Merge tag 'v14.0.6' into merge-14.0.6

CHANGELOG

@@ -2,10 +2,10 @@ minerva (15.0.0~alpha.2) stable; urgency=medium
   * Small improvement: data not compliant with database constraints (for
     instance too long species identifiers) will be automatically adjust instead
     of crashing project upload (#1041)
-  * Small improvement: reaction lines in SBML files without layout are set 
+  * Small improvement: reaction lines in SBML files without layout are set
     outside of the species (not in the center, #1023)
   * Bug fix: import from CellDesigner rounded alias dimension to integer
-  * Bug fix: old project with structural state couldn't be removed (regresion 
+  * Bug fix: old project with structural state couldn't be removed (regression
     15.0.0~alpha.1, #1021)
   * Bug fix: procseing sbgn file with render information was breaking sometimes
     (regresion 15.0.0~alpha.1, #1020)
@@ -29,8 +29,8 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
     about the plugins (name, version)
   * Small improvement: there is possibility to define default plugins loaded
     with every opening of a map (#967)
-  * Small improvement: support for annotations added: ChemIDplus, EcoGene, 
-    FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein, 
+  * Small improvement: support for annotations added: ChemIDplus, EcoGene,
+    FlyBase, GeneDB, Intact, Kegg Drug, KNApSAcK, LIPID MAPS, NCBI Protein,
     PATO, RGD, SPIKE, TTD Drug, ZFIN BioEntity
   * Bug fix: compartments limited by corner (left-top corner compartment, etc)
     are parsed properly from CellDesigner files
@@ -72,6 +72,24 @@ minerva (15.0.0~alpha.0) stable; urgency=medium
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 4 Nov 2019 11:00:00 +0200
 
+minerva (14.0.6) stable; urgency=medium
+  * Bug fix: opening map with no background overlays and search request in url
+    provides proper error message (#1046)
+  * Bug fix: search by identifier didn't consider identifiers added by
+    annotators (#1047)
+  * Bug fix: if map has SHOW OVERVIEW, the legend/comment/clear were not
+    displayed at all (regresion 14.0.5, #1045)
+  * Bug fix: when there is a problem with database during removing project,
+    project removal doesn't hang (#1058)
+  * Bug fix: coloring of the reaction wasn't applied to center of reaction
+    (regression 14.0.0, #1057)
+  * Bug fix: genetic variant overlay improperly processed elements identified
+    by miriam identifiers, like uniprot (#1059)
+  * Bug fix: invalid information was provided for genetic variants overlay when
+    map organism was defined (#1060)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 19 Dec 2019 13:00:00 +0200
+
 minerva (14.0.5) stable; urgency=medium
   * Bug fix: copy-paste of genetic-variant data overlay into Add overlay
     content dialog could crash upload (#1040)

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/reaction/ReactionConverter.java

@@ -296,8 +296,15 @@ public class ReactionConverter extends BioEntityConverter<Reaction> {
    *          {@link ColorSchema} to modify reaction
    */
   private void applyColorSchema(Reaction reaction, ColorSchema colorSchema) {
+    PolylineData pd = new PolylineData(reaction.getLine());
+    pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
+    if (colorSchema.getLineWidth() != null) {
+      pd.setWidth(colorSchema.getLineWidth());
+    }
+    reaction.setLine(pd);
+
     for (AbstractNode node : reaction.getNodes()) {
-      PolylineData pd = new PolylineData(node.getLine());
+      pd = new PolylineData(node.getLine());
       pd.setColor(colorExtractor.getNormalizedColor(colorSchema));
       if (colorSchema.getLineWidth() != null) {
         pd.setWidth(colorSchema.getLineWidth());

frontend-js/src/main/css/global.css

@@ -624,6 +624,10 @@ Plugin tabs
     float: left;
 }
 
+.minerva-overview-div {
+    display: inline;
+}
+
 .minerva-overview-button {
     color: #FFFFFF;
     height: 36px;

frontend-js/src/main/js/gui/topMenu/TopMenu.js

@@ -89,7 +89,7 @@ TopMenu.prototype._createGui = function () {
     style: "display:none;"
   }));
 
