new

common/aratiny/README.md

@@ -91,7 +91,7 @@ is at <http://localhost:17490/>
 ## Using the `aratinty` project for Cypher-based semantic motif queries.
 
 The neo4j mode uses Cypher-based queries for finding paths between genes to other entities. The queries are
-at [aratiny-ws/src/test/resources/knetminer-config/neo4j](aratiny-ws/src/test/resources/knetminer-config/neo4j). Any
+in the [test folder](aratiny-ws/src/test/resources/knetminer-dataset/config/neo4j). Any
 addition of .cypher files to this folder will be used by the `./run-ws-neo4j.sh` above to initially scan the 
 test data and find the paths specified by the queries.
 
@@ -103,7 +103,7 @@ UI).
 
 ### Rules for valid semantic motif queries 
 
-Let's look at [an example](aratiny-ws/src/test/resources/knetminer-config/neo4j/simple-protein-publication.cypher):
+Let's look at [an example](aratiny-ws/src/test/resources/knetminer-dataset/config/neo4j/simple-protein-publication.cypher):
 
 ```sql
 MATCH path =  

common/quickstart/cleanup-volume.sh

@@ -34,8 +34,13 @@ cd "$dataset_dir"
 cd config
 rm -Rf *
 
-echo -e "\tCleaning config"
+echo -e "\tCleaning data"
 cd ../data
 rm -Rf *.tab index map*
 
+echo -e "\tCleaning client-src"
+cd ..
+rm -Rf client-src
+
+echo -e "\t"
 echo -e "\n\tThe end\n"

common/quickstart/runtime-helper.sh

@@ -112,10 +112,10 @@ rm -Rf /tmp/aratiny-ws common/aratiny/aratiny-ws/target
 cp -Rf common/aratiny/aratiny-ws /tmp
 
 # We don't need the test queries used for aratiny, let's remove them from the build location
-rm -Rf /tmp/aratiny-ws/src/test/resources/knetminer-config/neo4j/*.cypher
+rm -Rf /tmp/aratiny-ws/src/test/resources/knetminer-dataset/config/neo4j/*.cypher
 
 # And then copy the dataset-specific config to the build place (in /tmp) 
-cp -Rf "$knet_dataset_dir/settings/ws/"* /tmp/aratiny-ws/src/test/resources/knetminer-config
+cp -Rf "$knet_dataset_dir/settings/ws/"* /tmp/aratiny-ws/src/test/resources/knetminer-dataset/config
 
 # Eventually, go to the build place and do mvn test-compile. This creates interpolated config files (ie, 
 # all the placeholders are instantiated with the values in maven settings or in ancestor POMS).  
@@ -125,7 +125,7 @@ cd /tmp/aratiny-ws
 mvn $MAVEN_ARGS --settings "$knet_dataset_dir/config/actual-maven-settings.xml" clean test-compile
 
 # End eventually, deploy the instantiated config files
-cp -Rf target/test-classes/knetminer-config/* "$knet_dataset_dir/config"
+cp -Rf target/test-classes/knetminer-dataset/config/* "$knet_dataset_dir/config"
 
 
 
@@ -172,7 +172,7 @@ cp target/knetminer-aratiny.war "$knet_tomcat_home/webapps/client.war"
 # --- And eventually run the server, which will have the ws.war (from the Docker build), the new client .war and the server config.
 # 
 
-if [ "$is_deploy_only" != '' ]; then
+if [ "$is_deploy_only" != '' ]; then
 	echo -e "\n\n\tFiles deployed at '$knet_tomcat_home/webapps/', not running Tomcat because of --deploy-only\n"
 	exit
 fi

common/server-datasource-ondexlocal/src/main/java/rres/knetminer/datasource/ondexlocal/OndexServiceProvider.java

@@ -698,7 +698,7 @@ public HashMap<ONDEXConcept, Float> searchLucene(String keywords, Collection<OND
             // Query qAccessions =
             // LuceneQueryBuilder.searchConceptByConceptAccessionExact(keyword,
             // false, dsAcc);
-            String fieldName = getFieldName("ConceptAccessions", dsAc);
+            String fieldName = getFieldName("ConceptAccession", dsAc);
             // QueryParser parser = new QueryParser(Version.LUCENE_36, fieldName, analyzer);
             QueryParser parser = new QueryParser(fieldName, analyzer);
             Query qAccessions = parser.parse(keyword);