| a8994a0 | Mark Hiner | 05 October 2023, 14:16:09 UTC | Merge pull request #120 from imagej/fix-loadannotations-npe Fixes a NPE when omeroAnnotations do not contain the pixelsID key | 05 October 2023, 14:16:09 UTC |
| 7e7e5d8 | Nicolas Chiaruttini | 05 October 2023, 13:49:59 UTC | Fixes a NPE when omeroAnnotations do not contain the pixelsID key | 05 October 2023, 13:49:59 UTC |
| e0b6857 | Nicolas Chiaruttini | 05 October 2023, 12:50:10 UTC | Update README.md Add OMERO 5.5-5.6 update site in the documentation | 05 October 2023, 12:50:10 UTC |
| ee0b585 | Curtis Rueden | 11 July 2023, 18:04:13 UTC | Happy New Year 2023 | 11 July 2023, 18:04:13 UTC |
| 3e2b494 | Curtis Rueden | 11 July 2023, 17:59:50 UTC | POM: update parent to pom-scijava 36.0.0 | 11 July 2023, 17:59:50 UTC |
| 2a17115 | Curtis Rueden | 10 March 2023, 02:53:42 UTC | Merge pull request #116 from mmongy/patch-1 Fix Java packages in command-line scripts. | 10 March 2023, 02:53:42 UTC |
| 51bada6 | mmongy | 08 March 2023, 16:06:38 UTC | Update run-script | 10 March 2023, 02:52:49 UTC |
| a39ffff | mmongy | 08 March 2023, 15:18:47 UTC | Update gen-scripts | 10 March 2023, 02:52:49 UTC |
| e2e675e | Curtis Rueden | 07 March 2023, 14:43:42 UTC | Merge pull request #115 from mmongy/patch-1 Update ScriptGenerator.java | 07 March 2023, 14:43:42 UTC |
| 8f5f12d | mmongy | 07 March 2023, 14:35:46 UTC | Update ScriptGenerator.java corrected a SyntaxError in line 224 | 07 March 2023, 14:35:46 UTC |
| 9337b98 | Curtis Rueden | 29 November 2022, 18:13:55 UTC | README: fix line wrapping | 29 November 2022, 18:13:55 UTC |
| f4a443d | Curtis Rueden | 29 November 2022, 18:13:22 UTC | Merge pull request #108 from jburel/update_readme small adjustments | 29 November 2022, 18:13:22 UTC |
| d5d8031 | Curtis Rueden | 18 August 2022, 20:51:22 UTC | README: change chat badge from gitter to zulip | 18 August 2022, 20:51:34 UTC |
| a3e635a | hinerm | 18 August 2022, 14:49:55 UTC | Change SNAPSHOT version Got auto-bumped to 6.6 but 5.7 seems more reasonable | 18 August 2022, 14:49:55 UTC |
| 7d3312a | hinerm | 18 August 2022, 14:44:03 UTC | Bump to next development cycle Signed-off-by: hinerm <hinerm@gmail.com> | 18 August 2022, 14:44:03 UTC |
| 0ebddb9 | hinerm | 18 August 2022, 14:42:50 UTC | Happy 2022 | 18 August 2022, 14:42:50 UTC |
| 96166d7 | hinerm | 18 August 2022, 14:42:22 UTC | POM: use HTTPS for schema location URL Maven no longer supports plain HTTP for the schema location. And using HTTP now generates errors in Eclipse (and probably other IDEs). | 18 August 2022, 14:42:22 UTC |
| e880487 | Mark Hiner | 18 August 2022, 14:41:28 UTC | Merge pull request #109 from imagej/omero-5.6 Update to OMERO 5.6 and Pom-SciJava 32 | 18 August 2022, 14:41:28 UTC |
| 7b13ff6 | hinerm | 18 August 2022, 14:37:40 UTC | Remove CTR note | 18 August 2022, 14:39:56 UTC |
| bafc0d6 | hinerm | 21 July 2022, 15:48:15 UTC | Remove IT from CI build This will have to be re-developed. See #113 | 18 August 2022, 14:39:56 UTC |
| b109563 | hinerm | 20 July 2022, 18:50:16 UTC | test.sh: set executable bit | 18 August 2022, 14:39:56 UTC |
| fea50bb | hinerm | 20 July 2022, 18:26:42 UTC | Split build and test steps | 18 August 2022, 14:39:56 UTC |
| 6cc53ee | hinerm | 20 July 2022, 18:20:04 UTC | Fix path to test.sh | 18 August 2022, 14:39:56 UTC |
| 1264d35 | hinerm | 20 July 2022, 17:29:51 UTC | Add missing javadoc tags | 18 August 2022, 14:39:56 UTC |
