match and then replace (parts) of document IDs before deletion using the docIdTransformBeforeDeletionReplacement parameter value. Can be used when deleteDocumentsBeforeIndexing is set to true. Then, a Matcher with the given regular expression is created and document IDs are transformed using Matcher.replaceAll(&lt;replacement&gt;) for the deletion step.</description>
+
+ <type>String</type>
+
+ <multiValued>false</multiValued>
+
+ <mandatory>false</mandatory>
+
+ </configurationParameter>
+
+ <configurationParameter>
+
+ <name>docIdTransformBeforeDeletionReplacement</name>
+
+ <description>Optional replacement String to be used to transform document IDs before deletion. Requires docIdTransformBeforeDeletionRegex to be specified. Then, document IDs used for deletion are matched with that regular expression and matches are replaced with this replacement String using Matcher.replace(&lt;replacement&gt;) where the Matcher was created with the regular expression.</description>
+
+ <type>String</type>
+
+ <multiValued>false</multiValued>
+
+ <mandatory>false</mandatory>
+
+ </configurationParameter>
+
  <configurationParameter>
 
  <name>documentIdField</name>
@@ -195,7 +223,7 @@
 
  <value>
 
- <string>gepi_1.0_3</string>
+ <string>gepi_1.0_2</string>
 
  </value>
 
@@ -253,7 +281,31 @@
 
  <value>
 
- <boolean>false</boolean>
+ <boolean>true</boolean>
+
+ </value>
+
+ </nameValuePair>
+
+ <nameValuePair>
+
+ <name>docIdTransformBeforeDeletionRegex</name>
+
+ <value>
+
+ <string>^([^_]+)_.*$</string>
+
+ </value>
+
+ </nameValuePair>
+
+ <nameValuePair>
+
+ <name>docIdTransformBeforeDeletionReplacement</name>
+
+ <value>
+
+ <string>$1</string>
 
  </value>
 

diff --git a/gepi/gepi-indexing/gepi-indexing-pubmed/descAll/JCore ElasticSearch Consumer.xml b/gepi/gepi-indexing/gepi-indexing-pubmed/descAll/JCore ElasticSearch Consumer.xml
@@ -195,7 +195,7 @@
 
  <value>
 
- <string>gepi_1.0_3</string>
+ <string>gepi_1.0_2</string>
 
  </value>
 

diff --git a/gepi/gepi-preprocessing/pmc/preprocessing/aeDescriptions.json b/gepi/gepi-preprocessing/pmc/preprocessing/aeDescriptions.json
@@ -1 +1 @@
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Schwartz and Marti A. Hearst: A Simple Algorithm For Identifying Abbreviation Definitions in Biomedical Text. 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+[{"uri":null,"location":"de.julielab.jcore.ae.jsbd.desc.jcore-jsbd-ae-biomedical-english","category":"ae","uimaDescPath":null,"metaDescription":{"description":"UIMA Wrapper for the JCoRe Sentence Boundary Detector (jcore-jsbd-ae) with a model trained on data from both the GENIA and PennBioIE corpus as well as additional material from MedLine abstracts.","group":"general","module":{"type":"GitHubRepository","name":"jcore-projects","version":"v2.4","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["ae"],"name":"JCoRe Sentence Annotator, Biomedical English","pear":false,"base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-jsbd-ae-biomedical-english","version":"2.6.1","classifier":null,"file":"/home/faessler/.m2/repository/de/julielab/jcore-jsbd-ae-biomedical-english/2.6.1/jcore-jsbd-ae-biomedical-english-2.6.1.jar","packaging":"jar"}},"name":"JCoRe Sentence Annotator","active":true},{"uri":null,"location":"de.julielab.jcore.ae.jtbd.desc.jcore-jtbd-ae-biomedical-english","category":"ae","uimaDescPath":null,"metaDescription":{"description":"UIMA Wrapper for the JCoRe Token Boundary Detector with a model trained on a special biomedical corpus which consists of data from (manually annotated) material which we took from MedLine abstracts and a modified version of PennBioIE's underlying tokenization.\n","group":"general","module":{"type":"GitHubRepository","name":"jcore-projects","version":"v2.5","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["ae"],"name":"JCoRe Token Annotator, Biomedical English","pear":false,"base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-jtbd-ae-biomedical-english","version":"2.6.0","classifier":null,"file":"/home/faessler/.m2/repository/de/julielab/jcore-jtbd-ae-biomedical-english/2.6.0/jcore-jtbd-ae-biomedical-english-2.6.0.jar","packaging":"jar"}},"name":"JCoRe Token Annotator","active":true},{"uri":null,"location":"de.julielab.jcore.ae.opennlp.postag.desc.jcore-opennlp-postag-ae-biomedical-english","category":"ae","uimaDescPath":null,"metaDescription":{"description":"This project employs the OpenNLP wrapper (jcore-opennlp-postag-ae) with a model trained on the PennBioIE corpus.","group":"general","module":{"type":"GitHubRepository","name":"jcore-projects","version":"v2.5","updateable":true,"type":"GitHubRepository","gitHubName":"JULIELab"},"base":null,"exposable":true,"categories":["ae"],"name":"JCoRe OpenNLP POS Tagger, Biomedical English","pear":false,"base-project":null,"maven-artifact":{"groupId":"de.julielab","artifactId":"jcore-opennlp-postag-ae-biomedical-english","version":"2.6.0","classifier":null,"file":"/home/faessler/.m2/repository/de/julielab/jcore-opennlp-postag-ae-biomedical-english/2.6.0/jcore-opennlp-postag-ae-biomedical-english-2.6.0.jar","packaging":"jar"}},"name":"JCoRe OpenNLP POS Tagger","active":true},{"uri":null,"location":"de.julielab.jcore.ae.acronymtagger.desc.jcore-acronym-ae","category":"ae","uimaDescPath":null,"metaDescription":{"description":"Arconym Tagger based on the SCHWARTZ & HEARST Algorithm: Ariel S. Schwartz and Marti A. Hearst: A Simple Algorithm For Identifying Abbreviation Definitions in Biomedical Text. 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