Updating settings for java, particularly to include jdk.internal.net.http in java.net.http calls, as it offers implementation for websocket communication

README.md

@@ -30,6 +30,9 @@ Create directory or copy appropriate database cluster to `labkeyDocker/postgresq
 mkdir -p labkeyDocker/postgresql/data
 ```
 
+Links are OK, too. Exact path is set in `bin/env.sh`, see below.
+
+
 Check if database runs:
 
 ```bash
@@ -40,14 +43,19 @@ labkeyDocker/bin/stopLabkey.sh
 
 ### Files and external modules for LabKey
 
-If old files and external modules are available, they should be either copied or linked to labkeyDocker/labkeyBase/files and labkeyDocker/labkeyBase/externalModules.
-
+The files and externalModules locations are set in `bin/env.sh`, see `bin/env.sh.sample`:
+```bash
+export EXTERNAL_MODULES=$HOME/externalModules
+export LABKEY_FILES=/data/labkey/files
+```
 
 ### Install LabKey binaries
 
-- run `labkeyDocker/bin/installLabkey.sh 22.3` to unzip the enclosed LabKey binary code and make appropriate links.
+- copy binaries from `https://labkey-public.fmf.uni-lj.si/labkey/Resources to `$HOME/packages`. Remember the version number for next step.
+- run `labkeyDocker/bin/installLabkey.sh 22` to unzip the LabKey binary code and make appropriate links.
 - copy `labkeyDocker/bin/env.sh.sample` to `labkeyDocker/bin/env.sh` and set a secret `$PGPASS`, other settings are probably OK, 
   check `$DOCKERCOMPOSE`
+- copy 
 - set the same value as `password` in `labkeyDocker/tomcat/conf/Catalina/localhost/labkey.xml` 
 
 ### Permissions

tomcat/bin/setenv.sh

@@ -3,4 +3,4 @@ export CATALINA_OPTS="-Dlog4j2.formatMsgNoLookups=true"
 export CATALINA_OPTS="${CATALINA_OPTS} -Duser.language.en -Duser.region=US -Ddevmode=true"
 export JAVA_OPTS="$JAVA_OPTS -Xms2g -Xmx2g -XX:-HeapDumpOnOutOfMemoryError"
 export JDK_JAVA_OPTIONS="$JDK_JAVA_OPTIONS --add-opens java.base/java.lang=ALL-UNNAMED --add-opens java.base/java.io=ALL-UNNAMED --add-opens java.base/java.util=ALL-UNNAMED --add-opens java.desktop/java.awt.font=ALL-UNNAMED --add-opens java.base/java.text=ALL-UNNAMED"
-export JDK_JAVA_OPTIONS="$JDK_JAVA_OPTIONS --add-exports java.net.http/jdk.internal.net.http.websocket=ALL-UNNAMED"
+export JDK_JAVA_OPTIONS="$JDK_JAVA_OPTIONS --add-exports java.net.http/jdk.internal.net.http.websocket=ALL-UNNAMED --add-exports java.net.http/jdk.internal.net.http=ALL-UNNAMED"