jalview

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Commits this week: 21
Total Committers: 73
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Commits this week: 21

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Monday 08 Aug
6:31 pm

Jim Procter

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

Options
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    • +2
    /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
    • -11
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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
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
    • -0
    • +27
    /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
11:06 am

Ben Soares

JAL-4036 removing the query field code from the dropdown indexes

Options
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    • +1
    /src/jalview/fts/core/FTSRestClient.java
Thursday 21 Jul
9:00 pm

Ben Soares

JAL-4036 Don't autosearch changing index when autosearch is de-selected

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    /src/jalview/fts/core/GFTSPanel.java
9:00 pm

Ben Soares

JAL-4036 add search fieldname to dropdown list

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    /src/jalview/fts/core/FTSRestClient.java
8:59 pm

Ben Soares

JAL-4036 removed often duplicated pluralisation in message

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    /resources/lang/Messages.properties
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    /resources/lang/Messages_es.properties
8:58 pm

Ben Soares

JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API

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    • +356
    /resources/fts/uniprot_data_columns-2022.txt
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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
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    /src/jalview/fts/service/uniprot/UniprotFTSPanel.java
Friday 01 Jul
1:44 pm

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

JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new

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    /help/help/html/features/uniprotsequencefetcher.html
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    /help/markdown/releases/release-2_11_2_3.md
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    /help/markdown/whatsnew/whatsnew-2_11_2_3.md
Thursday 30 Jun
5:37 pm

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

JAL-4036 use the legacy endpoint (and report the FTS query when debug/trace enabled)

Options
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    /src/jalview/fts/service/uniprot/UniProtFTSRestClient.java
Tuesday 28 Jun
1:32 pm

Ben Soares

Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

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    /src/jalview/jbgui/GDesktop.java
1:31 pm

Ben Soares

JAL-1988 Don't put Quit in the File menu if there's a handler for it

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    /src/jalview/jbgui/GDesktop.java
Thursday 23 Jun
4:02 pm

Ben Soares

Merge branch 'improvement/JAL-1988+JAL-3416_Java8_macOS_APQHandlers_and_FlatLaF_option' into develop

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    /src/jalview/jbgui/APQHandlers.java
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    /src/jalview/jbgui/GDesktop.java
3:28 pm

Ben Soares

JAL-1988 Check for setHandler capability to avoid About and Preferences menu options disappearing into a void

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    /src/jalview/jbgui/APQHandlers.java
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    /src/jalview/jbgui/GDesktop.java
Friday 17 Jun
5:10 pm

Ben Soares

JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

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    /src/jalview/jbgui/APQHandlers.java
Wednesday 15 Jun
4:17 pm

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

JAL-4012 release notes for JAL-1988,JAL-3416

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    /help/markdown/releases/release-2_11_2_3.md
3:54 pm

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

JAL-1988 JAL-3416 avoid unnecessary static flag

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    /src/jalview/jbgui/APQHandlers.java
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    /src/jalview/jbgui/GDesktop.java
3:54 pm

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

JAL-3418 JAL-1988 don’t need java version check anymore

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    /src/jalview/jbgui/GDesktop.java