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{5} Assigned, Active Tickets by Owner (Full Description) (35 matches)

List tickets assigned, group by ticket owner. This report demonstrates the use of full-row display.

atarkowska (2 matches)

Ticket Summary Component Milestone Type Created
Description
#888 Possible way to develope collaboration for Omero WebCollaboration 3.0-Beta4 story 03/05/08

OMERO.collaboration is the web application based on Django http://www.djangoproject.com/ - high-level Python Web framework and cooperates with Blitz server to manage and share datas from the OMERO.server.
The application is not only the "thin client" to manage images, datasets, projects, annotations, tags, etc., it will refer to a trend in web design and development - WEB 2.0 - a perceived second generation of web-based communities and hosted services (such as social-networking sites, wikis, blogs, and folksonomies) which aim to facilitate creativity, collaboration, and sharing between users.

The functionality and attitudes of the application:
Dictionary:
user - member of the system,
group - group with users,
people - users and rest of the world,
CMS - Content Management System.
Object – type of file or object which is supported by the server (image, container, attachment, tag, etc.)

1. Manage:

  1. Users Own images, files etc. no one has access to and not shared as default configuration.
  2. Multi-objects work.
  3. Permissions based on Unix approach - read, write for: private, group, everyone - default permissions for item is private can be changed if required.
  4. Accessible/available files stored inside the system by other users
    1. Intranet items - shared items for the place where system is installed.
    2. Internet items - shares and publications.
  5. Importing files.

2. View:

  1. Supported images by the viewer.
  2. Not supported file by the software installed on the user's computer like PDF, MsOffice? documents.
  3. Building user’s own viewer for printing out (for example to PDF)

3. Annotate:

  1. By attaching personal notes, remarks, links and relationships to other resources, terms from ontologies or controlled vocabularies, ratings and local files such as images, or PDF, MsOffice? documents.

4. Tagging.

5. Search:

  1. Search and analyze data to find relevant content.

6. Collaborate:

  1. Prepare package you would like to share with people.
  2. Define list of users who can have an access to this package (don't have to think about changing permissions for file if they are private).
  3. Collaborative discussions (over single thread) about the content with people from your contact list.

7. Publish:

  1. Finalize your work by the publishing chosen content.

8. History and tasks:

  1. Managing calendar
  2. Creating tasks

9. Custom area:

  1. Front page - place for information about institution, work, etc. (about us, what does lab do, etc.).

10. Private area:

  1. Pages for single user with CMS.
  2. Pages for groups with CMS.
#925 OMERO.web Html customization WebCollaboration 3.0-Beta4 story 05/02/08 
– Simple interface to customize for users 
– Quicker solution 
– Means: a series of prewritten queries “all images with XYZ in a ABC view” 
– Ola: configure application so you can extend template. Own viewer 
– Wiki pages with examples 
– Covers REST API (drop in a template)

callan (18 matches)

Ticket Summary Component Milestone Type Created
Description
#834 JBoss PermGen Errors ApplicationServer defect 11/12/07

JBoss is throwing java.lang.OutOfMemoryError: PermGen space exceptions: 

