jalview

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Commits this week: 17
Total Committers: 73
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Commits this week: 17

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Today
4 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4046 release on 9th August 2022

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    /help/markdown/releases/release-2_11_2_4.md
5 hrs ago

Jim Procter

5 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4046 JAL-3993 imports reformatting

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    /src/jalview/gui/SliderPanel.java
5 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4046 JAL-3993 patch for 2.11.2.4 release

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    /help/markdown/releases/release-2_11_2_4.md
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    /src/jalview/gui/SliderPanel.java
5 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4046 release notes for JAL-3991

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    /help/markdown/releases/release-2_11_2_4.md
5 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'task/JAL-3991_check_actual_JAVA_VERSION_against_build_properties_in_application_startup' into develop

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    /build.gradle
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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/bin/Cache.java
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    /src/jalview/bin/Jalview.java
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    /src/jalview/gui/Desktop.java
5 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4046 release notes for JAL-4014 - gecos colourschemes

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    /help/markdown/releases/release-2_11_2_4.md
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    /help/markdown/whatsnew/whatsnew-2_11_2_4.md
6 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'improvement/JAL-4014_gecos_colour_schemes' into develop

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6 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4056 documented in release notes for JAL-4043

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    /help/markdown/releases/release-2_11_2_4.md
6 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'patch/JAL-4036_uniprot_fts_legacy_endpoint' into develop

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    /resources/lang/Messages.properties
6 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4043 what’s new, updated help images and release notes for JAL-4034 (3d beacons button)

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    /help/help/html/features/3dbeacons_button.png
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    /help/help/html/features/schooser_main.png
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    /help/markdown/releases/release-2_11_2_4.md
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    /help/markdown/whatsnew/whatsnew-2_11_2_4.md
7 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

JAL-4034 show the loading spinner when switching between tabs

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    /src/jalview/gui/StructureChooser.java
8 hrs ago

Jim Procter <j.procter@dundee.ac.uk>

Merge branch 'features/JAL-4034_improve_3dbeacons_button_and_ux' into develop

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Monday 01 Aug
11:32 am

Ben Soares

JAL-4056 fixed tl;dr section of doc/building.md

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    /doc/building.md
Tuesday 26 Jul
6:01 pm

Ben Soares

JAL-4036 Fixed the virus_host_id query field

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    /resources/fts/uniprot_data_columns-2022.txt
6:01 pm

Ben Soares

JAL-4036 Added text to help about different number and date range acceptable formats

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    /help/help/html/features/uniprotsequencefetcher.html
Monday 25 Jul
5:09 pm

Ben Soares

JAL-4036 updated help about new UniProt API

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    /help/help/html/features/uniprotqueryfields.html
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    /help/help/html/features/uniprotsequencefetcher.html
11:00 am

Ben Soares

JAL-4036 moved a comment block

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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
10:57 am

Ben Soares

JAL-4034 button looks better also on other OSes with the 0 vertical insets

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    /src/jalview/jbgui/GStructureChooser.java
Sunday 24 Jul
5:37 pm

Ben Soares

JAL-4034 add round corners to 3DB confirmation button with icon on a mac

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    /src/jalview/jbgui/GStructureChooser.java
Friday 22 Jul
6:17 pm

Ben Soares

JAL-4036 Changes made from code review CR-JAL-265

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    /src/jalview/fts/core/GFTSPanel.java
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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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    /src/jalview/fts/service/uniprot/UniprotFTSPanel.java
4:40 pm

Ben Soares

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace. This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses...

I've now put in a warn with the e.getMessage(), but I've left in a debug with the full stacktrace.
This catch block is a little odd in that it's used as programmatic flow for non 200 HTTP responses. I notice that the new API server is sending back a 400 for bad input (including for non-existent query fields and wrong types for non-string query fields), which is invoking the warning triangle which puts the HTTP error message into the tooltip so this block is now getting more use!

The reason for wanting a full stacktrace in debug mode is that both the API and the changed client are new, so any errors in the next few months will be more quickly diagnosed if we can allow the user to easily obtain a stacktrace of the exception.

12:34 pm

Jim Procter

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a con...

after trying it out I think the old behaviour is better, unless 1) there's a really clear message in the UI explaining that now the field has changed, the search needs to be executed again 2) a convenient [search] button is shown so one doesn't have to click into the query field and press enter to trigger the search again.

12:32 pm

Jim Procter

should be Console.warn

should be Console.warn

12:31 pm

Jim Procter

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalvi...

Need to add logic that either 1) modifies config if an existing value of UNIPROT_DOMAIN is found that is legacy.uniprot.org or 2) uses UNIPROT_2022_DOMAIN as a config value so old versions of Jalview still work (up until legacy.uniprot.org goes away).

11:55 am

Ben Soares

JAL-4036 Add getDbName to the GFTSPanelI and add an index code message to the index dropdown tooltip as appropriate

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
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    /src/jalview/fts/api/GFTSPanelI.java
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    /src/jalview/fts/core/GFTSPanel.java
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    /src/jalview/fts/service/pdb/PDBFTSPanel.java
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    /src/jalview/fts/service/threedbeacons/TDBeaconsFTSPanel.java
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    /src/jalview/fts/service/uniprot/UniprotFTSPanel.java
11:38 am

Jim Procter

shouldn't this be a warn ?

shouldn't this be a warn ?

11:36 am

Jim Procter

this comment block should really be after the imports ?

this comment block should really be after the imports ?

11:35 am

Jim Procter

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

makes sense. I do wonder if there needs to be some indication that any results currently shown are stale, however ?

11:33 am

Jim Procter

JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API
JAL-4036: Jalview 2.11.2.2 and earlier no longer compatible with Uniprot REST API