fix #11877: move import logs to upload jobs instead of annotations #2055
Conversation
|
@mtbc: what is the impact of this PR in terms of upgrade from 5.0.0-rc1 to 5.0.0? In terms of upgrade documentation? |
|
Conflicting PR.Removed from build OMERO-5.0-merge-daily#564. See the console output for more details. |
|
@sbesson: I don't think this is worth any upgrade documentation. The system will work apparently the same with or without the upgrade script, and for good measure the same upgrade will be included in the 5.0.0 → 5.0.1 script. Clients don't currently offer access to "old" import logs so if some older imports can't be found, through the script not having yet been run, nobody will notice. Also, this PR doesn't remove clients' not listing old-style import logs among the file annotations. The conflict is with #2043 -- we both add the same import -- so I will wait for that to be merged, then rebase, fix, and force-push. |
| @@ -607,6 +607,56 @@ UPDATE image set archived = false where id in ( | |||
| AND i.archived | |||
| AND NOT EXISTS ( SELECT 1 FROM pixelsoriginalfilemap m WHERE m.child = p.id)); | |||
|
|
|||
|
|
|||
| -- #11877 move import logs to upload jobs so they are no longer file annotations | |||
| CREATE FUNCTION upgrade_import_logs() RETURNS void AS $$ | |||
There was a problem hiding this comment.
Not that it hurts, but I don't think this situation can occur: there would never be FS logs in a 4.4 DB.
There was a problem hiding this comment.
Ah, excellent, maybe I should just omit this then.
|
With a local build and server, import logs showed up in Insight fine, and there were no new entries in the filesetannotationlink table. Looks good! |
|
Conflicting PR.Removed from build OMERO-5.0-merge-daily#565. See the console output for more details. |
|
2043 is merged, @mtbc, if you want to rebase and kick off the daily build. |
omitting x- prefix for http://tools.ietf.org/html/bcp178
to repeat in OMERO5.0__1 for those already on OMERO5.0__0
Conflicts: components/blitz/src/ome/formats/importer/ImportLibrary.java
|
Functionally, this works as expected. Code seems fine, but (as with any big PR), I can only give a +1 (on the gerrit scale) - I'm not sure if there are any subtle implications that I'm missing. Another thing for viewing log files under Ubuntu - it doesn't work. Clicking the "View" button and then selecting the log file in the list only brings up an "Open file" modal and nothing happens. I wonder if it's some Java UI weirdness on Linux or is it connected to the MIME type? I'd expect the log file to open in a text editor, as it happens on OS X. |
|
Thanks for trying it. Which JVM? @jburel, any thoughts? |
|
The default text editor should be used unless none is set. I have started to modify the Open With section to integrate FLIMfit and other applications. I will do further tests. Not related to that PR. |
|
Deletion of filesets is broken due to the new original file link on the upload job. |
|
The delete tests should now be fixed. |
fix #11877: move import logs to upload jobs instead of annotations
|
@joshmoore: Should this be rebased, or is there a different plan for how import logs should be linked in 5.1? Or perhaps that plan is easier to reach after a rebase of this. |
|
Definitely rebase. Even if there were a different strategy, we should have this in place for the moment. |
|
@mtbc yes, db changes were the next item on my list, and I was going to ask you for some pointers. |
|
Once #1742 is merged will rebase against that. |
|
Now awaiting #2163. |
|
--rebased-to #2191 |
Fixes http://trac.openmicroscopy.org.uk/ome/ticket/11877 to make import logs attached to a fileset's upload job instead of being a file annotation on it; the import log's original file has a distinct MIME type. The upgrade script from RC1 now includes PL/pgSQL for moving legacy import logs accordingly.
Ensure that the new integration tests run and pass in http://ci.openmicroscopy.org/job/OMERO-5.0-merge-integration-java/lastCompletedBuild/testngreports/integration/integration.MetadataServiceTest/.
In testing, make sure that import logs can still be viewed from Insight, and that they indeed no longer exist as annotations in the database.