From d5f003d08ca67af199bb347d66aa80981db751d2 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Fri, 16 Feb 2018 11:26:41 +0100
Subject: [PATCH] Passing annotators descriptions to client, tooltips, fixes of
failing annotator tests
---
.../services/DrugbankHTMLParser.java | 2 +-
.../annotation/services/ModelAnnotator.java | 9 +-
.../services/annotators/ElementAnnotator.java | 17 +++-
.../services/annotators/KeggAnnotator.java | 6 ++
.../services/ModelAnnotatorTest.java | 3 +
.../annotators/CazyAnnotatorTest.java | 2 +-
.../annotators/ChebiAnnotatorTest.java | 6 +-
.../annotators/EnsemblAnnotatorTest.java | 2 +-
.../annotators/EntrezAnnotatorTest.java | 2 +-
.../annotators/HgncAnnotatorTest.java | 12 +--
.../annotators/TairAnnotatorTest.java | 2 +-
.../annotators/UniprotAnnotatorTest.java | 6 +-
frontend-js/src/main/css/global.css | 27 +++++-
.../js/gui/admin/ChooseAnnotatorsDialog.js | 17 ++--
.../src/main/js/gui/leftPanel/GuiUtils.js | 87 ++++++++++---------
.../src/main/js/map/data/Annotation.js | 30 +++++--
frontend-js/src/main/js/map/data/Annotator.js | 10 +++
.../java/lcsb/mapviewer/api/BaseRestImpl.java | 25 ++++--
.../configuration/ConfigurationRestImpl.java | 1 +
19 files changed, 175 insertions(+), 91 deletions(-)
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
index bfb4eb7ab8..8339571989 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/DrugbankHTMLParser.java
@@ -700,7 +700,7 @@ public class DrugbankHTMLParser extends DrugAnnotation implements IExternalServi
protienLinkPosition = protienLinkPosition + "/polypeptides/".length(); // 20;
int j = page.indexOf('"', protienLinkPosition);
String uniprotId = page.substring(protienLinkPosition, j);
- MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId);
+ MiriamData uniprotMiriam = new MiriamData(MiriamType.UNIPROT, uniprotId, UniprotAnnotator.class);
MiriamData hgncMiriam = uniprotAnnotator.uniProtToHgnc(uniprotMiriam);
if (hgncMiriam == null || !hgncMiriam.equals(hgncTarget)) {
logger.debug("Invalid target found. Expected " + hgncTarget + ", but found: " + hgncMiriam + " ("
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 8516fd4f6b..792c637103 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -17,7 +17,6 @@ import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorParamDefinition;
import lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator;
import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
import lcsb.mapviewer.annotation.services.annotators.CazyAnnotator;
@@ -360,9 +359,11 @@ public class ModelAnnotator {
for (ElementAnnotator elementAnnotator : list) {
try {
- List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());
- if (params != null) {
- elementAnnotator.annotateElement(element, params);
+ if (annotatorsParams != null){
+ List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());
+ if (params != null) {
+ elementAnnotator.annotateElement(element, params);
+ }
} else {
elementAnnotator.annotateElement(element);
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
index b353a3f86b..7be1c6bde1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotator.java
@@ -153,7 +153,16 @@ public abstract class ElementAnnotator extends CachableInterface {
*/
public abstract String getUrl();
-
+ /**
+ * Provides description of the extraction process
+ * for {@link ElementAnnotator} to be used in the front end.
+ * @return
+ * the description
+ */
+ public String getDescription(){
+ return "";
+ }
+
/**
* Provides description for {@link ElementAnnotator} and {@link MiriamType} pair
* to be used in the frontend.
@@ -161,9 +170,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* {@link MiriamType} annotated by this annotator.