-  var showOverviewDiv = Functions.createElement({type: "div"});
+  var showOverviewDiv = Functions.createElement({type: "div", className:"minerva-overview-div"});
   self.getElement().appendChild(showOverviewDiv);
 
   var showOverviewButton = Functions.createElement({

frontend-js/src/main/js/map/overlay/SearchDbOverlay.js

@@ -279,7 +279,7 @@ SearchDbOverlay.prototype.searchByCoordinates = function (params) {
       if (elements.length === 0) {
         return undefined;
       } else {
-        if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
+        if (self.getMap().getBackgroundDataOverlay() !== null && self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
           return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom(), coordinates);
         } else {
           return elements[0];

frontend-js/src/main/js/map/window/AliasInfoWindow.js

@@ -463,7 +463,11 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
     }
     if (geneticInformation) {
       if (genomeUrls.length === 0) {
-        contentElement.innerHTML = "No organism defined for this project, cannot display variant data";
+        if (self.getCustomMap().getProject().getOrganism() === undefined) {
+          contentElement.innerHTML = "No organism defined for this project, cannot display variant data.";
+        } else {
+          contentElement.innerHTML = "No reference genome defined for this MINERVA instance, cannot display variant data.";
+        }
       } else {
         for (i = 0; i < overlaysData.length; i++) {
           if (globalGeneVariants[i].length > 0) {

model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java

@@ -80,13 +80,17 @@ public class ColorModelCommand extends ModelCommand {
    * @throws InvalidColorSchemaException
    *           thrown when {@link Reaction} was already colored by other schema
    */
-  private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
+  void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
     if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
       throw new InvalidColorSchemaException(
           "At least two rows try to set color to reaction: " + reaction.getIdReaction());
     }
 
     Color color = colorExtractor.getNormalizedColor(schema);
+    reaction.getLine().setColor(color);
+    if (schema.getLineWidth() != null) {
+      reaction.getLine().setWidth(schema.getLineWidth());
+    }
     for (AbstractNode node : reaction.getNodes()) {
       node.getLine().setColor(color);
       if (schema.getLineWidth() != null) {
@@ -343,6 +347,7 @@ public class ColorModelCommand extends ModelCommand {
       element.setGlyph(null);
     }
     for (Reaction reaction : result.getReactions()) {
+      reaction.getLine().setColor(Color.BLACK);
       for (AbstractNode node : reaction.getNodes()) {
         node.getLine().setColor(Color.BLACK);
       }

model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java

@@ -2,9 +2,8 @@ package lcsb.mapviewer.commands;
 
 import static org.junit.Assert.*;
 
-import java.awt.*;
+import java.awt.Color;
 import java.util.*;
-import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -460,4 +459,21 @@ public class ColorModelCommandTest extends CommandTestFunctions {
     assertNotNull(factory.getModifiedElements().get(reaction));
   }
 
+  @Test
+  public void testApplyColorToReaction() throws Exception {
+    Model model = getModelForFile("testFiles/sample.xml", false);
+    Reaction re4 = model.getReactionByReactionId("re1");
+
+    ColorSchema schema = new GenericColorSchema();
+    schema.setElementId("re1");
+    schema.setColor(Color.YELLOW);
+    schema.setName(null);
+
+    ColorModelCommand factory = new ColorModelCommand(model, new ArrayList<>(), colorExtractor);
+
+    factory.applyColor(re4, schema);
+
+    assertEquals(Color.YELLOW, re4.getLine().getColor());
+  }
+
 }

model/src/main/java/lcsb/mapviewer/model/Project.java

@@ -80,7 +80,7 @@ public class Project implements Serializable {
   private List<Layout> layouts = new ArrayList<>();
 
   @Cascade({ CascadeType.SAVE_UPDATE })
-  @OneToOne(fetch = FetchType.LAZY, orphanRemoval = true)
+  @ManyToOne(fetch = FetchType.LAZY)
   @JoinColumn(name = "file_entry_id")
   private UploadedFileEntry inputData;
 

model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java

@@ -344,7 +344,8 @@ public class ModelFullIndexed implements Model {
     Set<BioEntity> result = new HashSet<>();
     for (Element element : getElements()) {
       for (MiriamData md : element.getMiriamData()) {
-        if (md.equals(miriamData)) {
+        if (Objects.equals(md.getResource().toLowerCase(), miriamData.getResource().toLowerCase())
+            && Objects.equals(md.getDataType(), miriamData.getDataType())) {
           result.add(element);
         }
       }
@@ -352,7 +353,8 @@ public class ModelFullIndexed implements Model {
 
     for (Reaction element : getReactions()) {
       for (MiriamData md : element.getMiriamData()) {
-        if (md.equals(miriamData)) {
+        if (Objects.equals(md.getResource().toLowerCase(), miriamData.getResource().toLowerCase())
+            && Objects.equals(md.getDataType(), miriamData.getDataType())) {
           result.add(element);
         }
       }

model/src/test/java/lcsb/mapviewer/model/map/model/ModelTest.java

@@ -115,6 +115,16 @@ public class ModelTest extends ModelTestFunctions {
     assertEquals(0, elements.size());
   }
 
