Mateusz Warowny

JAL-3878 Create WebServiceMenuBuilder which will replace PreferredServiceRegistry

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    /src/jalview/gui/WebServicesMenuBuilder.java
JAL-3878 Annotation comments and questions

JAL-3878 Add annotation operations to slivka discoverer.

JAL-3878 Fix sequences not being gathered when submitting without gaps.

JAL-3878 Rename annotation provider method to getAnnotations

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Set job status to cancelled on job cancellation.

Despite job cancellation not being implemented in slivka client,

the job status should be updated to cancelled for the event to

be emitted to the ui updater.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Start interactive job by registering them with calcManager

JAL-3878 Fix progress updater bar to account for cancelled state.

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    /src/jalview/ws2/gui/ProgressBarUpdater.java
Update annotation operation WIP

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
SequencesInfo which is an individual object is doable, but I feel like it would be just a wrapper around a Map. What additional functionality would SequencesInfo have over a traditional Map? I'm n...

SequencesInfo which is an individual object is doable, but I feel like it would be just a wrapper around a Map. What additional functionality would SequencesInfo have over a traditional Map?

I'm not very familiar with serialization in java, I know there are libraries that can serialize beans to json or xml, but what are your expectations in this case?

JAL-3899 Replace prints with logger messages.

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    /src/jalview/analysis/SeqsetUtils.java
What's wrong with static classes? They are just like regular classes but within other class' namespace. That's non-static inner classes that are special. About factory pattern, I think it would be ...

What's wrong with static classes? They are just like regular classes but within other class' namespace. That's non-static inner classes that are special.
About factory pattern, I think it would be an overkill for a class that is only used by SeqsetUtils' methods.

Because it's instantiated in a static context e.g. uniquify and it does not need an instance of SeqsetUtils object to work.

Because it's instantiated in a static context e.g. uniquify and it does not need an instance of SeqsetUtils object to work.

JAL-3899 Update usages of uniquify and deuniquify.

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    /src/jalview/io/packed/JalviewDataset.java
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    /src/jalview/ws/jws1/JPredThread.java
tmp

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    /src/jalview/io/packed/JalviewDataset.java
JAL-3899 Refactor sequence de/uniquification.

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    /src/jalview/analysis/SeqsetUtils.java
JAL-3878 Annotation operation skeleton.

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    /src/jalview/ws2/operations/AnnotationOperation.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Fix workers done condition to account for broken jobs.

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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/WebServiceWorkerI.java
JAL-3878 Skip getting results of failed jobs.

JAL-3878 Add job log messages reporting.

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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Fix null pointer exception when preparing empty sequences for job.

JAL-3878 Fetch sequences for alignment on menu action, not creation.

JAL-3878 Split web services menu entries by programs and hosts.

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    /src/jalview/ws2/operations/Operation.java
This is waiting for us to define the "language" of edam classifiers that we are going to support. Currently we only define services by what operation they perform but there is plenty of room for fi...

This is waiting for us to define the "language" of edam classifiers that we are going to support. Currently we only define services by what operation they perform but there is plenty of room for fine grained tuning of operations based on other classifiers.

Yes, there are pieces of code that can be reused across multiple if not all other workers. I suppose we can either add component classes that can be used by the workers that need them or we can cre...

Yes, there are pieces of code that can be reused across multiple if not all other workers. I suppose we can either add component classes that can be used by the workers that need them or we can create an abstract base class for all workers with implementations of common methods. The purpose of operation class is to provide metadata and create a worker, so the operation should stay as it is, but the worker needs to be tidied up. I absolutely agree that currently it is too bloated and should be split into smaller pieces but for now I wanted something that just works.
Regarding tuning, the whole point is that now the service is made of operations instead of extending one, so we can create new operations or add extra parameters to the existing operation classes that would alter worker behaviour without touching other parts of the code.

JAL-3878 Add isInteractive() method to Operation interface.

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    /src/jalview/ws2/operations/Operation.java
JAL-3878 Add getName() to Operation interface.

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    /src/jalview/ws2/operations/Operation.java
JAL-3878 Wire web services logic to UI elements.

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    /src/jalview/gui/AlignFrame.java
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    /src/jalview/gui/SlivkaPreferences.java
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    /src/jalview/ws2/WebServiceExecutor.java
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    /src/jalview/ws2/slivka/SlivkaWebService.java
JAL-3878 Fire service changed event after discovery task is done.