| 4b0b480 | hinerm | 20 July 2022, 15:20:45 UTC | pom.xml: remove newlines around argLine | 18 August 2022, 14:39:56 UTC |
| 44032c0 | hinerm | 20 July 2022, 15:10:43 UTC | OMEROFormat: preserve Key-Value pairs when writing An OMEROFormat.OMEROTranslator now copies the Metadata table between source and destination Metadata, which is then attached as a MapAnnotation to the final OMERO image. Closes #111 | 18 August 2022, 14:39:56 UTC |
| edeee53 | hinerm | 19 July 2022, 17:14:43 UTC | OMEROFormat: attach k-v pairs as global metadata See https://github.com/imagej/imagej-omero/issues/111 | 18 August 2022, 14:39:56 UTC |
| 1466dbf | hinerm | 19 July 2022, 15:34:28 UTC | Formatting | 18 August 2022, 14:39:56 UTC |
| 0e21388 | hinerm | 19 July 2022, 15:32:49 UTC | OMEROFormat: only create axes that are present This works around an issue where we always create a channel axis, which results in CompositeImages being created on the imagej-legacy side, which can have synchronization issues with the corresponding ImagePlus. | 18 August 2022, 14:39:56 UTC |
| 9a23ee8 | hinerm | 01 July 2022, 13:51:03 UTC | OpenFromOMERO: set rois as output This is necessary downstream for the imagej-omero-legacy postprocessing plugins to pick up and attach the rois to the active ImagePlus | 18 August 2022, 14:39:56 UTC |
| b3c0c51 | hinerm | 28 June 2022, 19:54:11 UTC | OMEROServer: ignore leading web protocol | 18 August 2022, 14:39:56 UTC |
| 63bd6c2 | hinerm | 27 June 2022, 19:28:30 UTC | SaveToOmero: use OMEROLocation to get ImageID Sources are not formatted the same as they were in previous iterations. | 18 August 2022, 14:39:55 UTC |
| a5723b0 | hinerm | 27 June 2022, 19:27:28 UTC | Move roiCache to OMEROService The workaround to keep it in OmeroSession is too extreme and quickly breaks down when we look at imagej-omero-legacy. | 18 August 2022, 14:39:55 UTC |
| 514a239 | hinerm | 27 June 2022, 15:43:56 UTC | Add imagej-ui-swing as test dependency This makes the Main test nicer when running from an IDE. | 18 August 2022, 14:39:55 UTC |
| f060bb9 | hinerm | 24 June 2022, 20:32:37 UTC | OmeroIT: remove workaround for Writer.close This is no longer necessary as OMEROFormat.Writer no longer closes its session. | 18 August 2022, 14:39:55 UTC |
| 114057a | hinerm | 24 June 2022, 20:31:46 UTC | OMEROFormat.Writer: don't close the session A writer has no business ending the session with OMERO. This should be managed by the OMEROService or other calling code. | 18 August 2022, 14:39:55 UTC |
| 18cf3b9 | hinerm | 22 June 2022, 19:00:14 UTC | Remove final from @Parameters | 18 August 2022, 14:39:55 UTC |
| e5f498e | hinerm | 17 June 2022, 17:41:16 UTC | OmeroIT: download table via tableId Not the image id | 18 August 2022, 14:39:55 UTC |
| 16eccda | hinerm | 17 June 2022, 17:17:57 UTC | OMEROFormat: set ImageID on Metadata OMEROSession grabs the image id off the Metadata to parse pixel data from OMERO, thus we need to set it in the Parser before passing control to the session. | 18 August 2022, 14:39:55 UTC |
| 395d896 | hinerm | 17 June 2022, 17:17:54 UTC | OMEROLocation: add getter for ImageID | 18 August 2022, 14:39:55 UTC |
| 3e9fff4 | hinerm | 16 June 2022, 19:46:49 UTC | OMEROFormat: attach server to metadata | 18 August 2022, 14:39:55 UTC |
| 85bcd02 | hinerm | 18 August 2022, 14:33:59 UTC | Update pom-scijava to 32.0.0-beta-5 This brings us to the latest SCIFIO version and removes the need for OMERO version properties. | 18 August 2022, 14:39:55 UTC |
