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Task #10755 (closed)

Opened 11 years ago

Closed 8 years ago

Add config key for OMERO.searcher storage path

Reported by: spli Owned by: spli
Priority: minor Milestone: Partner-1
Component: Scripting Version: 4.4.9
Keywords: searcher Cc: analysis@…, mtbcarroll
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.


In the short term we'll use the ContentDB (python pickle) file which OMERO.searcher stored independently of the OMERO filestore. The path should be configurable (it looks like the OMERO_CONTENTDB_PATH environment variable) isn't passed to scripts which are currently used for feature calculation.

Change History (9)

comment:1 Changed 11 years ago by spli

  • Cc analysis@… added
  • Status changed from new to accepted

comment:2 Changed 11 years ago by spli

I've tried

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE beans PUBLIC "-//SPRING//DTD BEAN//EN" "http://www.springframework.org/dtd/spring-beans.dtd">
  <bean class="ome.system.Preference" id="omerosearcher.data.dir">
    <property name="db" value="false"/>
    <property name="mutable" value="false"/>
    <property name="visibility" value="all"/>

as ome/services/blitz-config-omerosearcher.xml in lib/server/extensions.jar but the variable isn't readable by a non-admin (conn.getConfigService().getConfigValue('omerosearcher.data.dir') returns a SecurityViolation).

Also tried wrapping the bean in <bean id="preferenceContext" class="ome.system.PreferenceContext"><property name="preferences"><list>.
The XML is definitely read since it fails if there's a syntax error.

comment:3 Changed 11 years ago by jamoore

  • Cc mtbcarroll added

Simon: your bean definition looks very correct. The automatic lookup is not in place. Either a handler needs to be added as in https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/server/src/ome/services/scheduler/SchedulerFactoryBean.java or we will need to add a addPreference() method to https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/common/src/ome/system/PreferenceContext.java and have this preference inject itself.

If you'd like me to make either of those changes, just say so.

comment:4 Changed 11 years ago by spli

I've been having second thoughts on whether this is the best way of doing things. Having to change extensions.jar seems unnecessarily difficult, especially if you end up with more than one add-on from different groups. For now I'll just create a config file in the omero_searcher root dir- this works because omeroweb is on the OMERO PYTHONPATH, so can be found from within a script (import omeroweb.omero_searcher.omero_searcher_config), but maybe this isn't such a bad idea after all? Thoughts?

comment:5 Changed 11 years ago by jamoore

It's ok but not great. Moving forward, I would think bin/omero config will always be supported, across nodes, etc. One other option I've considered is making some namespace generally readable: omero_ext.*, omero.public.* or similar. Or perhaps even simpler, provide a way to list prefixes which should be readable: bin/omero config set omero.config.public_prefixes omero_searcher.

Last edited 11 years ago by jamoore (previous) (diff)

comment:6 Changed 10 years ago by spli

  • Keywords searcher added
  • Version set to 4.4.9

comment:7 Changed 10 years ago by spli

Referencing ticket #9945 has changed sprint.

comment:8 Changed 10 years ago by spli

  • Milestone changed from Unscheduled to Partner-1

comment:9 Changed 8 years ago by jamoore

  • Resolution set to wontfix
  • Status changed from accepted to closed

Cleaning up searcher backlog.

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