Changes to reflect simplier method of dataset instantiation

Updated class IVFLookup to support instantiation of dataset indexes
from the property metamaplite.index.directory.  Scripts, config files,
and README file where also updated to reflect change.

removed duplicate class IVFTermInfoLookup

README.md

@@ -257,12 +257,8 @@ These properties can be set using a System property
 ### Configuration properties
 
     | metamaplite.excluded.termsfile        | cui/terms pairs that are exclude from results (default: data/specialterms.txt)
-    | metamaplite.index.directory           | the directory the indexes resides (sets the following properties)
-    | metamaplite.ivf.cuiconceptindex       | cui/concept/preferredname index
-    | metamaplite.ivf.cuisourceinfoindex    | cui/sourceinfo index 
-    | metamaplite.ivf.cuisemantictypeindex  | cui/semantictype index
-
-    | opennlp.models.directory              | the directory the models resides (sets the following properties. default: data/models)
+    | metamaplite.index.directory           | the directory the indexes reside
+    | opennlp.models.directory              | the directory the models reside (sets the following properties. default: data/models)
     | opennlp.en-pos.bin.path               | (default: data/models/en-pos-maxent.bin)
     | opennlp.en-token.bin.path             | (default: data/models/en-token.bin)
     | opennlp.en-sent.bin.path              | (default: data/models/en-sent.bin)
@@ -484,11 +480,7 @@ Use the --indexdir=<directory> option:
 
 Or modify the configuration file config/metamap.properties:
 
-    metamaplite.ivf.cuiconceptindex: <ivfdir>/indices/cuiconcept
-    metamaplite.ivf.cuisourceinfoindex: <ivfdir>/indices/cuisourceinfo
-    metamaplite.ivf.cuisemantictypeindex: <ivfdir>/indices/cuist
-	metamaplite.ivf.varsindex: <ivfdir>/indices/vars
-    metamaplite.ivf.meshtcrelaxedindex: <ivfdir>/indices/meshtcrelaxed
+    metamaplite.index.directory: <ivfdir>
 
 ## Adding custom input document formats
 
@@ -582,8 +574,8 @@ directory and specify that in servlet:
         try {
           this.properties = new Properties();
           // default properties that can be overriden 
-          this.properties.setProperty("metamaplite.ivf.cuiconceptindex","data/ivf/strict/indices/cuiconcept");
-          ...
+          this.properties.setProperty("metamaplite.index.directory","data/ivf/strict");
+		  ...
           // load user properties
           this.properties.load(new FileReader(configPropertyFilename));
           this.metaMapLiteInst = new MetaMapLite(this.properties);

config/bioc.metamaplite.properties

@@ -8,11 +8,7 @@
 # metamaplite.varsindex: data/lucenedb/strict/vars
 
 # irutils indexes 
-metamaplite.ivf.cuiconceptindex: data/ivf/strict/indices/cuiconcept
-metamaplite.ivf.cuisourceinfoindex: data/ivf/strict/indices/cuisourceinfo
-metamaplite.ivf.cuisemantictypeindex: data/ivf/strict/indices/cuist
-metamaplite.ivf.varsindex: data/ivf/strict/indices/vars
-metamaplite.ivf.meshtcrelaxedindex: data/ivf/strict/indices/meshtcrelaxed
+metamaplite.index.directory=@@basedir@@/data/ivf/@@year@@/@@subset@@
 
 # OpenNLP model files
 opennlp.en-sent.bin.path:/net/indlx1/export/home/wjrogers/Projects/metamaplite/data/models/en-sent.bin

config/metamaplite.properties

@@ -8,11 +8,7 @@
 # metamaplite.varsindex: data/lucenedb/strict/vars
 
 # irutils indexes 
-metamaplite.ivf.cuiconceptindex: data/ivf/strict/indices/cuiconcept
-metamaplite.ivf.cuisourceinfoindex: data/ivf/strict/indices/cuisourceinfo
-metamaplite.ivf.cuisemantictypeindex: data/ivf/strict/indices/cuist
-metamaplite.ivf.varsindex: data/ivf/strict/indices/vars
-metamaplite.ivf.meshtcrelaxedindex: data/ivf/strict/indices/meshtcrelaxed
+metamaplite.index.directory: data/ivf/strict
 
 # default semantic.type.list: if not defined is empty (all semantic types) 
 #   semantic type abbreviations separated by commas.

