update lucene and content of nameindex based on dyntaxa and gbif-backbone taxonomy

Author: shahmanash

Makefile

@@ -237,8 +237,8 @@ build:
 	@docker build -t bioatlas/ala-apikey -t bioatlas/ala-apikey:v0.3 apikey
 	@docker build -t bioatlas/ala-cassandra -t bioatlas/ala-cassandra:v0.4 cassandra3
 	@docker build -t bioatlas/ala-solr -t bioatlas/ala-solr:v0.4 solr7
-	@docker build -t bioatlas/ala-dyntaxaindex -t bioatlas/ala-dyntaxaindex:v0.3 dyntaxa-index
-	@docker build -t bioatlas/ala-nameindex -t bioatlas/ala-nameindex:v0.3 nameindex
+	@docker build -t bioatlas/ala-dyntaxaindex -t bioatlas/ala-dyntaxaindex:v0.4 dyntaxa-index
+	@docker build -t bioatlas/ala-nameindex -t bioatlas/ala-nameindex:v0.4 nameindex
 #	@docker build -t bioatlas/ala-dashboard -t bioatlas/ala-dashboard:v0.3 dashboard
 
 up:
@@ -273,8 +273,8 @@ pull:
 	@docker pull bioatlas/ala-apikey:v0.3
 	@docker pull bioatlas/ala-cassandra:v0.4
 	@docker pull bioatlas/ala-solr:v0.4
-	@docker pull bioatlas/ala-dyntaxaindex:v0.3
-	@docker pull bioatlas/ala-nameindex:v0.3
+	@docker pull bioatlas/ala-dyntaxaindex:v0.4
+	@docker pull bioatlas/ala-nameindex:v0.4
 
 pull2:
 	@echo "Downloading other official docker images ..."
@@ -311,8 +311,8 @@ push:
 	@docker push bioatlas/ala-apikey:v0.3
 	@docker push bioatlas/ala-cassandra:v0.4
 	@docker push bioatlas/ala-solr:v0.4
-	@docker push bioatlas/ala-dyntaxaindex:v0.3
-	@docker push bioatlas/ala-nameindex:v0.3
+	@docker push bioatlas/ala-dyntaxaindex:v0.4
+	@docker push bioatlas/ala-nameindex:v0.4
 
 release: build push
 

dyntaxa-index/Dockerfile

@@ -16,13 +16,7 @@ RUN chmod 777 /usr/lib/nameindexer/nameindexer && \
 	cat /usr/lib/nameindexer/nameindexer.jar >> /usr/lib/nameindexer/nameindexer && \
 	ln -s /usr/lib/nameindexer/nameindexer /usr/bin/nameindexer
 
-RUN nameindexer --all --dwca /data/lucene/sources/dyntaxa --common /data/lucene/sources/dyntaxa/VernacularName.tsv
-
-ADD http://central.maven.org/maven2/org/apache/lucene/lucene-core/6.6.5/lucene-core-6.6.5.jar /tmp/
-ADD http://central.maven.org/maven2/org/apache/lucene/lucene-backward-codecs/6.6.5/lucene-backward-codecs-6.6.5.jar /tmp/
-
-RUN java -cp /tmp/lucene-core-6.6.5.jar:/tmp/lucene-backward-codecs-6.6.5.jar org.apache.lucene.index.IndexUpgrader -delete-prior-commits /data/lucene/namematching/cb
-RUN java -cp /tmp/lucene-core-6.6.5.jar:/tmp/lucene-backward-codecs-6.6.5.jar org.apache.lucene.index.IndexUpgrader -delete-prior-commits /data/lucene/namematching/vernacular
+RUN nameindexer --all --dwca /data/lucene/sources/dyntaxa --common /data/lucene/sources/dyntaxa/VernacularName.csv
 
 RUN rm -rf /data/lucene/sources/*
 

dyntaxa-index/nameindexer.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
-exec java -Dlog4j.configuration=file:/usr/lib/nameindexer/log4j.xml -Dfile.encoding=UTF8 -Djava.util.Arrays.useLegacyMergeSort=true -Xmx1g -Xms1g -jar $0 "$@"
+exec java -Dlog4j.configuration=file:/usr/lib/nameindexer/log4j.xml -Dfile.encoding=UTF8 -Djava.util.Arrays.useLegacyMergeSort=true -Xmx8g -Xms1g -jar $0 "$@"
 
 

nameindex/Dockerfile

@@ -23,13 +23,6 @@ RUN chmod 777 /usr/lib/nameindexer/nameindexer && \
 
 RUN nameindexer --all --dwca /data/lucene/sources/backbone --irmng /data/lucene/sources/IRMNG_DWC_HOMONYMS --common /data/lucene/sources/backbone/VernacularName.tsv
 
-ADD http://central.maven.org/maven2/org/apache/lucene/lucene-core/6.6.5/lucene-core-6.6.5.jar /tmp/
-ADD http://central.maven.org/maven2/org/apache/lucene/lucene-backward-codecs/6.6.5/lucene-backward-codecs-6.6.5.jar /tmp/
-
-RUN java -cp /tmp/lucene-core-6.6.5.jar:/tmp/lucene-backward-codecs-6.6.5.jar org.apache.lucene.index.IndexUpgrader -delete-prior-commits /data/lucene/namematching/cb
-RUN java -cp /tmp/lucene-core-6.6.5.jar:/tmp/lucene-backward-codecs-6.6.5.jar org.apache.lucene.index.IndexUpgrader -delete-prior-commits /data/lucene/namematching/irmng
-RUN java -cp /tmp/lucene-core-6.6.5.jar:/tmp/lucene-backward-codecs-6.6.5.jar org.apache.lucene.index.IndexUpgrader -delete-prior-commits /data/lucene/namematching/vernacular
-
 RUN rm -rf /data/lucene/sources/*
 
 VOLUME /data/lucene/namematching

nameindex/nameindexer.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
-exec java -Dlog4j.configuration=file:/usr/lib/nameindexer/log4j.xml -Dfile.encoding=UTF8 -Djava.util.Arrays.useLegacyMergeSort=true -Xmx1g -Xms1g -jar $0 "$@"
+exec java -Dlog4j.configuration=file:/usr/lib/nameindexer/log4j.xml -Dfile.encoding=UTF8 -Djava.util.Arrays.useLegacyMergeSort=true -Xmx8g -Xms1g -jar $0 "$@"