Merge branch '1365-change-active-tab-when-choosing-a-show-all-element-from-pin-popup' into 'master'

fix slider

Closes #1064

See merge request !1301

CHANGELOG

@@ -15,6 +15,10 @@ minerva (16.0.0~alpha.2) stable; urgency=medium
     their lines (#1471)
   * Bug fix: when selecting drug in the alias window the input text is updated
     (#1365)
+  * Bug fix: zoom slider was not updated when clicking on +/- in genome browser
+    (#1064)
+  * Bug fix: there was no possibility to see gene variants
+    (regression 16.0.0~alpha.1)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Mar 2021 10:00:00 +0200
 

frontend-js/src/main/js/map/data/DataOverlay.js

@@ -33,6 +33,10 @@ function DataOverlay(overlayId, name) {
     this.setGoogleLicenseConsent(object.googleLicenseConsent);
     this.setInputDataAvailable(object.inputDataAvailable);
     this.setType(object.type);
+    if (this.getType()===LayoutAlias.GENETIC_VARIANT) {
+      this.setGenomeVersion(object.genomeVersion);
+      this.setGenomeType(object.genomeType);
+    }
     if (!this.getInputDataAvailable()) {
       this.setInitialized(true);
     }
@@ -390,6 +394,38 @@ DataOverlay.prototype.setType = function (type) {
   this._type = type;
 };
 
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getGenomeType = function () {
+  return this._genomeType;
+};
+
+/**
+ *
+ * @param {string} type
+ */
+DataOverlay.prototype.setGenomeType = function (type) {
+  this._genomeType = type;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getGenomeVersion = function () {
+  return this._genomeVersion;
+};
+
+/**
+ *
+ * @param {string} version
+ */
+DataOverlay.prototype.setGenomeVersion = function (version) {
+  this._genomeVersion = version;
+};
+
 /**
  *
  * @param {boolean} value

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

@@ -403,35 +403,30 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
 
   overlays.forEach(function (overlay) {
     promises.push(overlay.getFullAliasesById(self.getAlias().getId()));
+    if (overlay.getType() === LayoutAlias.GENETIC_VARIANT) {
+      geneticInformation = true;
+      promises.push(self.getCustomMap().getTopMap().getReferenceGenome(overlay.getGenomeType(),
+        overlay.getGenomeVersion()).then(function (genome) {
+        if (genome.getUrl() !== null && genome.getUrl() !== undefined) {
+          if (genomes[genome.getUrl()] === undefined) {
+            genomes[genome.getUrl()] = genome;
+            genomeUrls.push(genome.getUrl());
+          }
+        } else {
+          logger.warn("Genome for " + overlay.getGenomeType() + ","
+            + overlay.getGenomeVersion() + " not loaded");
+        }
+      }, function () {
+        logger.warn("Genome for " + overlay.getGenomeType() + ","
+          + overlay.getGenomeVersion() + " not loaded");
+
+      }));
+    }
   });
   return Promise.all(promises).then(function (result) {
     promises = [];
     result.forEach(function (overlayEntries) {
       overlaysData = overlaysData.concat(overlayEntries);
-      for (var i = 0; i < overlayEntries.length; i++) {
-        var data = overlayEntries[i];
-        if (data !== null && data !== undefined && data.getType() === LayoutAlias.GENETIC_VARIANT) {
-          geneticInformation = true;
-          promises.push(Promise.each(data.getGeneVariants(), function (variant) {
-            return self.getCustomMap().getTopMap().getReferenceGenome(variant.getReferenceGenomeType(),
-              variant.getReferenceGenomeVersion()).then(function (genome) {
-              if (genome.getUrl() !== null && genome.getUrl() !== undefined) {
-                if (genomes[genome.getUrl()] === undefined) {
-                  genomes[genome.getUrl()] = genome;
-                  genomeUrls.push(genome.getUrl());
-                }
-              } else {
-                logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
-                  + variant.getReferenceGenomeVersion() + " not loaded");
-              }
-            }, function () {
-              logger.warn("Genome for " + variant.getReferenceGenomeType() + ","
-                + variant.getReferenceGenomeVersion() + " not loaded");
-
-            });
-          }));
-        }
-      }
     });
     return Promise.all(promises);
   }).then(function () {
@@ -521,7 +516,8 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
           var distDiff = Math.floor((range.stop - range.start + 1) / 4);
           range.start += distDiff;
           range.stop -= distDiff;
-
+          
+          $(".zoom-slider", contentElement).val(parseInt($(".zoom-slider", zoomControls).val()) + 1);
           self.pileup.setRange(range);
         });
         zoomIn.appendTo(zoomControls);
@@ -539,6 +535,7 @@ AliasInfoWindow.prototype.createGenomicDiv = function (params) {
             range.start = 0;
           }
 
