Indexer improvements

console.gradle

@@ -67,9 +67,10 @@ task createUIIndex(type: JavaExec) {
     main = 'org.zfin.indexer.UiIndexer'
 }
 
-task runChebiPhenotypeIndexer(type: JavaExec) {
+task runPhenotypeIndexer(type: JavaExec) {
     classpath = sourceSets.main.runtimeClasspath
     main = 'org.zfin.indexer.UiIndexer'
+    args 'TermPhenotype'
     args 'ChebiPhenotype'
 }
 

server_apps/DB_maintenance/build.xml

@@ -86,20 +86,6 @@
             <jvmarg value="${jvm.arg.log4j}"/>
         </java>
     </target>
-    <target name="update-ui-tables" description="">
-        <java classname="org.zfin.indexer.TermPageIndexer"
-              fork="yes"
-              classpathref="extended.classpath"
-              failonerror="true">
-            <arg value="-webrootDirectory"/>
-            <arg value="${web.dir}"/>
-            <arg value="-loadDir"/>
-            <arg value="server_apps/DB_maintenance/validatedata"/>
-            <arg value="-jobName"/>
-            <arg value="Regenerate-UI-Tables_d"/>
-            <jvmarg value="${jvm.arg.log4j}"/>
-        </java>
-    </target>
 
 
     <target name="load-gaf-goa" description="">

server_apps/DB_maintenance/warehouse/regenPhenotypeMart.sh

@@ -95,15 +95,15 @@ date;
 echo "done with pheno_term_regen()";
 
 
-echo "start gradle runChebiPhenotypeIndexer";
+echo "start gradle runPhenotypeIndexer";
 cd $SOURCEROOT
-gradle runChebiPhenotypeIndexer
+gradle runPhenotypeIndexer
 if ($? != 0) then
-   echo "gradle runChebiPhenotypeIndexer failed";
+   echo "gradle runPhenotypeIndexer failed";
 exit 1;
 endif
 date;
-echo "done with gradle runChebiPhenotypeIndexer";
+echo "done with gradle runPhenotypeIndexer";
 
 
 

source/org/zfin/db/postGmakePostloaddb/1145/db.changelog.master.xml

@@ -6,4 +6,5 @@
                       http://www.liquibase.org/xml/ns/dbchangelog/dbchangelog-3.1.xsd">
     <include file="source/org/zfin/db/postGmakePostloaddb/1145/ZFIN-8522.sql" />
     <include file="source/org/zfin/db/postGmakePostloaddb/1145/ZFIN-8625.sql" />
+    <include file="source/org/zfin/db/postGmakePostloaddb/1145/indexer-tuning.sql" />
 </databaseChangeLog>

source/org/zfin/db/postGmakePostloaddb/1145/indexer-tuning.sql

@@ -0,0 +1,44 @@
+--liquibase formatted sql
+--changeset cmpich:indexer-tuning.sql
+
+CREATE INDEX term_phenotype_display_term ON UI.TERM_PHENOTYPE_DISPLAY
+    (
+     tpd_term_zdb_id
+        );
+
+CREATE INDEX term_phenotype_display_fish ON UI.TERM_PHENOTYPE_DISPLAY
+    (
+     tpd_fish_zdb_id
+        );
+
+CREATE INDEX term_phenotype_display_fig ON UI.TERM_PHENOTYPE_DISPLAY
+    (
+     tpd_fig_zdb_id
+        );
+
+CREATE INDEX term_phenotype_display_pub ON UI.TERM_PHENOTYPE_DISPLAY
+    (
+     tpd_pub_zdb_id
+        );
+
+CREATE INDEX phenotype_warehouse_association_warehouse ON UI.PHENOTYPE_WAREHOUSE_ASSOCIATION
+    (
+     pwa_phenotype_warehouse_id
+    );
+
+CREATE INDEX phenotype_warehouse_association_phenotype ON UI.PHENOTYPE_WAREHOUSE_ASSOCIATION
+    (
+     pwa_phenotype_id
+    );
+
+CREATE INDEX phenotype_zfin_association_gene ON UI.PHENOTYPE_ZFIN_ASSOCIATION
+    (
+     pza_gene_zdb_id
+    );
+
+CREATE INDEX phenotype_zfin_association_phenotype ON UI.PHENOTYPE_ZFIN_ASSOCIATION
+    (
+     pza_phenotype_id
+    );
+
+