| 29c61ff | hinerm | 20 June 2022, 17:43:46 UTC | TEMP: pin to SCIFIO 0.43.2 | 18 August 2022, 14:39:55 UTC |
| 7296118 | hinerm | 13 June 2022, 20:06:45 UTC | OmeroIT: consolidate tests Remove the tests that required pre-existing data. | 18 August 2022, 14:39:55 UTC |
| ee7c141 | hinerm | 13 June 2022, 19:47:40 UTC | OmeroIT: ensure test image exists Each test that uploads an image or attachments to an image now uploads a new copy of blobs to the DB and operates on that particular image id. There is no longer an assumption of pre-exisiting data in the server for the IT. | 18 August 2022, 14:39:55 UTC |
| 92cfd57 | hinerm | 13 June 2022, 19:26:04 UTC | OmeroIT: rely on OMEROService's session cache Writing an image to the server will disconnect the session. By always using OMEROService.session() we will reconnect the session if needed. | 18 August 2022, 14:39:55 UTC |
| f6e92c4 | hinerm | 13 June 2022, 18:59:32 UTC | OMEROFormat: attach server in writer.setDest setDest is called immediately before writing to a location, thus the server should be updated in the OMEROFormat Metadata. | 18 August 2022, 14:39:55 UTC |
| 1200749 | hinerm | 13 June 2022, 18:59:12 UTC | OMEROFormat: add Metadata.setServer This field needs a way to actually be set | 18 August 2022, 14:39:55 UTC |
| 6532ce9 | hinerm | 13 June 2022, 18:58:01 UTC | OmeroIT: create session from service It should always be done in this direction to ensure the service knows of all active sessions. | 18 August 2022, 14:39:55 UTC |
| 83fd435 | hinerm | 10 June 2022, 20:11:39 UTC | OMEROFormat: claim OMEROLocations | 18 August 2022, 14:39:55 UTC |
| 261c5f2 | hinerm | 09 June 2022, 20:01:37 UTC | OmeroIT: update to current session API | 18 August 2022, 14:39:55 UTC |
| d5b39c3 | hinerm | 09 June 2022, 20:01:13 UTC | OMEROSession: set experimenter | 18 August 2022, 14:39:55 UTC |
| 794b896 | hinerm | 09 June 2022, 20:00:35 UTC | Add scijava-io-http dependency Required for opening remote images (in IT) | 18 August 2022, 14:39:55 UTC |
| 477d1e6 | hinerm | 09 June 2022, 20:00:26 UTC | Update to latest pom-scijava | 18 August 2022, 14:39:55 UTC |
| 5a67524 | hinerm | 08 June 2022, 19:10:40 UTC | OmeroIT: change server name to localhost | 18 August 2022, 14:39:55 UTC |
| 30b839f | hinerm | 08 June 2022, 17:33:21 UTC | DownloadROITest: update mock usage/service context | 18 August 2022, 14:39:55 UTC |
| 7d2887f | hinerm | 08 June 2022, 17:26:29 UTC | TreeNodeRPC conversion test - set session context | 18 August 2022, 14:39:55 UTC |
| 17717cc | hinerm | 08 June 2022, 17:17:34 UTC | TreeNodeToROIDCTest - set session context We need to set session contexts for conversion. | 18 August 2022, 14:39:55 UTC |
| bf92f86 | hinerm | 08 June 2022, 17:03:57 UTC | UploadROITest: update mock construction Use @Injectable Gateway and manually inject the OMEROService. | 18 August 2022, 14:39:55 UTC |
| db248b7 | hinerm | 08 June 2022, 17:02:51 UTC | OMEROSession empty constructor: init roiCache This is a trivial field that needs no connections to the context nor an OEMRO server. | 18 August 2022, 14:39:55 UTC |
| 4874fdf | hinerm | 08 June 2022, 17:02:00 UTC | DefaultOMEROService: add ThreadLocal initialValue Otherwise get() will return null, of course | 18 August 2022, 14:39:55 UTC |
| fcda5ad | hinerm | 08 June 2022, 16:51:22 UTC | UploadTableTest: update mock construction Use @Injectable Gateway and manually inject the OMEROService. Sadly we cannot auto-inject the service because doing so would trigger the single-param OMEROService constructor of OMEROSession. | 18 August 2022, 14:39:55 UTC |
