JAL-3848 Update slivka client library.

diff --git a/j11lib/slivka-client.jar b/j11lib/slivka-client.jar
index 68cc932..895366c 100644 (file)
Binary files a/j11lib/slivka-client.jar and b/j11lib/slivka-client.jar differ

diff --git a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
index b3509b0..3c80fbc 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaAnnotationServiceInstance.java
@@ -19,6 +19,7 @@ import jalview.ws.uimodel.AlignAnalysisUIText;
 import java.io.IOError;
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.List;
 import java.util.Map;
 
@@ -55,7 +56,7 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
   }
 
   @Override
-  public List<AlignmentAnnotation> getAnnotationResult(JobId job,
+  public List<AlignmentAnnotation> getAnnotationResult(JobId jobId,
           List<SequenceI> seqs, Map<String, FeatureColourI> featureColours,
           Map<String, FeatureMatcherSetI> featureFilters) throws Throwable
   {
@@ -63,14 +64,15 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
     RemoteFile featFile = null;
     try
     {
-      List<RemoteFile> files = client.getJobResults(job.getJobId());
+      var slivkaJob = client.getJob(jobId.getJobId());
+      Collection<RemoteFile> files = slivkaJob.getResults();
       for (RemoteFile f : files)
       {
-        if (f.getMimeType().equals("application/jalview-annotations"))
+        if (f.getMediaType().equals("application/jalview-annotations"))
         {
           annotFile = f;
         }
-        else if (f.getMimeType().equals("application/jalview-features"))
+        else if (f.getMediaType().equals("application/jalview-features"))
         {
           featFile = f;
         }
@@ -81,15 +83,21 @@ public class SlivkaAnnotationServiceInstance extends SlivkaWSInstance implements
     }
     Alignment aln = new Alignment(seqs.toArray(new SequenceI[0]));
     if (annotFile == null
-        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getURL().toString(), DataSourceType.URL))
+        || !new AnnotationFile().readAnnotationFile(aln, annotFile.getContentUrl().toString(), DataSourceType.URL))
     {
       Cache.log.debug("No annotation from slivka job\n" + annotFile);
     }
+    else {
+      Cache.log.debug("Annotation file loaded " + annotFile);
+    }
     if (featFile == null
-        || !new FeaturesFile(featFile.getURL().toString(), DataSourceType.URL).parse(aln, featureColours, true))
+        || !new FeaturesFile(featFile.getContentUrl().toString(), DataSourceType.URL).parse(aln, featureColours, true))
     {
       Cache.log.debug("No features from slivka job\n" + featFile);
     }
+    else {
+      Cache.log.debug("Features feil loaded " + featFile);
+    }
     return Arrays.asList(aln.getAlignmentAnnotation());
   }
 }

diff --git a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
index 9a33b04..03dda3f 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaMsaServiceInstance.java
@@ -1,5 +1,6 @@
 package jalview.ws.slivkaws;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -14,6 +15,7 @@ import jalview.ws.params.WsParamSetI;
 import java.io.IOError;
 import java.io.IOException;
 import java.rmi.ServerError;
+import java.util.Collection;
 import java.util.List;
 
 import compbio.data.msa.Category;
@@ -37,19 +39,20 @@ public class SlivkaMsaServiceInstance extends SlivkaWSInstance implements Multip
   @Override
   public AlignmentI getAlignmentFor(JobId jobId) throws InvalidArgumentException, ServerError, IOError
   {
-    List<RemoteFile> files;
+    Collection<RemoteFile> files;
     try
     {
-      files = client.getJobResults(jobId.getJobId());
+      var slivkaJob = client.getJob(jobId.getJobId());
+      files = slivkaJob.getResults();
       for (RemoteFile f : files)
       {
-        if (f.getMimeType().equals("application/clustal"))
+        if (f.getMediaType().equals("application/clustal"))
         {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Clustal);
+          return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
         }
-        else if (f.getMimeType().equals("application/fasta"))
+        else if (f.getMediaType().equals("application/fasta"))
         {
-          return new FormatAdapter().readFile(f.getURL().toString(), DataSourceType.URL, FileFormat.Fasta);
+          return new FormatAdapter().readFile(f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
         }
       }
     } catch (IOException e)

diff --git a/src/jalview/ws/slivkaws/SlivkaParamSet.java b/src/jalview/ws/slivkaws/SlivkaParamSet.java
index 7e81684..8a1d382 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaParamSet.java
+++ b/src/jalview/ws/slivkaws/SlivkaParamSet.java
@@ -9,85 +9,90 @@ import jalview.ws.params.simple.StringParameter;
 
