Merge branch '1434-annotations-missing-after-upload' into 'devel_15.1.x'

Resolve "No Protein annotations after uploading the map"

See merge request !1262

.gitlab-ci.yml

-image: node
+image: node:14
 
 stages:
   - build

CHANGELOG

+minerva (15.1.2) stable; urgency=medium
+  * Bug fix: automatic annotations are sometimes missing after project upload
+   (#1434)
+  * Bug fix: export to SBML failed if reactant/product line had length=0
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 7 Jan 2021 15:00:00 +0200
+
 minerva (15.1.1) stable; urgency=medium
   * Bug fix: export to CD maps with species containing ":" or "." in species id
     generated files that could not be opened in CellDesigner (#1363) 

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java

@@ -36,7 +36,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
   /**
    * Version of the rest API that is supported by this annotator.
    */
-  static final String SUPPORTED_VERSION = "13.0";
+  static final String SUPPORTED_VERSION = "13.1";
 
   /**
    * Url address of ensembl restful service.

annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java

@@ -14,6 +14,8 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
 import lcsb.mapviewer.annotation.services.annotators.ElementAnnotator;
 import lcsb.mapviewer.common.IProgressUpdater;
 import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.*;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.*;
@@ -49,15 +51,15 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
 
     model.addReaction(new Reaction());
 
-    Species proteinAlias1 = new GenericProtein("a1");
-    proteinAlias1.setName("SNCA");
+    Species protein1 = new GenericProtein("a1");
+    protein1.setName("SNCA");
 
-    Species proteinAlias2 = new GenericProtein("a2");
-    proteinAlias2.setName("PDK1");
-    proteinAlias2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
+    Species protein2 = new GenericProtein("a2");
+    protein2.setName("PDK1");
+    protein2.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CAS, "c"));
 
-    model.addElement(proteinAlias1);
-    model.addElement(proteinAlias2);
+    model.addElement(protein1);
+    model.addElement(protein2);
 
     modelAnnotator.annotateModel(model, updater, modelAnnotator.createDefaultAnnotatorSchema());
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporter.java

@@ -293,10 +293,14 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
     return createStyle(reaction.getLine());
   }
 
-  private void removeColinearPoints(ReactionGlyph glyph) {
+  void removeColinearPoints(ReactionGlyph glyph) {
     PolylineData line = createLine(glyph.getCurve());
     line = PolylineDataFactory.removeCollinearPoints(line);
-    Curve curve = createCurve(line, false, (int) glyph.getCurve().getCurveSegment(0).getStart().getZ());
+    int z = 0;
+    if (glyph.getCurve().getCurveSegmentCount() > 0) {
+      z = (int) glyph.getCurve().getCurveSegment(0).getStart().getZ();
+    }
+    Curve curve = createCurve(line, false, z);
     glyph.setCurve(curve);
   }
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java

@@ -81,4 +81,16 @@ public class SbmlReactionExporterTest {
     return exporter;
   }
 
+  @Test
+  public void removeColinearPointsForEmptyLine() throws InconsistentModelException {
+    ModelFullIndexed model = new ModelFullIndexed(null);
+
+    SbmlReactionExporter exporter = createExporter(model);
+    ReactionGlyph glyph = new ReactionGlyph("id", 3, 2);
+    glyph.setReaction("r_id");
+    glyph.setCurve(new Curve());
+    exporter.removeColinearPoints(glyph);
+    assertNotNull(glyph.getCurve());
+  }
+
 }

service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java

@@ -189,7 +189,7 @@ public class ModelService implements IModelService {
 
   @Override
   public void removeModelFromCache(Model model) {
-    models.remove(model.getProject().getProjectId());
+    removeModelFromCacheByProjectId(model.getProject().getProjectId());
 
   }
 
@@ -219,11 +219,26 @@ public class ModelService implements IModelService {
 
   @Override
   public void removeModelFromCache(ModelData model) {
-    models.remove(model.getProject().getProjectId());
+    removeModelFromCacheByProjectId(model.getProject().getProjectId());
   }
 
   @Override
   public void removeModelFromCacheByProjectId(String projectId) {
+    boolean waitForModel = false;
+    do {
+      synchronized (modelsInLoadStage) {
+        waitForModel = modelsInLoadStage.contains(projectId);
+      }
+      // if model is being loaded then wait until it's loaded
+      if (waitForModel) {
+        try {
+          Thread.sleep(100);
+        } catch (InterruptedException e) {
+          logger.fatal(e, e);
+        }
+      }
+    } while (waitForModel);
+
     models.remove(projectId);
   }
 

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -425,6 +425,7 @@ public class ProjectService implements IProjectService {
             // new session for db connection
             dbUtils.createSessionForCurrentThread();
           }
+          modelService.removeModelFromCacheByProjectId(params.getProjectId());
           modelService.getLastModelByProjectId(params.getProjectId());
         } finally {
           if (params.isAsync()) {