Insight connectors dev 4 4 #1321

jburel · 2013-06-28T15:32:14Z

This PR combines commit from gh-1278 and gh-1304. Not all commits are applicable to dev_4_4.
This should fix connection issue noticed on develop and at times on dev_4_4.
To test:

import data.
Browse dataset.
View images.
etc.

This might require to use the client for few days before the PR can be merged.

--rebased-from #1304
--rebased-from #1278
etc

pwalczysko · 2013-07-03T09:11:03Z

Bug: cannot create thumbs in importer.
Workflow:

login as user-6
ImportAs user-5, group read-write-1 (still logged in as user-6), dv folder on test_images_good
the import is successful, the images are okay and their thumbs are okay in Data Manager but
the thumbnails cannot be created error is in the importer window (see screenshot below)
if you import the same images into the same group, but this time as yourself (=user-6 as user-6), the thumbs in importer are okay (see second screenshot)

pwalczysko · 2013-07-03T09:25:07Z

Plates thumbs loading for big plates is still slow (much slower than small images). The 380 well plate loads in 4-5 minutes.

This did not repeat though - on other occassion, the loading was fast.

pwalczysko · 2013-07-03T09:36:37Z

Connection Destroyed after:

change channel name of a plate
in the middle of the process, go Switch User and confirm the dialog that you want to disconnect
connection destroyed popup appears and is not clickabel

Similar workflow already reported for develop, but I think the problem is sorted there now (see http://trac.openmicroscopy.org.uk/ome/ticket/11032 - the change is that channel name of plate was manipulated instead of big image viewing)

jburel · 2013-07-03T09:50:03Z

@pwalczysko: The last 4 commits should fix the thumbnail after import issue. They do not need to be ported to develop, they are related to the import sequence in dev_4_4

jburel · 2013-07-03T10:50:22Z

@pwalczysko: Few commits were not backported

pwalczysko · 2013-07-03T14:24:45Z

The two problems reported above (connection destroyed and cannot create thumb) are fixed. The problem with slow reading of the plate thumbs cannot be repeated. Works fine.

joshmoore · 2013-07-03T15:05:48Z

I'm slightly concerned about rushing this branch. Sorry, I just haven't had a chance to build this locally (and won't before leaving).

jburel · 2013-07-03T15:08:48Z

@joshmoore, @pwalczysko: I think the PR should remain opened for a while. No need to be merged now (cf. description) since we should not have any development happening

chris-allan · 2013-07-17T07:08:37Z

Excluded until we can get the required code from #1345 in. Then this branch can have dev_4_4 merged into it and conflicts resolved.

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Connector objects were being created without needed in some instances. Since the instantiation of an omero.clients object has high overhead, it's worth preventing this. Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Since all service access calls getConnector(), all logic for handling the checking of alive sessions and network has been refactored into the one location. This also prevents multiple calls. Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/util/NetworkChecker.java

Most likely, the synchronized methods on OMEROGateway were hiding this, but a race-condition during startup allowed dsFactory.getCredentials() to return null.

* Remove Connector.reconnect() since it leaves services dangling * Remove all get*Service() methods from OMEROGateway * Refactor all get*Service() methods in Connector * Use concurrent storage for services in Connector * Close all stateful services as quickly as possible. Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/agents/fsimporter/ImportResultLoader.java

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java components/insight/SRC/org/openmicroscopy/shoola/env/data/OmeroImageService.java components/insight/SRC/org/openmicroscopy/shoola/env/data/OmeroImageServiceImpl.java

Some thumbnails could take time to load. Display the progress bar so the user is notified of loading progress. Conflicts: components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/ThumbnailLoader.java

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/views/calls/ThumbnailLoader.java

The maximum size of a plane is 2000*2000 see 5b86032

The problem only occurs when import data for another user.

Method was invoked twice.

Resetting the channels name could take some time. if the user uses the switch user, service no longer valid could be used.

jburel · 2013-07-17T12:11:40Z

Rebased the branch and removed the exclude label

mtbc · 2013-07-21T09:20:54Z

Do we want to mark this "on hold" so it hangs around awhile quietly getting accidentally tested?

jburel · 2013-08-01T08:25:06Z

This PR is in the daily build so indirectly tested.

joshmoore · 2013-09-03T22:37:23Z

@jburel: is this a target for 4.4.9? If so, we should look to move it out of ON_HOLD.

jburel · 2013-09-04T05:22:05Z

@joshmoore: 4.4.9 target.This is a rebase, marked as onhold so it could test w/o specific review. Removing label.

pwalczysko · 2013-09-10T12:09:18Z

This is fine on Mac. Nevertheless, I wanted to give it a go on Windows (see #1453 (comment)). As the windows artifacts are not being built atm, I would wait till they do and give it a go.

joshmoore · 2013-09-11T08:30:59Z

Sounds good, @pwalczysko. I think the build has been fixed now: http://hudson.openmicroscopy.org.uk/view/2.%20Stable/job/OMERO-merge-stable/lastSuccessfulBuild/artifact/src/target/OMERO.insight-4.4.8-786-d0b4044-ice33-b360-win.zip

pwalczysko · 2013-09-11T15:54:40Z

Tested on Win 7 Java 1.6. No problems even when challenged (large plate & change settings & switch user).
Ready to merge.