15:12:51,890 ERROR [[jsp]] Servlet.service() for servlet jsp threw exception
java.lang.NoClassDefFoundError: org/eclipse/jdt/internal/compiler/codegen/CodeStream
        at org.eclipse.jdt.internal.compiler.ast.TypeDeclaration.generateCode(TypeDeclaration.java:508)
        at org.eclipse.jdt.internal.compiler.ast.TypeDeclaration.generateCode(TypeDeclaration.java:584)
        at org.eclipse.jdt.internal.compiler.ast.CompilationUnitDeclaration.generateCode(CompilationUnitDeclaration.java:214)
        at org.eclipse.jdt.internal.compiler.Compiler.process(Compiler.java:602)
        at org.eclipse.jdt.internal.compiler.Compiler.compile(Compiler.java:411)
        at org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:405)
        at org.apache.jasper.compiler.Compiler.compile(Compiler.java:308)
        at org.apache.jasper.compiler.Compiler.compile(Compiler.java:286)
        at org.apache.jasper.compiler.Compiler.compile(Compiler.java:273)
        at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:566)
        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:311)
        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:230)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
        at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:179)
        at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:84)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104)
        at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:157)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:241)
        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:844)
        at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:580)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447)
        at java.lang.Thread.run(Thread.java:619)
15:12:55,949 ERROR [[jsp]] Servlet.service() for servlet jsp threw exception
java.lang.NoClassDefFoundError: org/eclipse/jdt/internal/compiler/codegen/CodeStream
        at org.eclipse.jdt.internal.compiler.ast.TypeDeclaration.generateCode(TypeDeclaration.java:508)
        at org.eclipse.jdt.internal.compiler.ast.TypeDeclaration.generateCode(TypeDeclaration.java:584)
        at org.eclipse.jdt.internal.compiler.ast.CompilationUnitDeclaration.generateCode(CompilationUnitDeclaration.java:214)
        at org.eclipse.jdt.internal.compiler.Compiler.process(Compiler.java:602)
        at org.eclipse.jdt.internal.compiler.Compiler.compile(Compiler.java:411)
        at org.apache.jasper.compiler.JDTCompiler.generateClass(JDTCompiler.java:405)
        at org.apache.jasper.compiler.Compiler.compile(Compiler.java:308)
        at org.apache.jasper.compiler.Compiler.compile(Compiler.java:286)
        at org.apache.jasper.compiler.Compiler.compile(Compiler.java:273)
        at org.apache.jasper.JspCompilationContext.compile(JspCompilationContext.java:566)
        at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:311)
        at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:320)
        at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:266)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:230)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
        at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:179)
        at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:84)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:104)
        at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:157)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:241)
        at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:844)
        at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:580)
        at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:447)
        at java.lang.Thread.run(Thread.java:619)
15:51:43,148 ERROR [STDERR] Exception in thread "RMI TCP Connection(idle)"
15:51:43,151 ERROR [STDERR] java.lang.OutOfMemoryError: PermGen space
15:51:57,866 WARN  [RunnableTaskWrapper] Unhandled throwable for runnable: org.jnp.server.Main$BootstrapRequestHandler@723e94a6
java.lang.OutOfMemoryError: PermGen space
16:21:54,278 WARN  [RunnableTaskWrapper] Unhandled throwable for runnable: org.jnp.server.Main$BootstrapRequestHandler@53b69ca8
java.lang.OutOfMemoryError: PermGen space
16:22:24,906 WARN  [RunnableTaskWrapper] Unhandled throwable for runnable: org.jnp.server.Main$BootstrapRequestHandler@6264c005
java.lang.OutOfMemoryError: PermGen space
16:22:48,294 ERROR [STDERR] Exception in thread "WorkerThread#0[10.34.2.145:57702]"
16:22:48,294 ERROR [STDERR] java.lang.OutOfMemoryError: PermGen space
#115 OOM Errors Deployment Unscheduled story 05/24/06

This ticket is for tracking discussion and solutions to OOM errors during OMERO build.

#123 Importer Roadmap Import Unscheduled story 05/26/06
  • The initial design of the importer should run on the server as a command line tool, and handle the following formats (in rough order of importance):
    • Deltavision
    • Metamorph
    • Tiff
    • BioRad?
    • Zeiss LSM
  • After the command line tool is working, the next step will be to implement a standalone Client GUI for Importer, which should talk to a serverside demon to handle image imports
  • After the completion of this set of tools, the client should be intigrated with Shoola as a plugin tool.
  • The final step will be the introduction of additional file formats (to be decided later).

Additional information about the import story are captured in the Tiki and can be found here and here.

