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Task #10828 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 9 years ago

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

Reported by: mtbcarroll Owned by:
Priority: blocker Milestone: 5.0.0-beta1
Component: ApplicationServer Version: n.a.
Keywords: n.a. Cc: omero-team@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: FS demo 4.2

Description

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$ 

Attachments (1)

Blitz-0.log (101.5 KB) - added by mtbcarroll 9 years ago.

Download all attachments as: .zip

Change History (11)

comment:1 Changed 9 years ago by jamoore

Can you attach the full log, please?

comment:2 Changed 9 years ago by jamoore

  • Milestone changed from Unscheduled to OMERO-5
  • Sprint set to FS demo 4.1

Changed 9 years ago by mtbcarroll

comment:3 Changed 9 years ago by 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.

Last edited 9 years ago by bpindelski (previous) (diff)

comment:4 Changed 9 years ago by jamoore

  • Owner jamoore deleted
  • Sprint changed from FS demo 4.1 to FS demo 4.2

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

comment:5 Changed 9 years ago by bpindelski

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

Last edited 9 years ago by bpindelski (previous) (diff)

comment:6 Changed 9 years ago by 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.

comment:7 Changed 9 years ago by 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).

comment:8 Changed 9 years ago by jamoore

  • Resolution set to fixed
  • Status changed from new to closed

comment:9 Changed 9 years ago by Blazej Pindelski <bpindelski@…>

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

comment:10 Changed 9 years ago by 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)

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