| be47b5b | hinerm | 08 June 2022, 16:50:50 UTC | Update WellSampleData > WellData WellSampleData table columns are apparently no longer supported | 18 August 2022, 14:39:55 UTC |
| 41f040e | hinerm | 08 June 2022, 16:05:25 UTC | DownloadTableTest: use injectable gateway This appears to be the correct way to make the session use a mocked gateway. | 18 August 2022, 14:39:55 UTC |
| 023c3d0 | hinerm | 08 June 2022, 16:02:49 UTC | OMEROSession: add dummy constructor To test without an OMERO server we need a way to create a session that does not attempt to connect to OMERO. | 18 August 2022, 14:39:55 UTC |
| d754f08 | hinerm | 01 June 2022, 16:08:00 UTC | README: add link to omero docker | 18 August 2022, 14:39:55 UTC |
| 648107d | hinerm | 01 June 2022, 15:26:53 UTC | Formatting | 18 August 2022, 14:39:55 UTC |
| 01142d7 | hinerm | 01 June 2022, 15:26:42 UTC | OMEROSession: correct join/create logic | 18 August 2022, 14:39:55 UTC |
| a8c10fb | hinerm | 25 May 2022, 19:41:08 UTC | Tests: remove unnecessary OMEROLocation | 18 August 2022, 14:39:55 UTC |
| 245a148 | hinerm | 25 May 2022, 19:37:41 UTC | OmeroIT: update to latest API | 18 August 2022, 14:39:55 UTC |
| 74cff18 | hinerm | 25 May 2022, 19:37:31 UTC | UploadTableTest: update to latest API | 18 August 2022, 14:39:55 UTC |
| a2e278c | hinerm | 25 May 2022, 19:19:03 UTC | DownloadTableTest: update to new API | 18 August 2022, 14:39:55 UTC |
| a739f71 | hinerm | 25 May 2022, 19:15:19 UTC | UploadROITest: convert to new API | 18 August 2022, 14:39:55 UTC |
| 1b14a8d | hinerm | 25 May 2022, 19:09:20 UTC | DownloadROITest: convert to new API | 18 August 2022, 14:39:55 UTC |
| 36cec07 | hinerm | 25 May 2022, 18:52:00 UTC | OMEROFormatTest: remove testParseArguments This method no longer exists | 18 August 2022, 14:39:55 UTC |
| 361aa29 | hinerm | 25 May 2022, 18:51:39 UTC | OMEROFormatTest: Use OMEROLocation | 18 August 2022, 14:39:55 UTC |
| 81c267a | hinerm | 25 May 2022, 17:07:50 UTC | ModuleAdapter: use OMEROSession Minimal changes to get ModuleAdapter compiling. | 18 August 2022, 14:39:55 UTC |
| bf14614 | hinerm | 25 May 2022, 17:01:45 UTC | OMEROSession: update constructor documentation | 18 August 2022, 14:39:55 UTC |
| b1726f2 | hinerm | 25 May 2022, 17:01:12 UTC | OMEROSession: make client constructor public We shouldn't force a new client to be constructed, e.g. in the case of ModuleAdapter which has its own client. | 18 August 2022, 14:39:54 UTC |
| 0ec5f7a | hinerm | 25 May 2022, 16:52:06 UTC | OMEROService: remove thread note | 18 August 2022, 14:39:54 UTC |
| 96411e9 | hinerm | 24 May 2022, 18:32:15 UTC | Enable OMEROSession use by converters In cases we know converters will be used that require an active OMEROSession, we now set the current session in a ThreadLocal data structure within the OMEROService and retrieve it within the converters. | 18 August 2022, 14:39:54 UTC |
| 1d95e62 | hinerm | 24 May 2022, 18:30:15 UTC | OMEROService: add concept of ThreadLocal sessions This is important for contextual operations that require a session but only have access to the OMEROService (e.g. converters) | 18 August 2022, 14:39:54 UTC |
| cda0c32 | hinerm | 20 May 2022, 18:34:26 UTC | Update getting started notes | 18 August 2022, 14:39:54 UTC |
| 7e8a746 | hinerm | 20 May 2022, 18:30:40 UTC | OMEROSession: add log accessor | 18 August 2022, 14:39:54 UTC |