+  @Test
+  public void testElementsByAnnotationWithAnnotator() {
+    model = createModel();
+
+    Set<BioEntity> elements = model
+        .getElementsByAnnotation(new MiriamData(MiriamType.CHEMBL_TARGET, "CHEMBL12345", Object.class));
+    assertNotNull(elements);
+    assertEquals(1, elements.size());
+  }
+
   private Model createModel() {
     Model model = new ModelFullIndexed(null);
 

persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java

@@ -7,10 +7,12 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.hibernate.dialect.Dialect;
 import org.hibernate.query.NativeQuery;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 
 import lcsb.mapviewer.model.Project;
 import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.persist.dao.cache.UploadedFileEntryDao;
 
 /**
  * Data access object class for Project objects.
@@ -20,7 +22,10 @@ import lcsb.mapviewer.model.map.model.ModelData;
  */
 @Repository
 public class ProjectDao extends BaseDao<Project> {
-  Logger logger = LogManager.getLogger(ProjectDao.class);
+  Logger logger = LogManager.getLogger();
+
+  @Autowired
+  private UploadedFileEntryDao uploadedFileEntryDao;
 
   /**
    * Default constructor.
@@ -82,4 +87,14 @@ public class ProjectDao extends BaseDao<Project> {
     return ((BigInteger) sqlQuery.getResultList().get(0)).longValue();
 
   }
+
+  @Override
+  public void delete(Project project) {
+    super.delete(project);
+    if (project.getInputData() != null
+        && getElementsByParameter("file_entry_id", project.getInputData().getId()).size() == 0) {
+      uploadedFileEntryDao.delete(uploadedFileEntryDao.getById(project.getInputData().getId()));
+    }
+  }
+
 }

persist/src/main/resources/db/migration/14.0.6/V14.0.6.20191218__project_with_invalid_file.sql

+update project_table set file_entry_id = null where not file_entry_id in (select id from file_entry_table);
+
+ALTER TABLE project_table ADD CONSTRAINT project_file_constraint FOREIGN KEY (file_entry_id)
+      REFERENCES public.file_entry_table (id) MATCH SIMPLE
+      ON UPDATE NO ACTION ON DELETE NO ACTION;

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

@@ -54,7 +54,7 @@ public class SearchService implements ISearchService {
    * Default class logger.
    */
   @SuppressWarnings("unused")
-  private static Logger logger = LogManager.getLogger(SearchService.class.getName());
+  private static Logger logger = LogManager.getLogger();
 
   /**
    * Data access object for models.
@@ -91,7 +91,7 @@ public class SearchService implements ISearchService {
    * between String and List is stored. The key in this map is incomplete typed
    * word, and value list contains suggestions that should appear for this word.
    */
-  private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<Model, Map<String, List<String>>>();
+  private Map<Model, Map<String, List<String>>> autoCompleteLists = new HashMap<>();
 
   /**
    * Default constructor that set list of prefixes used in the search queries.

service/src/main/java/lcsb/mapviewer/services/utils/ColorSchemaReader.java

@@ -81,9 +81,7 @@ public class ColorSchemaReader {
     if (Integer.valueOf(params.get(TextFileUtils.COLUMN_COUNT_PARAM)) == 1) {
       return readSimpleNameColorSchema(colorInputStream);
     } else if (params.get(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE) == null) {
-      {
-        return readGenericColorSchema(colorInputStream);
-      }
+      return readGenericColorSchema(colorInputStream);
     } else {
       ColorSchemaType type = null;
       try {
@@ -393,10 +391,10 @@ public class ColorSchemaReader {
   private Collection<ColorSchema> mergeSchemas(Collection<ColorSchema> schemas) {
     Map<String, ColorSchema> schemasByName = new HashMap<>();
     for (ColorSchema colorSchema : schemas) {
-      ColorSchema mergedSchema = schemasByName.get(colorSchema.getName());
+      ColorSchema mergedSchema = schemasByName.get(getColorSchemaIdentifiablePart(colorSchema));
       if (mergedSchema == null) {
         mergedSchema = colorSchema.copy();
-        schemasByName.put(colorSchema.getName(), mergedSchema);
+        schemasByName.put(getColorSchemaIdentifiablePart(colorSchema), mergedSchema);
       } else {
         if (mergedSchema instanceof GeneVariationColorSchema) {
           if (colorSchema instanceof GeneVariationColorSchema) {
@@ -420,6 +418,16 @@ public class ColorSchemaReader {
     return schemasByName.values();
   }
 
