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Jim Procter
@foreveremain:matrix.org
[m]
Meeting at 2pm UK / 3pm Warsawa today ?
3 replies
Jim Procter
@foreveremain:matrix.org
[m]
Mateusz - if you want to change this it is straightforward - simply create a new XMLSchema spec or add optional components to the existing wsparamset storage spec. Alternatively you can simply reuse Slivka's existing JSON serialse/deserialise ?
you can decide YAGNI for external representations if you like. There will still be client specific glue code for mapping between jalview parameter objects and the client's parameter representation. Its a normative refactoring - which may or may not yield simpler code with fewer declarations.
benzoid
@benzoid
@foreveremain:matrix.org I'm trying to get my API branch up to date with develop. I think I've got the three overlapping classes merged okay (i.e. the ones with conflicts) and have those safely saved out of the repo, but I'm not getting a compiling Jalview! I remember you saying that when trying to merge the latest release to master you had to incant in a particular way -- was it merge release into master using a ... "ours" strategy? I've tried both ways but only with default strategy.
4 replies
Mateusz Warowny
@warownia1
Looks like we rely on javax.xml.bind to marshall and unmarshall jabaws options but it was removed in java 11 never mind, found it in j11lib. I'm wondering why eclipse doesn't detect it as a package.
3 replies
Jim Procter
@foreveremain:matrix.org
[m]
4 replies
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: is there any reason for keeping both FEATURE-3851 branches ? you seemed to have pushed your merge branch with develop to remote
1 reply
Mateusz Warowny
@warownia1
Accessing https://www.compbio.dundee.ac.uk/slivka/ throws 502 Proxy Error. I checked www-slivka on www-2 and all processes including apache daemon were dead. I restarted apache and slivka, but there is still something wrong in the upper layers.
7 replies
Jim Procter
@foreveremain:matrix.org
[m]
March 8 was when internal network was falling over.
@benzoid: feature/JAL-3982_mouseover_highlighting_viaJAL-3860 will give you structure highlighting. passed to you to test
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
how is the start of the week looking @benzoid @warownia1 ?
11 replies
Jim Procter
@foreveremain:matrix.org
[m]
@warownia1 @benzoid remember - usual 2pm catchup today ! (and ben - meeting 30 mins before to talk genomes/jalview!)
3 replies
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: patch wont quite happen tonight (no surprises I guess!) - most of the logic is extracted from VCFReader now but need a target pattern for the final step. Possibly something like StructureSelectionListener.mouseOverGenomic(species,assembly,chromosome,long..)
Jim Procter
@foreveremain:matrix.org
[m]
👏 @benzoid ! you survived the ensembl rest api going down in the middle of your demo. What are the chances ?
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: I've pushed a prototype for highlighting chromosomal location, but it needs a bit more work, and lots of testing. For human/Ensembl you need to use homo_sapiens in the species field, and I've verified it shows positions on an ENSG sequence. What doesn't work right now is highlighting of all regions mapped to the location (ie positions in the transcripts, CDS and peptide products) - the code is there (more or less) but should really be moved into StructureSelectionManager.
19 replies
Mateusz Warowny
@warownia1
What's a dataset of an alignment?
25 replies
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: it sounds like you've considerably broadened the scope of the API project.. that's good but remember that you also need to broaden your research about the use cases in that case, and it would be nice to at least stick to the roadmap in terms of first targetting what's needed for jalview+genome browsers, and subsequently what's needed for Jalview+Jupyter (that was the other REST API application)
6 replies
Mateusz Warowny
@warownia1
Is it possible to have multiple sub-jobs for an annotation job or is it always one?
10 replies
Jim Procter
@foreveremain:matrix.org
[m]
everything ok today @benzoid and @warownia1 ?
11 replies
Mateusz Warowny
@warownia1
What's the point of setting feature renderer on a AnnotationWsJob in SeqAnnotationServiceCalcWorker#poll() if it's never being retrieved?
10 replies
Mateusz Warowny
@warownia1

In SeqAnnotationServiceCalcWorker#updateResultAnnotaiton line ~704 what was this block supposed to do?

        SequenceI aseq = null;

        /**
         * transfer sequence refs and adjust gapmap
         */
        if (ala.sequenceRef != null)
        {
          SequenceI seq = running.getSeqNames()
                  .get(ala.sequenceRef.getName());
          aseq = seq;
          while (seq.getDatasetSequence() != null)
          {
            seq = seq.getDatasetSequence();
          }
        }

It looks like it was meant to get the original sequence dataset, but the variable seq, which the dataset is assigned to, is gone after leaving the if block. I'm not sure whether aseq should be a dataset and it's a bug, or an original sequence and the loop is redundant.

