From: Mateusz Warowny Date: Tue, 16 May 2023 12:47:01 +0000 (+0200) Subject: JAL-3954 Implement phmmer action and task as alignment actions X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=38d690aa3f6a75ec27ce55704602906d36d5847b JAL-3954 Implement phmmer action and task as alignment actions --- diff --git a/src/jalview/ws2/actions/hmmer/PhmmerAction.java b/src/jalview/ws2/actions/hmmer/PhmmerAction.java new file mode 100644 index 0000000..5e6ef08 --- /dev/null +++ b/src/jalview/ws2/actions/hmmer/PhmmerAction.java @@ -0,0 +1,73 @@ +package jalview.ws2.actions.hmmer; + +import java.util.List; +import java.util.Objects; + +import jalview.datamodel.AlignmentI; +import jalview.viewmodel.AlignmentViewport; +import jalview.ws.params.ArgumentI; +import jalview.ws2.actions.BaseAction; +import jalview.ws2.actions.api.TaskEventListener; +import jalview.ws2.actions.api.TaskI; +import jalview.ws2.api.Credentials; +import jalview.ws2.client.api.AlignmentWebServiceClientI; +import jalview.ws2.client.api.WebServiceClientI; + +/** + * Implementation of the {@link BaseAction} for the phmmer client. This is NOT + * how you should implement it. The action should be more generic and cover + * range of similar services. + * + * @author mmwarowny + * + */ +// FIXME: Not an alignment action (temporary hack) +public class PhmmerAction extends BaseAction +{ + public static class Builder extends BaseAction.Builder + { + protected AlignmentWebServiceClientI client; + + private Builder(AlignmentWebServiceClientI client) + { + super(); + Objects.requireNonNull(client); + this.client = client; + } + + public PhmmerAction build() + { + return new PhmmerAction(this); + } + } + + public static Builder newBuilder(AlignmentWebServiceClientI client) + { + return new Builder(client); + } + + protected final AlignmentWebServiceClientI client; + + public PhmmerAction(Builder builder) + { + super(builder); + client = builder.client; + } + + @Override + public TaskI perform(AlignmentViewport viewport, + List args, Credentials credentials, + TaskEventListener handler) + { + var task = new PhmmerTask(client, args, credentials, + viewport.getAlignmentView(true), handler); + task.start(viewport.getServiceExecutor()); + return task; + } + + @Override + public boolean isActive(AlignmentViewport viewport) + { + return false; + } +} diff --git a/src/jalview/ws2/actions/hmmer/PhmmerTask.java b/src/jalview/ws2/actions/hmmer/PhmmerTask.java new file mode 100644 index 0000000..0565300 --- /dev/null +++ b/src/jalview/ws2/actions/hmmer/PhmmerTask.java @@ -0,0 +1,66 @@ +package jalview.ws2.actions.hmmer; + +import static jalview.util.Comparison.GapChars; + +import java.io.IOException; +import java.util.List; + +import jalview.analysis.AlignSeq; +import jalview.bin.Console; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.AlignmentView; +import jalview.datamodel.Sequence; +import jalview.ws.params.ArgumentI; +import jalview.ws2.actions.AbstractPollableTask; +import jalview.ws2.actions.BaseJob; +import jalview.ws2.actions.ServiceInputInvalidException; +import jalview.ws2.actions.api.TaskEventListener; +import jalview.ws2.api.Credentials; +import jalview.ws2.api.JobStatus; +import jalview.ws2.client.api.AlignmentWebServiceClientI; + +class PhmmerTask extends AbstractPollableTask +{ + private final AlignmentWebServiceClientI client; + private final AlignmentView view; + + PhmmerTask(AlignmentWebServiceClientI client, List args, + Credentials credentials, AlignmentView view, + TaskEventListener eventListener) + { + super(client, args, credentials, eventListener); + this.client = client; + this.view = view; + } + + @Override + protected List prepare() throws ServiceInputInvalidException + { + Console.info("Preparing sequence for phmmer job"); + var sequence = view.getVisibleAlignment('-').getSequenceAt(0); + var seq = new Sequence(sequence.getName(), + AlignSeq.extractGaps(GapChars, sequence.getSequenceAsString())); + var job = new BaseJob(List.of(seq)) + { + @Override + public boolean isInputValid() + { + return true; + } + }; + job.setStatus(JobStatus.READY); + return List.of(job); + } + + @Override + protected AlignmentI done() throws IOException + { + var job = getSubJobs().get(0); + var jobId = job.getServerJob().getJobId(); + var status = job.getStatus(); + Console.info(String.format("phmmer finished job \"%s\" with status %s", + jobId, status)); + return client.getAlignment(job.getServerJob()); + } + +} diff --git a/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java b/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java index 11fbf2a..a20575d 100644 --- a/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java +++ b/src/jalview/ws2/client/ebi/JobDispatcherWSDiscoverer.java @@ -10,6 +10,7 @@ import jalview.bin.Console; import jalview.ws.params.ParamManager; import jalview.ws2.actions.NullAction; import jalview.ws2.actions.api.ActionI; +import jalview.ws2.actions.hmmer.PhmmerAction; import jalview.ws2.api.WebService; import jalview.ws2.client.api.AbstractWebServiceDiscoverer; import uk.ac.dundee.compbio.hmmerclient.PhmmerClient; @@ -73,18 +74,18 @@ public final class JobDispatcherWSDiscoverer extends AbstractWebServiceDiscovere @Override protected List> fetchServices(URL url) throws IOException { - PhmmerClient client; + PhmmerClient phmmerClient; try { - client = new PhmmerClient(url); + phmmerClient = new PhmmerClient(url); } catch (URISyntaxException e) { throw new MalformedURLException(e.getMessage()); } - if (!client.testEndpoint()) + if (!phmmerClient.testEndpoint()) throw new IOException( "unable to reach dispatcher server at " + url); // TODO change once a concrete action is implemented - var wsBuilder = WebService. newBuilder(); + var wsBuilder = WebService. newBuilder(); wsBuilder.url(url); wsBuilder.clientName("job dispatcher"); wsBuilder.category("Database search"); @@ -92,10 +93,11 @@ public final class JobDispatcherWSDiscoverer extends AbstractWebServiceDiscovere wsBuilder.description("Hmmer3 phmmer is used to search one or more query sequences against a sequence database."); wsBuilder.interactive(false); wsBuilder.paramDatastore(ParamStores.newPhmmerDatastore(url, paramManager)); - wsBuilder.actionClass(NullAction.class); + wsBuilder.actionClass(PhmmerAction.class); var webService = wsBuilder.build(); - var actionBuilder = NullAction.newBuilder(); + var client = new PhmmerWSClient(phmmerClient); + var actionBuilder = PhmmerAction.newBuilder(client); actionBuilder.webService(webService); actionBuilder.name(""); webService.addAction(actionBuilder.build());