#334 Rework RenderingEngine API 3.0-Beta4 story 09/07/06

Several times there have been difficulties with the RenderingEngine. See:

  • #194
  • #206
  • #330

This stems partly if not largely from the fact that the RE API was not designed for remote access, especially not for remote access to Hibernate. Taking this into mind, it may make sense to either split the API into stateful and stateless portions or to reintroduce DTOs in some capacity to prevent further troubles. Another alternative would be to implement a DeepCopy similar to ShallowCopy. (This could also be useful for: #80 if done properly, i.e. by passing in the paths for what should be copied/fetched. )

#1000 Thumbnail service: needed method Services 3.0-Beta4 task 06/02/08

I cannot find a ticket for that
For The Viewed By option, i will need to set the pixels and the userID something like service.setPixelsId(pixelsID, userID).

#670 Not setting the RGB channel correctly in the Importer Import defect 04/17/07

When importing RGB tiffs, the initial colors are not being preserved. TIFF files should be set the channel to the appropriate color during import

#1042 GC overhead limit exceeded out of memory exception General 3.0-Beta4 defect 07/14/08

Nightshade hit this error, causing the server to basically grind to a total halt: 

java.lang.OutOfMemoryError: GC overhead limit exceeded
17:03:13,557 INFO  [ServiceHandler]  Excp:      java.lang.OutOfMemoryError: GC overhead limit exceeded
17:20:50,217 INFO  [ServiceHandler]  Meth:      interface ome.services.util.Executor$Work.doWork
17:20:50,217 INFO  [ServiceHandler]  Args:      [null, null, ome.tools.spring.InternalServiceFactory@7847687d]
17:20:52,723 INFO  [EventHandler]   Auth:       user=0,group=0,event=19167046(Sessions)
17:20:55,223 INFO  [ServiceHandler]  Rslt:      true
17:20:55,223 INFO  [ServiceHandler]  Meth:      interface ome.services.util.Executor$Work.doWork
17:20:55,223 INFO  [ServiceHandler]  Args:      [null, null, ome.tools.spring.InternalServiceFactory@e88978b]
17:20:57,713 INFO  [EventHandler]   Auth:       user=0,group=0,event=19167047(Sessions)
17:21:00,196 WARN  [ServiceHandler] Unknown exception thrown.

java.lang.OutOfMemoryError: GC overhead limit exceeded
17:21:00,196 INFO  [ServiceHandler]  Excp:      java.lang.OutOfMemoryError: GC overhead limit exceeded
18:08:26,090 INFO  [ServiceHandler]  Meth:      interface ome.services.util.Executor$Work.doWork
18:08:26,090 INFO  [ServiceHandler]  Args:      [null, null, ome.tools.spring.InternalServiceFactory@434f7c8a]
18:08:28,596 INFO  [EventHandler]   Auth:       user=0,group=0,event=19167048(Sessions)
18:08:31,086 INFO  [ServiceHandler]  Rslt:      true
18:08:31,087 INFO  [ServiceHandler]  Meth:      interface ome.services.util.Executor$Work.doWork
18:08:31,087 INFO  [ServiceHandler]  Args:      [null, null, ome.tools.spring.InternalServiceFactory@5d980b4]
18:08:33,585 INFO  [EventHandler]   Auth:       user=0,group=0,event=19167049(Sessions)
18:08:36,079 WARN  [ServiceHandler] Unknown exception thrown.
#18 Import - Importer: Add in the priority import formats API Unscheduled story 05/05/06

Decide on the top 5 import formats and implement them.

#28 Externalize Util Package Bin-Services Future story 05/05/06

The rendering util package needs to be externalized (and added as a dependency) so that it can be used by Shoola.

#854 Rendering Settings Service Missing Return Values Services story 12/18/07

The paradigm of the existing return values for methods located in IRenderingSettings is that certain settings applications could fail or succeed. As such, we have methods such as: 

Map applySettingsToDataset(@NotNull long from, @NotNull long to);

where the <k,v> pairs are {true, List<Long>} and {false, List<Long>} signifying the above failure and success conditions. The methods in the service which reset rendering settings do not follow the paradigm because reseting of rendering settings should never fail. Failure conditions during methods which reset rendering settings are handled by throwing exceptions; in this case the entire transaction fails.

This said, it would be convenient for application developers to be able to know exactly which images have had their rendering settings reset when calling methods which take a Dataset, Category, etc.