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
-import uk.ac.dundee.compbio.slivkaclient.BooleanField;
-import uk.ac.dundee.compbio.slivkaclient.ChoiceField;
-import uk.ac.dundee.compbio.slivkaclient.DecimalField;
-import uk.ac.dundee.compbio.slivkaclient.FormField;
-import uk.ac.dundee.compbio.slivkaclient.IntegerField;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
+import uk.ac.dundee.compbio.slivkaclient.Parameter;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
-import uk.ac.dundee.compbio.slivkaclient.TextField;
-
-
 
 public class SlivkaParamSet implements WsParamSetI
 {
   private SlivkaService service;
+
   private List<ArgumentI> args = new ArrayList<>();
 
-  SlivkaParamSet(SlivkaService service) throws IOException {
+  SlivkaParamSet(SlivkaService service) throws IOException
+  {
     this.service = service;
-    SlivkaForm form = service.getForm();
-    for (FormField field : form.getFields())
+    for (Parameter param : service.getParameters())
     {
-      switch (field.getType()) {
-      case BOOLEAN:
-        BooleanField boolField = (BooleanField) field;
-        args.add(new BooleanOption(
-            field.getName(), field.getDescription(), field.getLabel(),
-            field.isRequired(), boolField.getDefault(), null
-        ));
-        break;
-      case TEXT:
-        TextField textField = (TextField) field;
-        args.add(new StringParameter(
-            field.getName(), field.getDescription(), field.isRequired(),
-            textField.getDefault(), textField.getDefault()
-        ));
-        break;
-      case INTEGER:
-        IntegerField intField = (IntegerField) field;
-        args.add(new IntegerParameter(
-            field.getName(), field.getDescription(), field.isRequired(),
-            intField.getDefault(), intField.getMin(), intField.getMax()
-        ));
-        break;
-      case DECIMAL:
-        DecimalField doubleField = (DecimalField) field;
-        args.add(new DoubleParameter(
-            field.getName(), field.getDescription(), field.isRequired(),
-            doubleField.getDefault(), doubleField.getMin(),
-            doubleField.getMax()
-        ));
-        break;
-      case CHOICE:
-        ChoiceField choiceField = (ChoiceField) field;
-        List<String> choices = new ArrayList<>(choiceField.getChoices());
-        if (field.hasMultipleValues()) {
-          int counter = 0;
-          for (String choice : choices) {
+      Object defaultValue = param.getDefault() instanceof List ? ((List<?>) param.getDefault()).get(0)
+          : param.getDefault();
+      if (param instanceof Parameter.FlagParameter)
+      {
+        args.add(new BooleanOption(param.getId(), param.getDescription(),
+            param.getName(), param.isRequired(), (Boolean) defaultValue, null));
+      }
+      else if (param instanceof Parameter.TextParameter)
+      {
+        args.add(new StringParameter(param.getId(), param.getDescription(),
+            param.isRequired(), (String) defaultValue, (String) defaultValue));
+      }
+      else if (param instanceof Parameter.IntegerParameter)
+      {
+        Integer min = ((Parameter.IntegerParameter) param).getMin();
+        Integer max = ((Parameter.IntegerParameter) param).getMax();
+        Integer defVal = defaultValue != null ? ((Number) defaultValue).intValue() : null;
+        args.add(new IntegerParameter(param.getId(), param.getDescription(),
+            param.isRequired(), defVal, (min == null) ? Integer.MIN_VALUE : min,
+            (max == null) ? Integer.MAX_VALUE : max));
+      }
+      else if (param instanceof Parameter.DecimalParameter)
+      {
+        Double min = ((Parameter.DecimalParameter) param).getMin();
+        Double max = ((Parameter.DecimalParameter) param).getMax();
+        Double defVal = defaultValue != null ? ((Number) defaultValue).doubleValue() : null;
+        args.add(new DoubleParameter(param.getId(), param.getDescription(),
+            param.isRequired(), defVal, (min == null) ? -Double.MAX_VALUE : min,
+            (max == null) ? Double.MAX_VALUE : max));
+      }
+      else if (param instanceof Parameter.ChoiceParameter)
+      {
+        List<String> choices = ((Parameter.ChoiceParameter) param)
+            .getChoices();
+        if (param.isArray())
+        {
+          int i = 0;
+          List<?> selected = param.getDefault() != null
+              ? (List<?>) param.getDefault()
+              : Collections.EMPTY_LIST;
+          for (String choice : choices)
+          {
             args.add(new BooleanOption(
-                String.format("%s$%d", field.getName(), counter++),
-                field.getDescription(), choice, field.isRequired(),
-                choice.equals(choiceField.getDefault()), choice,
-                null
-            ));
+                String.format("%s$%d", param.getId(), i++),
+                param.getDescription(), choice, param.isRequired(),
+                selected.contains(choice), choice, null));
           }
         }
         else
         {
           args.add(new StringParameter(
-              field.getName(), field.getDescription(),
-              field.isRequired(), choiceField.getDefault(), choiceField.getDefault(),
-              choices, choices
-          ));
+              param.getId(), param.getDescription(),
+              param.isRequired(), (String) param.getDefault(),
+              (String) defaultValue, choices, choices));
         }
-        break;
-      case FILE:
-      default:
-        continue;
+      }
+      else if (param instanceof Parameter.FileParameter)
+      {
+        // skip: files are provided from sequences
+      }
+      else
+      {
+        String defaultVal = param.getDefault() != null
+            ? param.getDefault().toString()
+            : null;
+        args.add(new StringParameter(param.getId(), param.getDescription(),
+            param.isRequired(), defaultVal, defaultVal));
       }
     }
   }
@@ -107,7 +112,7 @@ public class SlivkaParamSet implements WsParamSetI
   @Override
   public String[] getApplicableUrls()
   {
-    return new String[] { service.getURL().toString() };
+    return new String[] { service.getUrl().toString() };
   }
 