joshmoore · 2013-09-11T18:11:44Z

Thanks, @pwalczysko. (And, I guess, @jburel too 😄)

Insight connectors dev 4 4

jburel mentioned this pull request Jul 16, 2013

Use the reflected network check on non-Linux platforms #1345

Merged

joshmoore and others added 20 commits July 17, 2013 13:05

Refactor connectors to multimap

a850719

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Remove synchronized from isSessionAlive

ec07b98

Add caching to Connector

b655ae1

Connector objects were being created without needed in some instances. Since the instantiation of an omero.clients object has high overhead, it's worth preventing this. Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Remove ping since it doesn't check entryUnecrypted

33c0e29

Add static caching to NetworkChecker

c1bba2a

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/util/NetworkChecker.java

Fix race condition on UserDetails

b9fab95

Most likely, the synchronized methods on OMEROGateway were hiding this, but a race-condition during startup allowed dsFactory.getCredentials() to return null.

Increase keep alive check to 30 seconds

1ef82f8

Use cached Connector!

98b0594

Remove all synchronization from OMEROGateway methods

fd3626b

Fix concurrent modification err in Connector

8efe8ab

Review loading of thumbnails. (see #10748)

10ec5ac

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/agents/fsimporter/ImportResultLoader.java

Fix loading of thumbnails for bird eye view and fields (see #11071)

217047a

Do not set the default for the thumbnails.

85c3ee6

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java

Remove commented out code.

84efe04

Do not specify the user's ID.

f989941

Remove casting.

dda07fa

Create a thumbnail store.

167280b

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java components/insight/SRC/org/openmicroscopy/shoola/env/data/OmeroImageService.java components/insight/SRC/org/openmicroscopy/shoola/env/data/OmeroImageServiceImpl.java

Add support for multiple thumbnail loaders.

fcbc1f7

jburel added 16 commits July 17, 2013 13:09

Set the pixels Id.

1b6c2f9

Display the loading status

dffc4a1

Some thumbnails could take time to load. Display the progress bar so the user is notified of loading progress. Conflicts: components/insight/SRC/org/openmicroscopy/shoola/agents/dataBrowser/ThumbnailLoader.java

Do not go back to the intermediate state.

302b295

Adjust loader and message.

3375dc7

Conflicts: components/insight/SRC/org/openmicroscopy/shoola/env/data/views/calls/ThumbnailLoader.java

Roll back thumbnail dimension request.

cd683f6

Remove @OverRide annotation.

93f265c

Do not load the image after import for large plane.

d05045f

The maximum size of a plane is 2000*2000 see 5b86032

Log the exception.

37a863d

Refactor code to load the imported image.

6cbc292

Fix retrieval of thumbnail after import.

d782c61

The problem only occurs when import data for another user.

Fix retrieval of user photo (see #11110)

56ac1f3

Sort the list before splitting it.

e4a659f

Remove call to close method

eaccef1

Method was invoked twice.

Remove unused import.

f43e809

Add Java doc.

c15868d

TMP Solution to support long lasting call.

62a518f

Resetting the channels name could take some time. if the user uses the switch user, service no longer valid could be used.

Remove unused import.

3b34b43

jburel mentioned this pull request Sep 9, 2013

Thumbnail loader #1304

Merged

joshmoore mentioned this pull request Sep 9, 2013

Remove synchronization from insight connectors/gateway #1278

Merged

joshmoore added a commit that referenced this pull request Sep 11, 2013

Merge pull request #1321 from jburel/insight-connectors-dev_4_4

5db22f6

Insight connectors dev 4 4

joshmoore merged commit 5db22f6 into ome:dev_4_4 Sep 11, 2013

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Insight connectors dev 4 4 #1321

Insight connectors dev 4 4 #1321

jburel commented Jun 28, 2013

pwalczysko commented Jul 3, 2013

pwalczysko commented Jul 3, 2013

pwalczysko commented Jul 3, 2013

jburel commented Jul 3, 2013

jburel commented Jul 3, 2013

pwalczysko commented Jul 3, 2013

joshmoore commented Jul 3, 2013

jburel commented Jul 3, 2013

chris-allan commented Jul 17, 2013

jburel commented Jul 17, 2013

mtbc commented Jul 21, 2013

jburel commented Aug 1, 2013

joshmoore commented Sep 3, 2013

jburel commented Sep 4, 2013

pwalczysko commented Sep 10, 2013

joshmoore commented Sep 11, 2013

pwalczysko commented Sep 11, 2013

joshmoore commented Sep 11, 2013

Insight connectors dev 4 4 #1321

Insight connectors dev 4 4 #1321

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jburel commented Jun 28, 2013

pwalczysko commented Jul 3, 2013

pwalczysko commented Jul 3, 2013

pwalczysko commented Jul 3, 2013

jburel commented Jul 3, 2013

jburel commented Jul 3, 2013

pwalczysko commented Jul 3, 2013

joshmoore commented Jul 3, 2013

jburel commented Jul 3, 2013

chris-allan commented Jul 17, 2013

jburel commented Jul 17, 2013

mtbc commented Jul 21, 2013

jburel commented Aug 1, 2013

joshmoore commented Sep 3, 2013

jburel commented Sep 4, 2013

pwalczysko commented Sep 10, 2013

joshmoore commented Sep 11, 2013

pwalczysko commented Sep 11, 2013

joshmoore commented Sep 11, 2013