config/metamaplite.properties.in

@@ -8,12 +8,7 @@ metamaplite.cuisemantictypeindex: @@basedir@@/data/lucenedb/cui_st
 metamaplite.varsindex: @@basedir@@/data/lucenedb/vars
 
 # Inverted Files
-metamaplite.ivf.cuiconceptindex: @@basedir@@/data/ivf/@@year@@/@@subset@@/indices/cuiconcept
-metamaplite.ivf.firstwordsofonewideindex: @@basedir@@/data/ivf/@@year@@/@@subset@@/indices/first_words_of_one_WIDE
-metamaplite.ivf.cuisourceinfoindex: @@basedir@@/data/ivf/@@year@@/@@subset@@/indices/cuisourceinfo
-metamaplite.ivf.cuisemantictypeindex: @@basedir@@/data/ivf/@@year@@/@@subset@@/indices/cuist
-metamaplite.ivf.varsindex: @@basedir@@/data/ivf/@@year@@/@@subset@@/indices/vars
-metamaplite.ivf.meshtcrelaxedindex: @@basedir@@/data/ivf/@@year@@/@@subset@@/indices/meshtcrelaxed
+metamaplite.index.directory=@@basedir@@/data/ivf/@@year@@/@@subset@@
 
 # default semantic.type.list: if not defined is empty (all semantic types) 
 #   semantic type abbreviations separated by commas.

metamaplite.bat

@@ -1,5 +1,8 @@
 ::
-echo off
+:: A simplified metamaplite batch script using metamaplite standalone
+:: jar, should work in Command Prompt and maybe PowerShell on Windows.
+
+@echo off
 
 set projectdir=%cd%
 
@@ -10,7 +13,7 @@ set CONFIGDIR=$PROJECTDIR/config
 
 set MML_JVM_OPTS=-Xmx12g
 
-set METAMAPLITE=%projectdir%/target/metamaplite-%MML_VERSION%%-standalone.jar
+set METAMAPLITE=%projectdir%/target/metamaplite-%MML_VERSION%-standalone.jar
 
 set JARSPATH=%METAMAPLITE%
 
@@ -24,13 +27,11 @@ set JVMOPTS=-Den-sent.bin.path=%OPENNLP_MODELS%/en-sent.bin ^
 -Dlog4j.configurationFile=file:///%projectdir%/config/log4j2.xml ^
 -Dmetamaplite.property.file=%CONFIGDIR%/metamaplite.properties ^
 -Dmetamaplite.entitylookup.resultlength=1500 ^
--Dmetamaplite.ivf.cuiconceptindex=%projectdir%/data/ivf/strict/cuiconcept ^
--Dmetamaplite.ivf.firstwordsofonewideindex=%projectdir%/data/ivf/strict/first_words_of_one_WIDE ^
--Dmetamaplite.ivf.cuisourceinfoindex=%projectdir%/data/ivf/strict/cuisourceinfo ^
--Dmetamaplite.ivf.cuisemantictypeindex=%projectdir%/data/ivf/strict/cuist ^
--Dmetamaplite.ivf.varsindex=%projectdir%/data/ivf/strict/vars ^
--Dmetamaplite.ivf.meshtcrelaxedindex=$PROJECTDIR/data/ivf/strict/indices/meshtcrelaxed
-
-java -cp %projectdir%/target/classes;%projectdir%/build/classes;%projectdir%/classes;%JARSPATH%;%CONFIGDIR% ^
+-Dmetamaplite.index.directory=%projectdir%/data/ivf/2019AB/USAbase ^
+-Dmetamaplite.excluded.termsfile=%projectdir%/data/specialterms.txt
+
+java -cp %projectdir%/target/classes;%projectdir%/build/classes;%projectdir%/classes;%JARSPATH%;%projectdir% ^
      %JVMOPTS% gov.nih.nlm.nls.ner.MetaMapLite %* 
 
