fix execution to use target runtime; add documentation

.gitignore

@@ -0,0 +1,8 @@
+target
+
+# IntelliJ project files
+*.iml
+
+# Temporary execution files
+*.log
+

README.md

@@ -0,0 +1,19 @@
+# Run on Linux
+
+Update UMLS account settings
+
+```
+cd ctakes-temporal-demo
+mvn clean install
+export ctakes_umlsuser='<your-username>'
+export ctakes_umlspw='<your-password>'
+./configure.sh
+MAVEN_OPTS="-Xmx4096m -Xms3072m -Xss128M -XX:+CMSClassUnloadingEnabled -XX:-UseGCOverheadLimit" mvn jetty:run
+mvn jetty:run
+```
+
+You don't need to re-export the `umlsuser` and `umlspassword` after the configuration has been updated. You need to run `./configure.sh` every time `mvn clean` was issued.
+
+
+
+

ctakes-temporal-demo/configure.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+
+cTAKES_DICTIONARY_HOME=target/ctakes-web-client/WEB-INF/classes/org/apache/ctakes/dictionary
+DICTIONARY_FAST_HOME=${cTAKES_DICTIONARY_HOME}/lookup/fast
+
+cTAKESHSQL_CONF=${DICTIONARY_FAST_HOME}/cTakesHsql.xml
+SNO_RX_16AB_CONF=${DICTIONARY_FAST_HOME}/sno_rx_16ab.xml
+
+CHANGEME_FILES=( "${cTAKESHSQL_CONF}" "${SNO_RX_16AB_CONF}" )
+
+for changeme_file in "${CHANGEME_FILES[@]}"; do
+  if [ ! -f "${changeme_file}" ]; then
+    echo "dictionary ${changeme_file} could not be found"
+    continue
+  fi
+
+  echo "updating credentials in dictionary configuration ${changeme_file}"
+
+  # updating umlsUser
+  sed -i "s/\(<property key=\"umlsUser\" value=\"\)CHANGEME/\1${ctakes_umlsuser}/g" "${changeme_file}"
+
+  # updating umlsPass
+  sed -i "s/\(<property key=\"umlsPass\" value=\"\)CHANGEME/\1${ctakes_umlspassword}/g" "${changeme_file}"
+done

ctakes-temporal-demo/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab.xml

@@ -30,7 +30,7 @@ Though JdbcConnectionFactory will attempt to "find" a db based upon the parent d
 for the sake of ide ease-of-use, the user should be aware of these hsql limitations.
 -->
          <property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
-         <property key="jdbcUrl" value="jdbc:hsqldb:file:src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
+         <property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
          <property key="jdbcUser" value="sa"/>
          <property key="jdbcPass" value=""/>
          <property key="rareWordTable" value="cui_terms"/>
@@ -48,7 +48,7 @@ for the sake of ide ease-of-use, the user should be aware of these hsql limitati
       <implementationName>org.apache.ctakes.dictionary.lookup2.concept.JdbcConceptFactory</implementationName>
       <properties>
          <property key="jdbcDriver" value="org.hsqldb.jdbcDriver"/>
-         <property key="jdbcUrl" value="jdbc:hsqldb:file:src/main/resources/org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
+         <property key="jdbcUrl" value="jdbc:hsqldb:file:org/apache/ctakes/dictionary/lookup/fast/sno_rx_16ab/sno_rx_16ab"/>
          <property key="jdbcUser" value="sa"/>
          <property key="jdbcPass" value=""/>
          <property key="umlsUrl" value="https://uts-ws.nlm.nih.gov/restful/isValidUMLSUser"/>