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
WIP

JAL-3878 Use slivka client's URL when building web service

JAL-3878 Add conservation service discovery

JAL-3878 Build interactive services menu

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    /src/jalview/ws2/gui/WebServicesMenuManager.java
JAL-3878 Implement prot. seq. an. discovery for slivka.

JAL-3878 Implement gui elements for annotation servicces

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    /src/jalview/ws2/gui/AnnotationServiceGuiHandler.java
JAL-3878 Create SlivkaAnnotationWSClient

JAL-3878 Add full name getter to ActionI

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    /src/jalview/ws2/actions/api/ActionI.java
JAL-3878 Log status changes in annotation task

JAL-3878 Allow null value for action name

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    • +1
    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Add action and task for annotation services

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    /src/jalview/util/Pair.java
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    /src/jalview/ws2/actions/annotation/AnnotationAction.java
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    /src/jalview/ws2/actions/annotation/AnnotationJob.java
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    /src/jalview/ws2/actions/annotation/AnnotationResult.java
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    /src/jalview/ws2/actions/annotation/AnnotationTask.java
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    /src/jalview/ws2/client/api/AnnotationWebServiceClientI.java
JAL-3878 Introduce IProgressIndicator#addProgressBar

addProgressBar adds a bar to the panel if it doesn't exist

ensuring that the bar is present after the call contrary

to setProgressBar which toggles the progress bar on and off.

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    • +15
    /src/jalview/gui/IProgressIndicator.java
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    /src/jalview/gui/ProgressBar.java
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    • +6
    /src/jalview/gui/StructureChooser.java
JAL-3878 Fix method name to fireTaskRestarted

JAL-3878 Add char[] constructor to Sequence

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    • +15
    /src/jalview/datamodel/Sequence.java
JAL-3878 Make BaseJob setters public so they can be accessed by other tasks.

JAL-3878 Add fullName to BaseAction class which combines service and action name

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    • +14
    /src/jalview/ws2/actions/BaseAction.java
JAL-3878 Move status precedence list to JobStatus class

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    /src/jalview/ws2/api/JobStatus.java
JAL-3878 Add uid to WS Tasks

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    • +7
    /src/jalview/ws2/actions/api/TaskI.java
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
make AlignFrame the parent of FeatureEditor dialog, and have parent Component request focus after...
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.
JAL-3975 forced re-focus to alignframe after Create Sequence Feature dialog.