+
+

metamaplite.bat.in

@@ -10,12 +10,12 @@ set CONFIGDIR=$PROJECTDIR/config
 
 set MML_JVM_OPTS=-Xmx12g
 
-set METAMAPLITE=%projectdir%/target/metamaplite-%MML_VERSION%%-standalone.jar
+set METAMAPLITE=%projectdir%/target/metamaplite-%MML_VERSION%-standalone.jar
 
 set JARSPATH=%METAMAPLITE%
 
 set OPENNLP_MODELS=%projectdir%/data/models
-set CONFIGDIR=%projectdir%/config
+set CONFIGDIR=%projectdir%
 
 set JVMOPTS=-Den-sent.bin.path=%OPENNLP_MODELS%/en-sent.bin ^
 -Den-token.bin.path=%OPENNLP_MODELS%/en-token.bin ^
@@ -24,14 +24,10 @@ set JVMOPTS=-Den-sent.bin.path=%OPENNLP_MODELS%/en-sent.bin ^
 -Dlog4j.configurationFile=file:///%projectdir%/config/log4j2.xml ^
 -Dmetamaplite.property.file=%CONFIGDIR%/metamaplite.properties ^
 -Dmetamaplite.entitylookup.resultlength=1500 ^
--Dmetamaplite.ivf.cuiconceptindex=%projectdir%/data/ivf/@@year@@/@@subset@@/indices/cuiconcept ^
--Dmetamaplite.ivf.firstwordsofonewideindex=%projectdir%/data/ivf/@@year@@/@@subset@@/first_words_of_one_WIDE ^
--Dmetamaplite.ivf.cuisourceinfoindex=%projectdir%/data/ivf/@@year@@/@@subset@@/cuisourceinfo ^
--Dmetamaplite.ivf.cuisemantictypeindex=%projectdir%/data/ivf/@@year@@/@@subset@@/cuist ^
--Dmetamaplite.ivf.varsindex=%projectdir%/data/ivf/@@year@@/@@subset@@/vars ^
--Dmetamaplite.ivf.meshtcrelaxedindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/meshtcrelaxed
-
-java -cp %projectdir%/target/classes;%projectdir%/build/classes;%projectdir%/classes;%JARSPATH%;%CONFIGDIR% ^
+-Dmetamaplite.index.directory=%projectdir%/data/ivf/2019AB/USAbase ^
+-Dmetamaplite.excluded.termsfile=%projectdir%/data/specialterms.txt
+
+java -cp %projectdir%/target/classes;%projectdir%/build/classes;%projectdir%/classes;%JARSPATH%;%projectdir% ^
      %JVMOPTS% gov.nih.nlm.nls.ner.MetaMapLite %* 
 
 

metamaplite.sh

@@ -3,7 +3,6 @@
 # A simplified metamaplite bash script using metamaplite standalone
 # jar, should work on MINGW bash (and GIT bash) on Windows.
 # 
-
 PROJECTDIR=$(dirname $0)
 
 MML_VERSION=3.6.2rc5
@@ -20,14 +19,11 @@ MMLPROPS="-Dopennlp.en-sent.bin.path=$OPENNLP_MODELS/en-sent.bin \
     -Dopennlp.en-chunker.bin.path=$OPENNLP_MODELS/en-chunker.bin \
     -Dlog4j.configurationFile=$PROJECTDIR/config/log4j2.xml \
     -Dmetamaplite.entitylookup.resultlength=1500 \
-    -Dmetamaplite.ivf.cuiconceptindex=$PROJECTDIR/data/ivf/strict/indices/cuiconcept \
-    -Dmetamaplite.ivf.firstwordsofonewideindex=$PROJECTDIR/data/ivf/strict/indices/first_words_of_one_WIDE \
-    -Dmetamaplite.ivf.cuisourceinfoindex=$PROJECTDIR/data/ivf/strict/indices/cuisourceinfo \
-    -Dmetamaplite.ivf.cuisemantictypeindex=$PROJECTDIR/data/ivf/strict/indices/cuist \
-    -Dmetamaplite.ivf.varsindex=$PROJECTDIR/data/ivf/strict/indices/vars \
-    -Dmetamaplite.ivf.meshtcrelaxedindex=$PROJECTDIR/data/ivf/strict/indices/meshtcrelaxed \
+    -Dmetamaplite.index.directory=$PROJECTDIR/data/ivf/2019AB/USAbase \
     -Dmetamaplite.excluded.termsfile=$PROJECTDIR/data/specialterms.txt"
 
