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JAL-3878 Fix typo in slivka host urls variable name.

JAL-3878 Move listeners list from the WebServiceDiscoverer interface.

Listeners list defined in the interface was globally shared

among all discoverer instances. Listeners should be kept by

the discoverer instance instead.

  1. … 2 more files in changeset.
JAL-3878 Add jpred operation and worker to the services.

  1. … 4 more files in changeset.
JAL-3878 Add annotation operation and worker to the services.

  1. … 4 more files in changeset.
JAL-3878 Add multiple sequence operation.

  1. … 6 more files in changeset.
JAL-3878 Add slivka's implementations of web service and discoverer.

    • -0
    • +210
    ./SlivkaWSDiscoverer.java
    • -0
    • +304
    ./SlivkaWebService.java
JAL-3878 Add RNAalifold service discovery.

  1. … 1 more file in changeset.
JAL-3878 Separate gui elements from operations.

Separation went well for alignment operation but not so much

for the annotations. GUI progress bar needs to be moved outside

the operation and be controlled by the worker listener.

Addition of the results to the frame needs to be moved out from

the #done method, but it's strongly wired to the align frame

code and cannot be nicely packed into AnnotationResult object.

  1. … 13 more files in changeset.
JAL-3878 Add annotation operations to slivka discoverer.

JAL-3878 Rename annotation provider method to getAnnotations

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.

JAL-3878 Add dataset and viewport arguments to ResultSupplier.

  1. … 2 more files in changeset.
JAL-3878 Annotation operation skeleton.

  1. … 1 more file in changeset.
JAL-3878 Add job log messages reporting.

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.

after taking a look at the rest I can see that the next step is to split this class up further. There's plenty of code that will be used by many different operations - e.g. job state management - i...

after taking a look at the rest I can see that the next step is to split this class up further. There's plenty of code that will be used by many different operations - e.g. job state management - is that the plan ?

not really the recommended way - see e.g. https://docs.oracle.com/en/java/javase/11/docs/api/java.desktop/java/beans/PropertyChangeSupport.html *do you need to expose the generic binders ? what k...

not really the recommended way - see e.g. https://docs.oracle.com/en/java/javase/11/docs/api/java.desktop/java/beans/PropertyChangeSupport.html

  • do you need to expose the generic binders ? what kind of events need to be monitored ?
is utils really the right name ? suggest the classes are used in several different places

is utils really the right name ? suggest the classes are used in several different places

this is going to get much more complex. there are plenty of additional attributes - e.g. input type (dna, protein, rna) - none of them are currently being configured on the operation.

this is going to get much more complex. there are plenty of additional attributes - e.g. input type (dna, protein, rna) - none of them are currently being configured on the operation.

this class seems to contain a bunch of hard coded stuff taken from the original web services configuration code rather than provide a way for a web services provider to configure an instance of Ali...

this class seems to contain a bunch of hard coded stuff taken from the original web services configuration code rather than provide a way for a web services provider to configure an instance of AlignmentOperation tuned to the alignment service that the provider is offering.

first review of Web Services overhaul for 2.12
first review of Web Services overhaul for 2.12
JAL-3878 Wire web services logic to UI elements.

  1. … 5 more files in changeset.
JAL-3878 Fire service changed event after discovery task is done.

JAL-3878 Fix incorrect value of isRunning in SlivkaWSDiscoverer

JAL-3878 Move operation type from WebService to Operation.

  1. … 3 more files in changeset.
JAL-3878 Code reformatting.

  1. … 7 more files in changeset.
JAL-3878 Move WSJob instantiation out of WebService classes.

  1. … 2 more files in changeset.