+  private String getColorSchemaIdentifiablePart(ColorSchema colorSchema) {
+    List<String> identifiers = new ArrayList<>();
+    for (MiriamData md : colorSchema.getMiriamData()) {
+      identifiers.add(md.toString());
+    }
+    Collections.sort(identifiers);
+
+    return StringUtils.join(identifiers, "\n") + "\n" + colorSchema.getName();
+  }
+
   /**
    * Gets color that should be assigned to {@link GeneVariationColorSchema}.
    * 
@@ -771,7 +779,7 @@ public class ColorSchemaReader {
       if (schema.getLineWidth() != null) {
         result.add(ColorSchemaColumn.LINE_WIDTH);
       }
-      if (schema.getName() != null) {
+      if (getColorSchemaIdentifiablePart(schema) != null) {
         result.add(ColorSchemaColumn.NAME);
       }
       if (schema.getModelName() != null) {

service/src/test/java/lcsb/mapviewer/services/utils/ColorSchemaReaderTest.java

@@ -376,4 +376,18 @@ public class ColorSchemaReaderTest extends ServiceTestFunctions {
     reader.readColorSchema(fis, TextFileUtils.getHeaderParametersFromFile(fis2));
 
   }
+
+  @Test
+  public void testGeneticVariantByUniprotIdentifier() throws Exception {
+    File f = new File("testFiles/coloring/uniprot-identifiers.txt");
+    byte[] data = fileToByteArray(f);
+
+    ByteArrayInputStream bin = new ByteArrayInputStream(data);
+
+    Collection<ColorSchema> schemas = reader.readColorSchema(bin,
+        TextFileUtils.getHeaderParametersFromFile(new ByteArrayInputStream(data)));
+    assertNotNull(schemas);
+    assertEquals(2, schemas.size());
+  }
+
 }

service/testFiles/coloring/uniprot-identifiers.txt

+#TYPE=GENETIC_VARIANT						
+#GENOME_VERSION=hg19						
+#GENOME_TYPE=UCSC						
+position	original_DNA	alternative_DNA	contig	allele_frequency	color	identifier_uniprot
+90648003	T	G	4	0.3750000	#e58e00	P14416
+90656320	T	C	4	0.7034621	#e58e00	P14416
+90755218	G	A	4	0.1379310	#e58ec5	P02511
+161709831	G	T	6	0.6025862	#e58ec5	P02511
+162525131	G	T	6	0.7025762	#e58ec5	P02511

web/src/test/java/lcsb/mapviewer/web/ProjectControllerIntegrationTestWithoutTransaction.java

@@ -2,6 +2,7 @@ package lcsb.mapviewer.web;
 
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.patch;
 import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
+import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.delete;
 import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.status;
 
 import java.nio.file.Files;
@@ -179,4 +180,75 @@ public class ProjectControllerIntegrationTestWithoutTransaction extends Controll
     }
   }
 
+  @Test
+  public void addProjectWithInvalidFileId() throws Exception {
+    String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+        new BasicNameValuePair("file-id", "-1"),
+        new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+        new BasicNameValuePair("parser",
+            "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
+
+    RequestBuilder request = post("/projects/" + TEST_PROJECT)
+        .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+        .content(body)
+        .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+
+    mockMvc.perform(request).andExpect(status().isBadRequest());
+  }
+
+  @Test
+  public void removeProjectWithUsedFile() throws Exception {
+    String testProject2 = "test2";
+    User admin = userService.getUserByLogin(BUILT_IN_ADMIN_LOGIN);
+    try {
+      UploadedFileEntry fileEntry = createFileInSeparateThread(
+          new String(Files.readAllBytes(Paths.get("./src/test/resources/generic.xml")), "UTF-8"),
+          admin);
+
+      String body = EntityUtils.toString(new UrlEncodedFormEntity(Arrays.asList(
+          new BasicNameValuePair("file-id", String.valueOf(fileEntry.getId())),
+          new BasicNameValuePair("mapCanvasType", "OPEN_LAYERS"),
+          new BasicNameValuePair("parser",
+              "lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser"))));
+
+      RequestBuilder request = post("/projects/" + TEST_PROJECT)
+          .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+          .content(body)
+          .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+      mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+
+      request = post("/projects/" + testProject2)
+          .contentType(MediaType.APPLICATION_FORM_URLENCODED)
+          .content(body)
+          .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+      mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+
+      callInSeparateThread(() -> {
+        try {
+          waitForProjectToFinishLoading(testProject2);
+        } catch (InterruptedException e) {
+          e.printStackTrace();
+        }
+        return null;
+      });
+
+      request = delete("/projects/" + testProject2)
+          .session(createSession(BUILT_IN_ADMIN_LOGIN, BUILT_IN_ADMIN_PASSWORD));
+      
+      mockMvc.perform(request).andExpect(status().is2xxSuccessful());
+
+    } finally {
+      callInSeparateThread(() -> {
+        try {
+          waitForProjectToFinishLoading(TEST_PROJECT);
+        } catch (InterruptedException e) {
+          e.printStackTrace();
+        }
+        return null;
+      });
+      removeProjectInSeparateThread(TEST_PROJECT);
+      removeProjectInSeparateThread(testProject2);
+    }
+  }
+
 }