3 replies
Jim Procter
@foreveremain:matrix.org
[m]
morning @warownia1 - everything going OK ?
2 replies
Jim Procter
@foreveremain:matrix.org
[m]
Meeting at 2pm UK/3pm Warsawa @warownia1 ?
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
great talk @warownia1 ! I'm sure it'll be referred to by a few people in the group :D
Jim Procter
@foreveremain:matrix.org
[m]
hi @warownia1 - are you on holiday today ?
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid happy post-chocolate day!
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: I saw an update via email to https://issues.jalview.org/browse/JAL-3288 about you having found a workaround - but it doesn't seem to actually be on the issue tracker.. is there something wrong with the server ?
16 replies
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: I'm considering pushing a patch release for tomorrow's training that addresses https://issues.jalview.org/browse/JAL-3365 ? there's a branch with a fix that I think works, but there's another with a failing test highlighting an issue with exporting and re-importing sequence associated secondary structure annotation that I couldn't fathom. Could you have a look at the failing test ?
Jim Procter
@foreveremain:matrix.org
[m]
I'd like to have a very short meeting today @warownia1 @benzoid 2pm-2.30pm only.
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: I'm not going to be able to answer the question on the forum until after the training course is done this evening, but please do chat with @gjbarton about a good answer :)
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
hi @warownia1 we're meeting at 3pm UK - 4pm Europe time today. Hope that works.
Jim Procter
@foreveremain:matrix.org
[m]
afternoon(nearly) @warownia1 and @benzoid - hope all is well. as promised I'm working on the TODO for the website today.
2 replies
Jim Procter
@foreveremain:matrix.org
[m]
Morning/afternoon @benzoid & @warownia1 .. meeting as usual at 2pm UK/3pm PL today.
2 replies
Mateusz Warowny
@warownia1
should I convert my http client into gradle or maven project?
10 replies
Jim Procter
@foreveremain:matrix.org
[m]
Hi @benzoid currently rebooting the atlassian vm
9 replies
Jim Procter
@foreveremain:matrix.org
[m]
@warownia1: meeting today at 4pm UK time as usual.
3 replies
Jim Procter
@foreveremain:matrix.org
[m]
greetings from a misty Tay. I'm focusing on catching up on writing and (of course) the website this week. let me know if I've forgotten to do something I said I would :)
Mateusz Warowny
@warownia1
Hi, what are the best practises of organising tests into classes. I have a Foo class that I want to test. The consensus is to put all Foo-related tests into a public TestFoo class. Now, let's consider a following scenario, I want to perform two distinct sets of tests on two Foo instances one initialised with dataset A and the other with B. I can't have them in a single class with a single @BeforeClass any more. What's the right way to group tests in testng so they have different setups?
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
@warownia1 @benzoid meeting in 3-4 mins !
Mateusz Warowny
@warownia1
I'm taking two days off, I'm sick. I hope it's not Covid
4 replies
Jim Procter
@foreveremain:matrix.org
[m]
@warownia1: hope you are feeling better !
1 reply
@benzoid: just saw https://issues.jalview.org/browse/JAL-4007 - FWIW you might want to edit out the bit about "Theoretically this may lead to a problem with the actual build, though since nothing's actually changed this is unlikely, but it most likely leads to tasks being re-run that don't need to be leading to a less efficient build process." - since the whole point of that 'optimisations disabled' message is that gradle has disabled incremental caching so the build runs correctly.
7 replies
Jim Procter
@foreveremain:matrix.org
[m]
oops. sorry for lateness. online now.
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: slight feature creep for the website - I've noticed the menu minibar that appears when you scroll down the page in widescreen doesn't get shown when you are in mobile mode. Sidebar based navigation is also lost - I guess we can ensure the text on each page duplicates the links to the sidebar (it mostly does, but I would love to thin it down), but it would be cool to still have the minibar for navigation, since the header looks a bit naff right now
6 replies
Jim Procter
@foreveremain:matrix.org
[m]
guess so
Jim Procter
@foreveremain:matrix.org
[m]
@benzoid: is the build server stuck ? Tests are taking more than 10 mins to run, and appear to be failing.
3 replies
Jim Procter
@foreveremain:matrix.org
[m]
but.. it looks like Gradle suite > Gradle test > jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence FAILED 10-May-2022 18:34:48 java.lang.AssertionError at SeqPanelTest.java:1037 is a reliable issue.
1 reply
Jim Procter
@foreveremain:matrix.org
[m]
sorry - no mice advice - but we are now on jitsi for the team meeting
1 reply
benzoid
@benzoid
@warownia1 Jim’s on holiday and I’m getting journal club ready for tomorrow, let’s call it a google-doc-update-only meeting...
1 reply