BUG: Importing LEI

[cxallan]

Problems with "used files" and lookups on certain platforms.

[bwzloranger]

Much of the metadata for these files is missing such as Filters, some Detector information, voltages, etc. Channel colors are also wrong. See nightshade/brian's tests/lei/ for 4.1 examples to compare with mage/root/brian's test/lei 4.2 examples.

[cxallan]

Replying to bwzloranger:

Much of the metadata for these files is missing such as Filters, some Detector information, voltages, etc. Channel colors are also wrong. See nightshade/brian's tests/lei/ for 4.1 examples to compare with mage/root/brian's test/lei 4.2 examples.

Data types appear to be being parsed incorrectly in parseInstrumentData().

[cxallan]

(In [7069]) Updating to ​bio-formats:r6356; fixes issues with LEI metadata. (See #2410)

[cxallan]

Problems inserting the newly populated metadata from r7069:

2010-05-21 12:49:42,666 147396     [2-thread-1] INFO   ormats.importer.gui.LoggingImportMonitor  - INTERNAL_EXCEPTION: /Users/callan/testimages/lei/seq_colon_dapi_phalloidinA488.lei
java.lang.RuntimeException: omero.ValidationException
    serverStackTrace = "ome.conditions.ValidationException: could not insert: [ome.model.acquisition.LightPathEmissionFilterLink]; SQL [insert into lightpathemissionfilterlink (child, creation_id, external_id, group_id, owner_id, permissions, update_id, parent, version, id) values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)]; constraint [lightpathemissionfilterlink_parent_key]; nested exception is org.hibernate.exception.ConstraintViolationException: could not insert: [ome.model.acquisition.LightPathEmissionFilterLink]
                                at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:637)
                                at org.springframework.orm.hibernate3.HibernateAccessor.convertHibernateAccessException(HibernateAccessor.java:412)
                                at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:117)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:175)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:111)
                                at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                                at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                                at $Proxy54.doWork(Unknown Source)
                                at ome.services.util.Executor$Impl.execute(Executor.java:339)
                                at ome.services.throttling.Adapter.run(Adapter.java:51)
                                at ome.services.throttling.InThreadThrottlingStrategy.runnableCall(InThreadThrottlingStrategy.java:89)
                                at ome.services.blitz.impl.AbstractAmdServant.runnableCall(AbstractAmdServant.java:146)
                                at ome.services.blitz.impl.MetadataStoreI.saveToDB_async(MetadataStoreI.java:167)
                                at omero.api._MetadataStoreTie.saveToDB_async(_MetadataStoreTie.java:85)
                                at omero.api._MetadataStoreDisp.___saveToDB(_MetadataStoreDisp.java:211)
                                at omero.api._MetadataStoreDisp.__dispatch(_MetadataStoreDisp.java:333)
                                at IceInternal.Incoming.invoke(Incoming.java:159)
                                at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
                                at Ice.ConnectionI.message(ConnectionI.java:972)
                                at IceInternal.ThreadPool.run(ThreadPool.java:577)
                                at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
                                at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
                        "

[cxallan]

(In [7071]) Ensuring that duplicate references are not possible but that order is maintained by checking reference existence before adding a new one. (See #2410)

[cxallan]

Filter metadata now seems to have an odd order or mixed up indexing with Filter "SP mirror 3" having the cut in/cut out values that Filter "SP mirror 1" did previously.

[cxallan]

(In [7074]) Updating to ​bio-formats:r6359; fixes LEI issues with files missing from getUsedFiles(). (See #2410)

[cxallan]

Resolved with the closing of #2440 (r7107).