Bug: omero.data.dir ignored in current develop branch

[mtbcarroll]

mark@ls27175:~/src/openmicroscopy$ ls dist/var/log/
mark@ls27175:~/src/openmicroscopy$ omero config get omero.data.dir
/Users/mark/var/omero/
mark@ls27175:~/src/openmicroscopy$ omero admin start
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
mark@ls27175:~/src/openmicroscopy$ grep /OMERO dist/var/log/Blitz-0.log | head -n 2
2013-05-01 10:35:53,929 INFO  [      o.s.blitz.repo.AbstractRepositoryI] (      main) Initializing repository in /OMERO/
org.springframework.beans.factory.access.BootstrapException: Unable to return specified BeanFactory instance: factory key [OMERO.blitz], from group with resource name [classpath*:beanRefContext.xml]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'OMERO.blitz' defined in URL [jar:file:/Users/mark/src/openmicroscopy/dist/lib/server/blitz.jar!/beanRefContext.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.system.OmeroContext]: Constructor threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'legacyRepository' defined in URL [jar:file:/Users/mark/src/openmicroscopy/dist/lib/server/blitz.jar!/ome/services/blitz-repositories.xml]: Instantiation of bean failed; nested exception is org.springframework.beans.BeanInstantiationException: Could not instantiate bean class [ome.services.blitz.repo.LegacyRepositoryI]: Constructor threw exception; nested exception is java.lang.IllegalArgumentException: Invalid directory specified for file system service./OMERO
mark@ls27175:~/src/openmicroscopy$ 

[jamoore]

Can you attach the full log, please?

[bpindelski]

This still happens on develop. The exception thrown comes from AbstractFileSystemService. It seems that the legacyRepository bean in blitz-repositories.xml is the culprit. Josh's suggestion: a change to PreferenceContext? for logback work has somehow changed the order of operations in Spring. That causes a null to be passed to the bean ctor and the default value of /OMERO/ is taken from omero.properties.

[jamoore]

Open bug which needs to be looked at. Removing my name in case anyone else wants to pick it up.

[bpindelski]

Suggestion from Josh: adding "lazy-init=..." or "depends-on=..." in the bean parameters might fix the issue of operation order.

[mtbcarroll]

In case it's any help, I seem to have created /OMERO/ on the morning of May 8th, so it's probably a PR merged shortly beforehand that caused the problem.

[bpindelski]

After laborious debugging and Josh's help, it came out that PreferencesContext? subclasses PropertyPlaceholderConfigurer? subclasses PropertyResourceConfigurer? subclasses PropertiesLoaderSupport? and systemPropertiesMode is in PropertyPlaceholderConfigurer? and mergeProperties is in PropertiesLoaderSupport?. That tells us that if the omero.data.dir property is already set in the System.properties, we should ignore the return value from mergeProperties(). Some changes in the mentioned classes might have been a result of work needed to get Logback working (especially the logback.xml file).

[jamoore]

PR filed (​https://github.com/openmicroscopy/openmicroscopy/pull/1201) and tested locally.

[Blazej Pindelski <bpindelski@…>]

(In [1faee00473ad4cb519b12b0faff7ccc9bc0edf6f/ome.git] on branch develop) Don't overwrite System properties (see #10828).

[Josh Moore <josh@…>]

(In [83bc0ff5498c0933620d832d7ff8ac8831abd29c/ome.git] on branch develop) Merge pull request #1201 from bpindelski/data-dir

Fix omero.data.dir ignored in current develop branch (see #10828)