-CLASSPATH=$CONFIGDIR
-java $MML_JVM_OPTS $MMLPROPS -cp $PROJECTDIR/target/metamaplite-${MML_VERSION}-standalone.jar gov.nih.nlm.nls.ner.MetaMapLite $* 
+MML_JAR=$PROJECTDIR/target/metamaplite-${MML_VERSION}-standalone.jar
+MML_CLASSPATH=$PROJECTDIR/target/classes:$PROJECTDIR/build/classes:$PROJECTDIR/classes:$PROJECTDIR:$MML_JAR
+
+java $MML_JVM_OPTS $MMLPROPS -cp $MML_CLASSPATH gov.nih.nlm.nls.ner.MetaMapLite $* 
 

metamaplite.sh.in

@@ -20,14 +20,13 @@ MMLPROPS="-Dopennlp.en-sent.bin.path=$OPENNLP_MODELS/en-sent.bin \
     -Dopennlp.en-chunker.bin.path=$OPENNLP_MODELS/en-chunker.bin \
     -Dlog4j.configurationFile=$PROJECTDIR/config/log4j2.xml \
     -Dmetamaplite.entitylookup.resultlength=1500 \
-    -Dmetamaplite.ivf.cuiconceptindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/cuiconcept \
-    -Dmetamaplite.ivf.firstwordsofonewideindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/first_words_of_one_WIDE \
-    -Dmetamaplite.ivf.cuisourceinfoindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/cuisourceinfo \
-    -Dmetamaplite.ivf.cuisemantictypeindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/cuist \
-    -Dmetamaplite.ivf.varsindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/vars \
-    -Dmetamaplite.ivf.meshtcrelaxedindex=$PROJECTDIR/data/ivf/@@year@@/@@subset@@/indices/meshtcrelaxed \
+    -Dmetamaplite.index.directory=$PROJECTDIR/data/ivf/@@year@@/@@subset@@ \
     -Dmetamaplite.excluded.termsfile=$PROJECTDIR/data/specialterms.txt"
 
-CLASSPATH=$CONFIGDIR
-java $MML_JVM_OPTS $MMLPROPS -cp $PROJECTDIR/target/metamaplite-${MML_VERSION}-standalone.jar gov.nih.nlm.nls.ner.MetaMapLite $* 
+MML_CLASSPATH=$PROJECTDIR/target/classes:$PROJECTDIR/build/classes:$PROJECTDIR/classes:$PROJECTDIR:$MML_JAR
+
+MML_JAR=$PROJECTDIR/target/metamaplite-${MML_VERSION}-standalone.jar
+MML_CLASSPATH=$PROJECTDIR/target/classes:$PROJECTDIR/build/classes:$PROJECTDIR/classes:$PROJECTDIR:$MML_JAR
+
+java $MML_JVM_OPTS $MMLPROPS -cp $MML_CLASSPATH gov.nih.nlm.nls.ner.MetaMapLite $* 
 

src/main/java/gov/nih/nlm/nls/metamap/lite/IVFLookup.java

@@ -72,6 +72,16 @@ public IVFLookup(Properties properties) {
 
   // Implementation of gov.nih.nlm.nls.metamap.lite.DictionaryLookup
 
+  public static void expandIndexDir(Properties properties, String indexDirName) {
+    if (indexDirName != null) {
+      properties.setProperty("metamaplite.ivf.cuiconceptindex", indexDirName + "/indices/cuiconcept");
+      properties.setProperty("metamaplite.ivf.firstwordsofonewideindex", indexDirName + "/indices/first_words_of_one_WIDE");
+      properties.setProperty("metamaplite.ivf.cuisourceinfoindex", indexDirName + "/indices/cuisourceinfo");
+      properties.setProperty("metamaplite.ivf.cuisemantictypeindex", indexDirName + "/indices/cuist");
+      properties.setProperty("metamaplite.ivf.varsindex", indexDirName + "/indices/vars");
+      properties.setProperty("metamaplite.ivf.meshtcrelaxedindex", indexDirName + "/indices/meshtcrelaxed");
+    }
+  }
 
   public void init(Properties properties) {
     try {
@@ -84,6 +94,8 @@ public void init(Properties properties) {
 	Integer.parseInt(properties.getProperty("metamaplite.entitylookup3.maxtokensize",
 						Integer.toString(MAX_TOKEN_SIZE)));
 
+      // fill-in properties for individual indexes
+      expandIndexDir(properties, properties.getProperty("metamaplite.index.directory"));
       this.mmIndexes = new MetaMapIvfIndexes(properties);
       this.cuiPreferredNameCache = new CuiPreferredNameCache(this, properties);
       this.cuiSemanticTypeSetIndex = new CuiSemanticTypeSetIndex(mmIndexes);