* @return
* the description
- */
+ */
public String getDescription(MiriamType mt){
- return getCommonName();
+ return "";
}
/**
@@ -177,7 +186,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* the description
*/
public String getDescription(MiriamType mt, MiriamRelationType relationType){
- return getCommonName();
+ return "";
}
/**
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
index 2097537be8..180871318e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotator.java
@@ -271,6 +271,12 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
public String getUrl() {
return "http://www.genome.jp/kegg/";
}
+
+ @Override
+ public String getDescription() {
+ return "Annotations extracted from KEGG ENZYME Database based on species EC numbers. "
+ + "Annotation include relevant publications and homologous genes for given EC numbers.";
+ }
@Override
protected WebPageDownloader getWebPageDownloader() {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
index 17af451888..0efd208ec9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -88,6 +88,8 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
assertTrue(model.getElementByElementId("a1").getMiriamData().size() > 0);
assertTrue(model.getElementByElementId("a2").getMiriamData().size() >= 1);
+
+ modelAnnotator.annotateModel(model, updater, null);
} catch (Exception e) {
e.printStackTrace();
@@ -129,6 +131,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
}
}
+
@Test
public void testCopyMissingAnnotationsInCD() throws Exception {
try {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
index 66f7e4f58f..e00ab89303 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
@@ -41,7 +41,7 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testUniprotToCazy() throws Exception {
try {
- assertEquals(new MiriamData(MiriamType.CAZY, "GH5_7"),
+ assertEquals(new MiriamData(MiriamType.CAZY, "GH5_7", CazyAnnotator.class),
cazyAnnotator.uniprotToCazy(new MiriamData(MiriamType.UNIPROT, "Q9SG95")));
} catch (Exception e) {
e.printStackTrace();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
index a000cdc242..0c25808d4f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
@@ -59,7 +59,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
public void testGetIdByName() throws Exception {
try {
MiriamData id = backend.getChebiForChebiName("adenine");
- assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"), id);
+ assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:16708", ChebiAnnotator.class), id);
id = backend.getChebiForChebiName("asdf bvclcx lcxj vxlcvkj");
assertNull(id);
assertNull(backend.getChebiForChebiName(null));
@@ -250,7 +250,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
try {
// easy tests with some molecule
MiriamData result = backend.getChebiForChebiName("Ca2+");
- assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:29108"), result);
+ assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:29108", ChebiAnnotator.class), result);
} catch (Exception e) {
e.printStackTrace();
@@ -271,7 +271,7 @@ public class ChebiAnnotatorTest extends AnnotationTestFunctions {
assertNotNull(res);
assertTrue(res.size() > 1);
assertTrue(
- res.contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:24431")));
+ res.contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:24431", ChebiAnnotator.class)));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
index 8366b4f6c7..6c92f99481 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
@@ -240,7 +240,7 @@ public class EnsemblAnnotatorTest extends AnnotationTestFunctions {
try {
MiriamData ensembl = new MiriamData(MiriamType.ENSEMBL, "ENSG00000154930");
MiriamData entrez = ensemblAnnotator.ensemblIdToEntrezId(ensembl);
- assertEquals(new MiriamData(MiriamType.ENTREZ, "84532"), entrez);
+ assertEquals(new MiriamData(MiriamType.ENTREZ, "84532", EnsemblAnnotator.class), entrez);
} catch (Exception e) {
e.printStackTrace();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
index be988ab502..b83f4b449e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotatorTest.java
@@ -172,7 +172,7 @@ public class EntrezAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testGetHgncFromEntrez() throws Exception {
try {
- assertEquals(new MiriamData(MiriamType.HGNC, "11179"), entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, "6647")));