   @Override

diff --git a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
index e849f97..accb40d 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSDiscoverer.java
@@ -215,7 +215,7 @@ public class SlivkaWSDiscoverer implements WSDiscovererI
     {
       List<?> services = new SlivkaClient(url).getServices();
       return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
-    } catch (IOException e)
+    } catch (IOException | org.json.JSONException e)
     {
       Cache.log.error("Slivka could not retrieve services list", e);
       return STATUS_INVALID;

diff --git a/src/jalview/ws/slivkaws/SlivkaWSInstance.java b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
index 75e5722..658d99e 100644 (file)
--- a/src/jalview/ws/slivkaws/SlivkaWSInstance.java
+++ b/src/jalview/ws/slivkaws/SlivkaWSInstance.java
@@ -13,6 +13,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.ParamDatastoreI;
 import jalview.ws.params.ParamManager;
 import jalview.ws.params.WsParamSetI;
+import javajs.http.ClientProtocolException;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -20,22 +21,18 @@ import java.io.IOError;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.EnumMap;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Optional;
 import java.util.Set;
 
-import uk.ac.dundee.compbio.slivkaclient.FieldType;
-import uk.ac.dundee.compbio.slivkaclient.FileField;
-import uk.ac.dundee.compbio.slivkaclient.FormField;
-import uk.ac.dundee.compbio.slivkaclient.FormValidationException;
-import uk.ac.dundee.compbio.slivkaclient.JobState;
+import uk.ac.dundee.compbio.slivkaclient.Job;
+import uk.ac.dundee.compbio.slivkaclient.JobRequest;
+import uk.ac.dundee.compbio.slivkaclient.Parameter;
 import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaForm;
 import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
-import uk.ac.dundee.compbio.slivkaclient.ValidationException;
 
 public abstract class SlivkaWSInstance extends ServiceWithParameters
     implements JalviewServiceEndpointProviderI, JalviewWebServiceI
@@ -46,19 +43,19 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
 
   protected SlivkaDatastore store = null;
 
-  protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
+  protected static final EnumMap<Job.Status, WsJob.JobState> stateMap = new EnumMap<>(Job.Status.class);
   {
-    stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
-    stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
-    stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
-    stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
-    stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
-    stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
-    stateMap.put(JobState.INTERRUPTED, WsJob.JobState.CANCELLED);
-    stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
-    stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
-    stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
-    stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
+    stateMap.put(Job.Status.PENDING, WsJob.JobState.QUEUED);
+    stateMap.put(Job.Status.REJECTED, WsJob.JobState.INVALID);
+    stateMap.put(Job.Status.ACCEPTED, WsJob.JobState.QUEUED);
+    stateMap.put(Job.Status.QUEUED, WsJob.JobState.QUEUED);
+    stateMap.put(Job.Status.RUNNING, WsJob.JobState.RUNNING);
+    stateMap.put(Job.Status.COMPLETED, WsJob.JobState.FINISHED);
+    stateMap.put(Job.Status.INTERRUPTED, WsJob.JobState.CANCELLED);
+    stateMap.put(Job.Status.DELETED, WsJob.JobState.CANCELLED);
+    stateMap.put(Job.Status.FAILED, WsJob.JobState.FAILED);
+    stateMap.put(Job.Status.ERROR, WsJob.JobState.SERVERERROR);
+    stateMap.put(Job.Status.UNKNOWN, WsJob.JobState.UNKNOWN);
   }
   protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
       WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
@@ -67,7 +64,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
 
