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Fix bug; Lookupname for omero home dir was overwritten #156

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merged 4 commits into from
Jul 30, 2020

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dominikl
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@dominikl dominikl commented Jul 28, 2020

The USER_MDE_PATH LookupName conflicted with the USER_HOME_OMERO one, which caused issues #154 and #153.

Test:
See travis builds of last two commits to check that the units test works.
Check that Insight still works as expected.
And check that Insight now picks up the correct location for its files again, e.g. the log file, see #153 .

@dominikl
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If it's not too urgent to merge, I'll add a test which checks uniqueness of the LookupNames to prevent this in future.

@dominikl
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There were actually two more LookupNames with identical values. See commit 1382779 , added unit test, which failed. Then commit a5b2d19 with the fixed names, test passed.

@joshmoore
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This is great, @dominikl . With the passing test, I'm inclined to get this in (and released). I can't overly speak to the removed fields though in terms of breakingness. (If you have any concerns, any option would be to deprecate them instead)

@dominikl
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True, I added them again as deprecated. Intellij flagged them up as unused, but I'll check again properly and remove them after the next release.

@pwalczysko
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Testing the functionality.

Try to repeat the problems:

Mac OS, release insight 5

  1. Repeat the failure of script: Run Batch image Export script, then try to download the attached zip. Failure below.
java.lang.Exception: omero.gateway.exception.DSAccessException: Cannot create file  /Applications/OMERO.insight.app/Contents/Java/config/filesOmero/file annotation 144975
	at org.openmicroscopy.shoola.env.data.OMEROGateway.download(OMEROGateway.java:3347)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:3291)
	at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.downloadFile(OmeroMetadataServiceImpl.java:1658)
	at org.openmicroscopy.shoola.env.data.views.calls.FilesLoader$1.doCall(FilesLoader.java:98)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.FileNotFoundException: /Applications/OMERO.insight.app/Contents/Java/config/filesOmero/file annotation 144975 (No such file or directory)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:162)

  1. Repeat the failure of download of Import log

Mac OS, insight 5.5.11 release.
The import log download after successful import fails, short message about impossibility of downloading the file.
From insight log:

Data Retrieval Failure: omero.gateway.exception.DSAccessException: Cannot create file  /Applications/OMERO.insight.app/Contents/Java/config/filesOmero/importLog_285793
	at org.openmicroscopy.shoola.env.data.OMEROGateway.download(OMEROGateway.java:3347)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.downloadFile(OMEROGateway.java:3291)
	at org.openmicroscopy.shoola.env.data.OmeroMetadataServiceImpl.downloadFile(OmeroMetadataServiceImpl.java:1658)
,,,

Note: I am also not sure which script did the users run, but possibly the problem they were hitting was the subsequent inability to download the resulting file (attachment to the image on which the script was run). I am repeating the failure of downloading (any) attachment from insight in Ad 1. above.

@pwalczysko
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So insight 5.5.11 is failing to download any attachments, with the error reported in #156 (comment) - I think this upgrades significantly the seriousness of the issue here...

@pwalczysko
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Tested the insight from merge-ci.

All problems reported in #156 (comment) are fixed.
Ready to merge fmpov.

@joshmoore
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Releasing as 5.5.13

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3 participants