#218 Rendering tests need an ImportFixture Bin-Services 3.0-Beta4 task 07/14/06

RenderingEngineTest will always fail because there are no valid rendering defs in the DB. A fixture to create one is needed.

#831 Thumbnail Service: Compression level Services 3.0-Beta4 task 11/06/07

Add method or new constructor to set the compression level

#876 Screen Plate Well model support General 3.0-Beta4 task 02/15/08

The SPW (Screen Plate Well) model from OME XML (defined in SWP.xml) should be propagated to OMERO DSL for inclusion into the OMERO Hibernate mappings and model.

#1023 Renderer: set settings Services 3.0-Beta4 task 06/24/08

See ticket 621 on shoola trac. I found a workaround, but the method set the model to "rgb" and should be set to "hsb" in order to fix the problem described in ticket 621. See this probably linked to the fact that we no longer have a HSB strategy but we still "hsb" as the default model i.e. the first time the image is launched the 

renderer.getModel()  is hsb
#852 GC Out of Memory Errors ApplicationServer defect 12/13/07

Out of memory errors during pre-Beta-2.3 testing with r1966: 

12:31:49,681 ERROR [STDERR] Exception in thread "WorkerThread#4[10.44.0.126:63565]"
12:31:49,681 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:36:17,042 ERROR [STDERR] Exception in thread "WorkerThread#5[194.117.10.254:62081]"
12:36:17,042 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:38:05,295 ERROR [STDERR] Exception in thread "WorkerThread#6[10.44.0.126:63582]"
12:38:05,295 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:38:23,279 ERROR [STDERR] Exception in thread "WorkerThread#3[10.34.1.204:1711]"
12:38:23,279 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:41:05,706 ERROR [STDERR] Exception in thread "WorkerThread#7[10.44.0.126:63610]"
12:41:05,706 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:42:18,017 ERROR [STDERR] Exception in thread "WorkerThread#2[10.44.0.53:51576]"
12:42:18,017 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:42:37,511 ERROR [STDERR] Exception in thread "WorkerThread#8[194.117.10.254:22401]"
12:42:37,511 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:42:56,327 ERROR [STDERR] Exception in thread "WorkerThread#11[134.36.37.80:51002]"
12:42:56,327 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:43:26,762 ERROR [STDERR] Exception in thread "WorkerThread#12[194.117.10.254:1665]"
12:43:26,762 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:44:18,385 ERROR [STDERR] Exception in thread "WorkerThread#13[134.36.37.80:51020]"
12:44:18,386 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:45:36,349 ERROR [STDERR] Exception in thread "WorkerThread#14[134.36.37.80:51031]"
12:45:36,349 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
12:49:25,809 ERROR [STDERR] Exception in thread "WorkerThread#15[134.36.37.80:51050]"
12:49:25,809 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:27:59,668 ERROR [STDERR] Exception in thread "WorkerThread#16[10.44.0.126:63740]"
13:27:59,668 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:32:26,840 ERROR [STDERR] Exception in thread "WorkerThread#17[10.44.0.126:63811]"
13:32:26,840 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:33:57,940 ERROR [ServerThread] Worker thread initialization failure
java.io.EOFException
        at org.jboss.remoting.transport.socket.ServerThread.processInvocation(ServerThread.java:526)
        at org.jboss.remoting.transport.socket.ServerThread.dorun(ServerThread.java:369)
        at org.jboss.remoting.transport.socket.ServerThread.run(ServerThread.java:165)
13:34:08,031 ERROR [STDERR] Exception in thread "WorkerThread#18[134.36.37.80:51181]"
13:34:08,031 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:38:43,801 ERROR [STDERR] Exception in thread "WorkerThread#19[134.36.37.80:51227]"
13:38:43,801 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:45:10,783 ERROR [STDERR] Exception in thread "WorkerThread#20[134.36.37.80:49172]"
13:45:10,783 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:46:15,122 ERROR [STDERR] Exception in thread "WorkerThread#21[134.36.37.80:49179]"
13:46:15,122 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:46:54,647 ERROR [STDERR] Exception in thread "WorkerThread#22[134.36.37.80:49184]"
13:46:54,648 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:50:04,863 ERROR [STDERR] Exception in thread "WorkerThread#23[10.34.1.204:1741]"
13:50:04,863 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
13:55:33,221 ERROR [STDERR] Exception in thread "WorkerThread#24[10.34.2.182:57284]"
13:55:33,221 ERROR [STDERR] java.lang.OutOfMemoryError: GC overhead limit exceeded
#12 Allow individual user images to be imported Resurrect Future story 05/05/06