+ assertEquals(new MiriamData(MiriamType.HGNC, "11179", EntrezAnnotator.class), entrezAnnotator.getHgncIdFromEntrez(new MiriamData(MiriamType.ENTREZ, "6647", EntrezAnnotator.class)));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index 2a28675529..71347a9620 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -289,8 +289,8 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
try {
List<MiriamData> result = hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "11138"));
assertEquals(1, result.size());
- assertEquals(new MiriamData(MiriamType.UNIPROT, "P37840"), result.get(0));
- assertEquals(0, hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "1")).size());
+ assertEquals(new MiriamData(MiriamType.UNIPROT, "P37840", HgncAnnotator.class), result.get(0));
+ assertEquals(0, hgncAnnotator.hgncToUniprot(new MiriamData(MiriamType.HGNC, "1", HgncAnnotator.class)).size());
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -300,8 +300,8 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testHgncIdToName() throws Exception {
try {
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "FSD2"), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "18024")));
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "LMOD1"), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "6647")));
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "FSD2", HgncAnnotator.class), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "18024")));
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "LMOD1", HgncAnnotator.class), hgncAnnotator.hgncIdToHgncName(new MiriamData(MiriamType.HGNC, "6647")));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -430,13 +430,13 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
MiriamData data1 = new MiriamData(MiriamType.HGNC_SYMBOL, "PTGS1");
MiriamData entrez = hgncAnnotator.hgncToEntrez(data1);
assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "5742").equals(entrez));
+ assertTrue(new MiriamData(MiriamType.ENTREZ, "5742", HgncAnnotator.class).equals(entrez));
// check by id
data1 = new MiriamData(MiriamType.HGNC, "11138");
entrez = hgncAnnotator.hgncToEntrez(data1);
assertNotNull(entrez);
- assertTrue(new MiriamData(MiriamType.ENTREZ, "6622").equals(entrez));
+ assertTrue(new MiriamData(MiriamType.ENTREZ, "6622", HgncAnnotator.class).equals(entrez));
} catch (Exception e) {
e.printStackTrace();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
index 10d1bb10e7..c7700dbb95 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -154,7 +154,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testTairToUniprot() throws Exception {
try {
- assertEquals(new MiriamData(MiriamType.UNIPROT, "Q9MAN1"),
+ assertEquals(new MiriamData(MiriamType.UNIPROT, "Q9MAN1", TairAnnotator.class),
tairAnnotator.tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030")));
} catch (Exception e) {
e.printStackTrace();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
index aec70cf429..18172cd7d1 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
@@ -87,8 +87,8 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
Collection<MiriamData> mds = uniprotAnnotator.uniProtToEC(new MiriamData(MiriamType.UNIPROT, "P12345"));
assertEquals(mds.size(), 2);
- MiriamData md1 = new MiriamData(MiriamType.EC, "2.6.1.1");
- MiriamData md2 = new MiriamData(MiriamType.EC, "2.6.1.7");
+ MiriamData md1 = new MiriamData(MiriamType.EC, "2.6.1.1", UniprotAnnotator.class);
+ MiriamData md2 = new MiriamData(MiriamType.EC, "2.6.1.7", UniprotAnnotator.class);
for (MiriamData md: mds) {
assertTrue(md.compareTo(md1) == 0 || md.compareTo(md2) == 0);
}
@@ -244,7 +244,7 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testUniprotToHgnc() throws Exception {
try {
- assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "KDR"), uniprotAnnotator.uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, "P35968")));
+ assertEquals(new MiriamData(MiriamType.HGNC_SYMBOL, "KDR", UniprotAnnotator.class), uniprotAnnotator.uniProtToHgnc(new MiriamData(MiriamType.UNIPROT, "P35968")));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index b0b3be3a99..0c3e27b0be 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -582,9 +582,8 @@ h1 {
font-weight: bold;
