macdev : config for running on a mac

[rtaylorzfin]

Some notes from trying to get this set up:

Notes on Setting Up Local Dev Env:

Trying to mirror cell as closely as possible. I created /opt/research instead of /research since mac doesn't allow creating /research.

unzipped macos java tar file to /opt/jvm with a symlink of java-openjdk so the JAVA_HOME becomes:

export JAVA_HOME=/opt/jvm/java-openjdk/Contents/Home

I created commons/env/macdev.env and macdev.properties

ant rebuildProperties failed somehow, so i created it by hand.

Create a symlink:

$ cd /opt/zfin/source_roots/
$ ln -s zfin.org macdev

Did a brew install postgres

Symlink:

mkdir /opt/postgres
ln -s /usr/local/Cellar/postgresql/14.6_1 /opt/postgres/postgresql

Ran into pg 14 compatibility issue and fixed with code change

Ran into this compile error:

     [copy] Copying 289 files to /opt/zfin/source_roots/zfin.org/home/WEB-INF/classes
    [javac] Compiling 2120 source files to /opt/zfin/source_roots/zfin.org/home/WEB-INF/classes
    [javac] /opt/zfin/source_roots/zfin.org/source/org/zfin/mapping/GenomeLocation.java:202: error: cannot find symbol
    [javac]         ZFIN("ZfinGbrowseStartEndLoader", true, "ZFIN Gbrowse", "/" + ZfinPropertiesEnum.GBROWSE_PATH_FROM_ROOT + "?name="),

This was due to needing to rebuildProperties with ant

Got this error:

gwt:
     [java] [WARN] Can't create directory: /opt/zfin/www_homes/macdev/pre-home/gwt-unitCache

don't know why. the directory seems to exist.

Got issue starting tomcat:

FIX:
    <property name="tomcat-script-mutant" value="${env.CATALINA_HOME}/bin/catalina.sh"/>

and fixed with change to tomcat.xml

tomcat issue:

HTTP Status 500 – Internal Server Error
Type Exception Report

Message Unable to acquire JDBC Connection

Description The server encountered an unexpected condition that prevented it from fulfilling the request.

Fix?:

scp 'bent:/opt/apache/apache-tomcat/lib/postgres*' /opt/apache/apache-tomcat/lib/