Currently, Resurrect imports all images from a user. This should be changed to allow individual images to be imported.

#452 Removal of RGB Rendering Model Bin-Services 3.0-Beta4 story 10/26/06

The RGB rendering model is a holdover from the client side rendering engine that doesn't fit well with the colour choices one would like to make. Having to flip the rendering model when one wants to assign channel 0 to blue, channel 1 to green and channel 2 to blue explicitly is less than ideal.

The real benefit this has is allowing an optimization to be enabled when you don't have colour component overlap in the user's colour choices. The rendering engine should be smart enough to enable this optimization based on the user's colour choices and not have to have the rendering model flipped by the API user.

In short, the model should be removed and the optimization enabled intelligently by the rendering engine.

#434 Rendering Engine: set default color. Bin-Services Unscheduled task 10/18/06

The default color of a channel should correspond to the emission wavelenght of the channel (if info available) The code invoking the public method of ColorFactory? doesn't seem to work. Put a tempo solution client side.

jmoore (15 matches)

Ticket Summary Component Milestone Type Created
Description
#118 Hibernate session.merge() is updating non-changed entities. API 3.0-Beta4 defect 05/25/06

It was found in r582 that calls to session.merge() were cascading to all instances so that versions in Experimenter, EventTypes, etc. are being incremented. This was hellish for clients trying to deal with optimistic locks.

This is a hibernate bug. See http://opensource.atlassian.com/projects/hibernate/browse/HHH-1401 (version 3.2 may help)

Revisions r590, r591, and r597 made temporary fixes so work could continue without versions.

Before we close this, we need to re-instate versions and finish the update tests (like DetachedPixelsGraphTest) which test the possible combinations of transient/detached graphs.

  • Transient root with:
    • transient entity
    • "transient" collection
    • unloaded entity
    • filtered collection (ERROR)
  • Detached root with:
    • transient entities/collections
    • detached entities/collections
    • filtered entities/collections

Also we need to make sure that the bug fix really worked, i.e.:

  • re-merging unchanged detached --> no version increment
  • re-merging changed --> version++ (also re: collections)

A possible Abstract test would be of the form: 

  class {
    createGraph();
    saveGraph();
    checkIds();
    checkVersions();
    checkLogs();
  }

Originally http://bugs.openmicroscopy.org.uk/show_bug.cgi?id=646

#975 Search.onlyType() can return different types Search 3.0-Beta4 defect 05/18/08

Under some circumstances: 

        Class[] klass = new Class[1];
        klass[0] = TagAnnotation.class;
        search.onlyAnnotatedWith(klass);
        search.onlyType(Image.class);
        search.bySomeMustNone(new String[] { "an*" }, null, null);

can return more than images.

#800 OMERO properties rework for simplification and central administration Configuration 3.0-Beta4 story 09/14/07

This ticket subsumes:

  • #437 - Remove local.properties.default
  • #556 - Ability to store omero.data.dir in local.properties rather than omero.properties
  • #660 - Copying local.properties into the ear file
  • #718 - Preferences based configuration
  • #734 - Location for LDAP read/write values
  • #741 - proper defaults
  • #746 - sensible javac|javadoc.maxmem values
  • #753 - central administration
  • #754 - A writable configuration store for ldap

And will also include the merging of ice.config & glacier2.config with omero.properties (with overrides in local.properties).

