jalview

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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).

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-4024 only render partially when new view overlaps with last rendered annotation panel view

    • -12
    • +14
    /src/jalview/gui/AnnotationPanel.java
Merge branch 'patch/JAL-4008_jabaws_2_2_1_patch' into doc/release_2_11_2_3

JAL-4012 JAL-4008 release notes for Jalview 2.11.2.3

JAL-4008 update jabaws client to 2.2.1 - definitely no log4j references !

    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j11lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.0.jar
    • binary
    /j8lib/jabaws-min-client-NO_LOG4J-2.2.1.jar
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3992 bump version and report updates in 2.11.2.2 release notes

Merge branch 'bug/JAL-3997_NPE_in_wrapped_mode' into develop

Merge branch 'bug/JAL-3365_extendedDSSP_via_stockholm' into develop

JAL-3997 check for tooltip being null before checking equivalence to last tooltip string

Merge branch 'task/JAL-3992_update_docs' into bug/JAL-3365_extendedDSSP_via_stockholm

JAL-3992 fix path

    • -1
    • +1
    /help/help/html/features/cursorMode.html
JAL-3365 expand range of allowed DSSP secondary structure symbols in Stockholm files

    • -0
    • +12
    /test/jalview/io/StockholmFileTest.java
JAL-3992 shift+arrow to jump to next gap/residue in cursor/keyboard editing mode

    • -8
    • +12
    /help/help/html/features/cursorMode.html
Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 release notes and what’s new

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3981 patch tests and remove errant imports

Merge branch 'develop' into releases/Release_2_11_2_Branch

JAL-3990 gradle spotlessApply

JAL-3990 release notes for 2.11.2.1 patch release

Merge branch 'bug/JAL-3980_JAL-3981_tooltips_sequence_details' into develop