+          $(".zoom-slider", contentElement).val(parseInt($(".zoom-slider", zoomControls).val()) - 1);
           self.pileup.setRange(range);
         });
         zoomOut.appendTo(zoomControls);

model/src/main/java/lcsb/mapviewer/model/overlay/GeneVariant.java

@@ -7,6 +7,8 @@ import javax.persistence.*;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
 import lcsb.mapviewer.common.exception.NotImplementedException;
 
 /**
@@ -72,6 +74,7 @@ public class GeneVariant implements Serializable {
    */
   private String variantIdentifier;
 
+  @JsonIgnore
   @ManyToOne
   private GeneVariantDataOverlayEntry dataOverlayEntry;
 

rest-api/src/main/java/lcsb/mapviewer/api/projects/overlays/OverlayRestImpl.java

@@ -7,6 +7,7 @@ import java.util.stream.Collectors;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.hibernate.Hibernate;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
@@ -431,6 +432,7 @@ public class OverlayRestImpl extends BaseRestImpl {
       case "genevariations":
         if (overlayEntry instanceof GeneVariantDataOverlayEntry) {
           value = ((GeneVariantDataOverlayEntry) overlayEntry).getGeneVariants();
+          Hibernate.initialize(((GeneVariantDataOverlayEntry) overlayEntry).getGeneVariants());
         } else {
           value = new Object[] {};
         }

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

@@ -42,6 +42,7 @@ import org.springframework.web.context.WebApplicationContext;
 
 import lcsb.mapviewer.api.projects.chemicals.ChemicalRestImpl;
 import lcsb.mapviewer.common.*;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
 import lcsb.mapviewer.model.*;
 import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.graphics.*;
@@ -560,6 +561,11 @@ abstract public class ControllerIntegrationTest {
   }
 
   protected DataOverlay createOverlay(Project project, User admin, String content) throws Exception {
+    return createOverlay(project, admin, content, DataOverlayType.GENERIC);
+  }
+
+  protected DataOverlay createOverlay(Project project, User admin, String content, DataOverlayType type)
+      throws Exception {
     UploadedFileEntry file = new UploadedFileEntry();
     file.setFileContent(content.getBytes());
     file.setLength(content.getBytes().length);
@@ -568,7 +574,7 @@ abstract public class ControllerIntegrationTest {
     ColorSchemaReader reader = new ColorSchemaReader();
 
     DataOverlay overlay = new DataOverlay();
-    overlay.setColorSchemaType(DataOverlayType.GENERIC);
+    overlay.setColorSchemaType(type);
     overlay.setInputData(file);
     overlay.setProject(project);
     overlay.setName("test title");
@@ -576,6 +582,7 @@ abstract public class ControllerIntegrationTest {
     overlay.setCreator(admin);
     Map<String, String> headers = new HashMap<>();
     headers.put(TextFileUtils.COLUMN_COUNT_PARAM, "2");
+    headers.put(ZipEntryFileFactory.LAYOUT_HEADER_PARAM_TYPE, type.toString());
     overlay.addEntries(reader.readColorSchema(new ByteArrayInputStream(content.getBytes()), headers));
     dataOverlayDao.add(overlay);
     return overlay;

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

@@ -1483,7 +1483,6 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
   }
 
   @Test
-
   public void testRemoveUserOverlayAsAnonymous() throws Exception {
     DataOverlay overlay = createOverlayInSeparateThread(TEST_PROJECT, user);
     RequestBuilder request = delete("/projects/" + TEST_PROJECT + "/overlays/" + overlay.getId());
@@ -1492,4 +1491,37 @@ public class OverlayControllerIntegrationTest extends ControllerIntegrationTest
         .andExpect(status().isForbidden());
   }
 
+  @Test
+  public void testFetchGeneticDataOverlayData() throws Exception {
+    MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+    DataOverlay overlay = callInSeparateThread(() -> {
+      try {
+        return createOverlay(project, user, "#TYPE=GENETIC_VARIANT\n" +
+            "#GENOME_TYPE=UCSC\n" +
+            "#GENOME_VERSION=xenLae2\n" +
+            "position\toriginal_dna\talternative_dna\tgene_name\tdescription\tcolor\tcontig\n" +
+            "10146\tAC\tA\tGSTA4\tupstream\t#ff0000\tchr1", DataOverlayType.GENETIC_VARIANT);
+      } catch (Exception e) {
+        e.printStackTrace();
+        return null;
+      }
+    });
+    assertNotNull(overlay);
+    for (Element element_iterator : map.getElements()) {
+      if (element_iterator.getName().equals("GSTA4")) {
+        element = element_iterator;
+      }
+    }
+    assertEquals(element.getName(), "GSTA4");
+
+    RequestBuilder request = get(
+        "/projects/{projectId}/overlays/{overlayId}/models/{mapId}/bioEntities/elements/{elementId}/",
+        TEST_PROJECT, overlay.getId(), map.getId(), element.getId())
+            .session(session);
+
+    mockMvc.perform(request)
+        .andExpect(status().is2xxSuccessful());
+  }
+
 }