Other possibilities:

  • Allow comma separated values in OMERO_CONFIG for prefs.class
  • Allow a path value in OMERO_CONFIG for prefs.class
  • Failover to using $HOME/.omero.config when Java not present from Python
  • Warn when Java preferences or .omero.config are not umask 077
  • Use IConfig as the central configurator which is injected into beans. This would allow hot-swapping properties
  • Outline all environment properties which are of importance for OmeroBuild, OmeroBlitz, OmeroGrid, etc. (ICE_CONFIG in grid?, OMERO_CONFIG, OMERO_MASTER, OMERO_NODE, ..., NOMAKE, ...)
#77 Unspecified behavior if two QueryParameters with same name are entered. Queries 3.0-RC1 defect 05/18/06

As we begin using QueryParameters internally (for example with the uniqueResult clause from #72), it will become important to check for any namespace clashes.

The initialization of Queries should throw an exception on duplicate QP names.

#307 Hibernate improperly handles Permissions components that are null ORM 3.0-RC1 defect 08/25/06

For #182, it is important to set Permissions to null by default. However, Hibernate has some quirks when an interceptor un-nulls a null-valued component. See HHH-2027 for more. Until this is fixed, we'll workaround.

#964 Possible "corrupted" Lucene index after stale reader exception. Search 3.0-Beta4 defect 05/15/08

The following exception was thrown during a run of the JobHandleTest. We need to guarantee that when such an exception is thrown, that the related Event is re-indexed to prevent a stale index (e.g. a still present entry which has already been deleted.) 

25547      [r_Worker-2] ERROR  rg.hibernate.transaction.JDBCTransaction  - exception calling user Synchronization
org.hibernate.search.SearchException: Unable to remove from Lucene index: class ome.model.meta.GroupExperimenterMap#250
	at org.hibernate.search.backend.impl.lucene.LuceneWorker.remove(LuceneWorker.java:109)
	at org.hibernate.search.backend.impl.lucene.LuceneWorker.performWork(LuceneWorker.java:80)
	at org.hibernate.search.backend.impl.lucene.LuceneWorker.performWork(LuceneWorker.java:46)
	at org.hibernate.search.backend.impl.lucene.LuceneBackendQueueProcessor.run(LuceneBackendQueueProcessor.java:98)
	at org.hibernate.search.backend.impl.BatchedQueueingProcessor.performWorks(BatchedQueueingProcessor.java:132)
	at org.hibernate.search.backend.impl.PostTransactionWorkQueueSynchronization.afterCompletion(PostTransactionWorkQueueSynchronization.java:50)
	at org.hibernate.transaction.JDBCTransaction.notifyLocalSynchsAfterTransactionCompletion(JDBCTransaction.java:243)
	at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:121)
	at ome.services.fulltext.FullTextIndexer.doWork(FullTextIndexer.java:99)
	at ome.services.util.Executor$Interceptor$1$1.doInHibernate(Executor.java:241)
	at org.springframework.orm.hibernate3.HibernateTemplate.execute(HibernateTemplate.java:373)
	at ome.services.util.Executor$Interceptor$1.doInTransaction(Executor.java:238)
	at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:128)
	at ome.services.util.Executor$Interceptor.invoke(Executor.java:236)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at $Proxy58.doWork(Unknown Source)
	at sun.reflect.GeneratedMethodAccessor166.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:301)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:112)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:169)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:92)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.interceptor.JamonPerformanceMonitorInterceptor.invokeUnderTrace(JamonPerformanceMonitorInterceptor.java:105)
	at org.springframework.aop.interceptor.AbstractTraceInterceptor.invoke(AbstractTraceInterceptor.java:110)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at $Proxy58.doWork(Unknown Source)
	at ome.services.util.Executor.execute(Executor.java:169)
	at ome.services.fulltext.FullTextThread.doRun(FullTextThread.java:124)
	at ome.services.util.ExecutionThread.run(ExecutionThread.java:58)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:585)
	at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:283)
	at org.springframework.scheduling.quartz.MethodInvokingJobDetailFactoryBean$MethodInvokingJob.executeInternal(MethodInvokingJobDetailFactoryBean.java:272)
	at org.springframework.scheduling.quartz.QuartzJobBean.execute(QuartzJobBean.java:86)
	at org.quartz.core.JobRunShell.run(JobRunShell.java:203)
	at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:520)
Caused by: org.apache.lucene.index.StaleReaderException: IndexReader out of date and no longer valid for delete, undelete, or setNorm operations
	at org.apache.lucene.index.IndexReader.acquireWriteLock(IndexReader.java:648)
	at org.apache.lucene.index.IndexReader.deleteDocument(IndexReader.java:672)
	at org.hibernate.search.backend.impl.lucene.LuceneWorker.remove(LuceneWorker.java:104)
	... 49 more
#86 Create ITypes interface for meta-work with model. API GatherReqs story 05/22/06

