jalview

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JAL-4036 Fixed the virus_host_id query field

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    /resources/fts/uniprot_data_columns-2022.txt
JAL-4036 Added text to help about different number and date range acceptable formats

JAL-4036 updated help about new UniProt API

JAL-4036 moved a comment block

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

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.

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.

should be Console.warn

should be Console.warn

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).

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_es.properties
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    /src/jalview/fts/core/GFTSPanel.java
shouldn't this be a warn ?

shouldn't this be a warn ?

this comment block should really be after the imports ?

this comment block should really be after the imports ?

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 ?

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

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    /src/jalview/fts/core/FTSRestClient.java
JAL-4036 Don't autosearch changing index when autosearch is de-selected

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    /src/jalview/fts/core/GFTSPanel.java
JAL-4036 add search fieldname to dropdown list

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    /src/jalview/fts/core/FTSRestClient.java
JAL-4036 removed often duplicated pluralisation in message

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    /resources/lang/Messages_es.properties
JAL-4036 New configuration, target and pagination process for 2022-07 new Uniprot API

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    /resources/fts/uniprot_data_columns-2022.txt
JAL-4036 JAL-4012 note about Uniprot FTS workaround in search documentation, and update to release notes and what’s new

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

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

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

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

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    /src/jalview/jbgui/APQHandlers.java
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
JAL-3027 Avoid FlatLAF Desktop class is JalviewJS

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

JAL-1988 JAL-3416 avoid unnecessary static flag

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