   public SlivkaWSInstance(SlivkaClient client, SlivkaService service, String action)
   {
-    super(action, action, service.getLabel(), "Slivka", client.getUrl().toString());
+    super(action, action, service.getName(), "Slivka", client.getUrl().toString());
     this.client = client;
     this.service = service;
   }
@@ -75,16 +72,17 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   protected final JobId submit(List<SequenceI> sequences,
           WsParamSetI preset, List<ArgumentI> args) throws Throwable
   {
-    SlivkaForm form = service.getForm();
-    for (FormField field : form.getFields())
+    var parameters = service.getParameters();
+    var request = new JobRequest();
+    for (Parameter param : parameters)
     {
-      if (field.getType() == FieldType.FILE)
+      if (param instanceof Parameter.FileParameter)
       {
         FormatAdapter fa = new FormatAdapter();
         fa.setNewlineString("\r\n");
-        FileField fileField = (FileField) field;
+        Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
         FileFormat format;
-        switch (fileField.getMediaType())
+        switch (fileParam.getMediaType())
         {
         case "application/pfam":
           format = FileFormat.Pfam;
@@ -100,9 +98,7 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
         InputStream stream = new ByteArrayInputStream(
             fa.formatSequences(format, sequences.toArray(new SequenceI[0]))
                 .getBytes());
-        RemoteFile rf = client.uploadFile(stream, "input",
-            fileField.getMediaType());
-        form.insert(field.getName(), rf);
+        request.addFile(param.getId(), stream);
       }
     }
     if (args != null)
@@ -111,22 +107,22 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
       {
         // multiple choice field names are name$number to avoid duplications
         // the number is stripped here
-        String fieldName = arg.getName().split("\\$", 2)[0];
-        FormField field = form.getField(fieldName);
-        if (field.getType() == FieldType.BOOLEAN)
-        {
-          form.insert(fieldName,
-                  (arg.getValue() != null && !arg.getValue().isBlank())
-                          ? true
-                          : false);
+        String paramId = arg.getName().split("\\$", 2)[0];
+        Parameter param = service.getParameter(paramId);
+        if (param instanceof Parameter.FlagParameter) {
+          if (arg.getValue() != null && !arg.getValue().isBlank())
+            request.addData(paramId, true);
+          else
+            request.addData(paramId, false);
         }
         else
         {
-          form.insert(fieldName, arg.getValue());
+          request.addData(paramId, arg.getValue());
         }
       }
     }
-    return new JobId(service.getName(), service.getName(), form.submit());
+    var job = service.submitJob(request);
+    return new JobId(service.getName(), service.getName(), job.getId());
   }
 
   @Override
@@ -134,7 +130,8 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   {
     try
     {
-      job.setState(stateMap.get(client.getJobState(job.getJobId())));
+      var slivkaJob = client.getJob(job.getJobId());
+      job.setState(stateMap.get(slivkaJob.getStatus()));
     } catch (IOException e)
     {
       throw new IOError(e);
@@ -143,8 +140,9 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
 
   @Override
   public final boolean updateJobProgress(WsJob job) throws IOException
-  {
-    List<RemoteFile> files = client.getJobResults(job.getJobId());
+  {      
+    var slivkaJob = client.getJob(job.getJobId());
+    Collection<RemoteFile> files = slivkaJob.getResults();
     RemoteFile logFile=null;
     for (RemoteFile f : files)
     {
@@ -196,17 +194,10 @@ public abstract class SlivkaWSInstance extends ServiceWithParameters
   @Override
   public final boolean handleSubmitError(Throwable _lex, WsJob j, WebserviceInfo wsInfo)
   {
-    if (_lex instanceof FormValidationException)
+    if (_lex instanceof ClientProtocolException)
     {
-      FormValidationException formError = (FormValidationException) _lex;
-      String[] messages = new String[formError.getErrors().size()];
-      int i = 0;
-      for (ValidationException e : formError.getErrors())
-      {
-        messages[i++] = String.format("%s: %s,", e.getField().getName(), e.getMessage());
-      }
       j.setState(WsJob.JobState.INVALID);
-      j.setStatus(String.join(", ", messages));
+      j.setStatus(_lex.getMessage());
       return true;
     }
     return false;