A service is needed for working with the model at a meta-level and perhaps working with the meta-model (ha ha).

See http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=ApiRequestsOMERO for use cases.

Other possible methods include:

  • IEnum iTypes.enum( Class k, String value )
  • Permissions iTypes.permissions( Class k )

Originally : http://bugs.openmicroscopy.org.uk/show_bug.cgi?id=656

#237 Have Hibernate events fire Spring events General 3.0-Beta4 story 07/17/06

With the EventMethodInterceptor (r788) it would be easy to raise Spring events (or even JMS messages) if we ever were to start using them internally.

#982 Develop our own ActiveServant container with eviction Services 3.0-Beta4 task 05/21/08

#883 shows that the servant logic in ServiceFactoryI has gotten too complicated and should be abstracted, especially as we add more types (Processors, Process, Callbacks, etc.) which need to be managed. Look into using FreezeEvictor?, but this must work properly with OmeroSessions.

#1063 Adding multi-image delete methods to IDelete Services 3.0-Beta4 task 08/25/08

Extend DeleteService? (#857) with two methods for deleting images:

  • by id set
  • by dataset id
#779 Dist's "ant update" sometimes fails to update jars Deployment 3.0-Beta4 defect 08/24/07

Assuming one is trying to update etc/local.properties into omero.ear!local.properties, the update is done only when:

  • time(etc/local.properties) > time(omero.ear!local.properties)

and time(omero.ear) plays no role. Therefore to ensure that the update occurs on has to touch etc/local.properties (something of a hack, but there appears to be no other way).

Ref: http://issues.apache.org/bugzilla/show_bug.cgi?id=10755

Note: this arose when a user had moved omero.ear to a system with a different timezone. The jar was silently NOT updated, causing issues.

#1072 loadContainerHierarchy - ome.conditions.SecurityViolation: Cannot read ome.model.containers.Dataset Services 3.0-Beta4 defect 08/31/08

loadContainerHierarchy cannot load hierarchy when project permissions is rwr--- and contains dataset with permissions (rw----).
I am not sure about different use cases.

#55 Define a "selftest" command for distribution diagnostics. Deployment 3.0-Beta4 task 05/18/06

As mentioned in Pragmatic Project Automation, a self-test ant target of the form: 

  java omero self-test

or 

  bin/omero self-test

which checks Java version, file/directory sanity (existence, permissions, etc.), database availablility, and other requirements for a production system. See <check-system/> for a first draft.

#814 Improve install/deploy experience Deployment 3.0-Beta4 task 10/17/07

Currently there are several situations and warnings which are only printed during or after JBoss start up. These could be performed during "ant deploy" or some future "ant install" target:

  • #444 check for postgres.jar in JBOSS_HOME/server/lib (or copy it)
  • check for omero.data.dir (/OMERO)
  • check dbpatch level
  • check Java version (and possible existence of _jboss-remoting.jar if needed)

This might should be just large warnings or possibly errors to prevent startup. If we ever replace JBOSS_HOME/bin/run.sh with a call to "ant jboss", then

#886 StructuredAnnotation: FileAnnotation General 3.0-Beta4 task 03/05/08

It will be really useful to load the original file object linked to the 

FileAnnotation

when the annotation is retrieved otherwise it is not really practical to play with client side. I have a solution for now.

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