| b7f2a6d | hinerm | 20 May 2022, 18:23:26 UTC | OMEROFormat: remove completed TODO | 18 August 2022, 14:39:54 UTC |
| a1e0234 | hinerm | 20 May 2022, 18:22:42 UTC | OMEROFormat: use OMEROException | 18 August 2022, 14:39:54 UTC |
| 7b90f7f | hinerm | 19 May 2022, 17:22:47 UTC | Add support for re-establishing OMERO sessions - sessionID is now cached by the OMEROSession instead of OMEROCredentials - OMEROService will try to use credentials if available when creating a session, but they are no longer strictly necessary if the session has a cached sessionID - OMEROSession now has a restore() method optionally accepting an OMEROCredentials, which are preferred if present to a cached sessionID | 18 August 2022, 14:39:54 UTC |
| 928ae6d | hinerm | 19 May 2022, 13:27:51 UTC | Apply SciJava formatter | 18 August 2022, 14:39:54 UTC |
| 75ce031 | hinerm | 19 May 2022, 13:26:27 UTC | OMEROSession: public API throws OMEROException | 18 August 2022, 14:39:54 UTC |
| e3be8d4 | hinerm | 18 May 2022, 20:09:43 UTC | OMEROSession: consolidate service dependencies | 18 August 2022, 14:39:54 UTC |
| 60101ab | Curtis Rueden | 17 May 2022, 17:29:18 UTC | Add notes for getting started | 18 August 2022, 14:39:54 UTC |
| 9e5f6d5 | Curtis Rueden | 17 May 2022, 17:16:08 UTC | Add FIXME for FileLocation | 18 August 2022, 14:39:54 UTC |
| 22cd6f3 | Curtis Rueden | 17 May 2022, 17:15:54 UTC | test.sh: switch from git:// to https:// GitHub doesn't support the git protocol anymore. | 18 August 2022, 14:39:54 UTC |
| 757651f | Curtis Rueden | 11 May 2022, 21:34:38 UTC | Improve OMERO session constructs * An OMEROServer is a host+port * An OMEROLocation is an OMEROServer + resource path (e.g. image/23) * An OMEROCredentials is a user+pass or sessionID * An OMEROSession is an active omero.client connection backed by OMEROServer+OMEROCredentials. OMEROService was a beast. And OMEROSession publicly exposed a ton of implementation details. These changes aim to dramatically improve encapsulation. | 18 August 2022, 14:39:54 UTC |
| ffb6dfb | hinerm | 20 June 2022, 17:50:03 UTC | Flesh out OMEROLocation | 18 August 2022, 14:39:54 UTC |
| 7572998 | jmoore | 01 September 2020, 11:08:05 UTC | Update omero-test-infra to v0.6.3 | 18 August 2022, 14:39:54 UTC |
| 84150cb | Curtis Rueden | 12 June 2020, 23:52:59 UTC | Remove SSLUtils hack It's no longer necessary with OMERO 5.5+. | 18 August 2022, 14:39:54 UTC |
| 0567569 | Curtis Rueden | 07 June 2020, 15:09:54 UTC | Travis: update test to OMERO 5.6 Co-authored-by: Josh Moore <josh@glencoesoftware.com> | 18 August 2022, 14:39:54 UTC |
| b8f4ff5 | Mark Hiner | 04 June 2020, 19:02:22 UTC | Update to the new SCIFIO API This updates the parent POM to pom-scijava 29.0.0-beta-2. We don't have String ids any more, but rather Locations and DataHandles. This commit also removes OMEROSession from the JMockit Expectations. Having instantiation without assignment appears to be non-kosher in the latest JMockit. Removing this invocation did not cause tests to fail, so it's not clear why it was originally needed. See also: * https://stackoverflow.com/q/16576177 * https://gitmemory.com/issue/jmockit/jmockit1/630/531445943 * https://gitmemory.com/issue/jmockit/jmockit1/630/531494884 Signed-off-by: Curtis Rueden <ctrueden@wisc.edu> | 18 August 2022, 14:39:54 UTC |
| b97c596 | Mark Hiner | 04 June 2020, 19:01:29 UTC | Add javaagent parameter for testing from mvn See https://stackoverflow.com/a/53926201 | 18 August 2022, 14:39:54 UTC |