}
-.minerva-annotator-param-name .annotator-tooltip {
- visibility: hidden;
- width: 50%;
+.minerva-annotator-param-name .annotator-tooltip, .minerva-annotation-group .annotator-tooltip{
+ visibility: hidden;
background-color: rgba(0, 0, 0, .5);
color: #fff;
text-align: left;
@@ -596,7 +595,27 @@ h1 {
z-index: 1;
}
-.minerva-annotator-param-name:hover .annotator-tooltip {
+.minerva-annotator-param-name .annotator-tooltip {
+ width: 50%;
+}
+
+.minerva-annotation-group .annotator-tooltip {
+ width: 250px;
+}
+
+.minerva-annotator-param-name>span:hover .annotator-tooltip, .minerva-annotation-group-header>span:hover .annotator-tooltip {
visibility: visible;
}
+.minerva-annotation-group-header>span {
+ position: relative;
+}
+
+.minerva-annotation-group .tooltip-icon, .minerva-annotator-param-name .tooltip-icon{
+ font-size: 0.8em;
+ left: 3px;
+ top: -3px;
+ font-weight: 700;
+}
+
+
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 9c4e8b9c56..aafcd38207 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -88,7 +88,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
className: "minerva-multi-select"
});
- var annotators = configuration.getElementAnnotators(elementType);
+ var annotators = configuration.getElementAnnotators(elementType);
var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
@@ -149,14 +149,21 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
className: "minerva-annotator-param-name",
content: param.name
});
-
- var toolTip = Functions.createElement({
+
+ var tooltipContainer = Functions.createElement({
+ type: "span"
+ });
+ tooltipContainer.appendChild(Functions.createElement({
+ type: "span",
+ className: "glyphicon glyphicon-question-sign tooltip-icon"
+ }));
+ tooltipContainer.appendChild(Functions.createElement({
type: "span",
className: "annotator-tooltip",
content: param.description
- });
+ }));
- paramName.appendChild(toolTip)
+ paramName.appendChild(tooltipContainer)
paramElement.appendChild(paramName);
var paramValue;
diff --git a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
index 1ac0e50928..2e1caa0851 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GuiUtils.js
@@ -182,23 +182,56 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
var self = this;
var result = document.createElement("div");
+ var annotators = this.getConfiguration().getAnnotators();
+ var annotatorsClassMapping = {};
+ for (var i = 0; i < annotators.length; i++) {
+ annotatorsClassMapping[annotators[i].getClassName()] = annotators[i];
+ }
+
var grouppedAnnotations = {};
for (var i = 0; i < annotations.length; i++) {
- var desc = annotations[i].getDescription();
- if (desc == "") desc = "Annotated by curator"
- if (!(desc in grouppedAnnotations)) grouppedAnnotations[desc] = [];
- grouppedAnnotations[desc].push(annotations[i])
+ var clazz = annotations[i].getAnnotatorClassName();
+ if (!(clazz in grouppedAnnotations)) grouppedAnnotations[clazz] = [];
+ grouppedAnnotations[clazz].push(annotations[i])
}
+ // = annotatorClasName ? annotatorsClassMapping[annotatorClasName].getName() : "Annotated by curator";
+
var cntAnnotations = 0;
- // for (var i = 0; i < grouppedAnnotations.keys().length; i++) {
- Object.keys(grouppedAnnotations).sort().forEach(function(desc){
+
+ Object.keys(grouppedAnnotations).sort().forEach(function(annotatorClass){
// var desc = grouppedAnnotations.keys()[i];
var groupContainer = (inline ? document.createElement("span") : document.createElement("div"));
var descContainer = (inline ? document.createElement("span") : document.createElement("div"));
- descContainer.innerHTML = (inline ? desc + ': ' : desc);
+ var annotatorName = annotatorClass ? annotatorsClassMapping[annotatorClass].getName() : "Annotated by curator";
+
+ if (inline) {
+ descContainer.innerHTML = annotatorName + ': ';
+ } else {
+ descContainer.innerHTML = annotatorName;
+
+ if (annotatorClass) {
+ var annotatorDescription = annotatorsClassMapping[annotatorClass].getDescription();
+ if (annotatorDescription) {
+ var tooltipContainer = Functions.createElement({
+ type: "span"
+ });
+ tooltipContainer.appendChild(Functions.createElement({
+ type: "span",
+ className: "glyphicon glyphicon-question-sign tooltip-icon"
+ }));
+ tooltipContainer.appendChild(Functions.createElement({
+ type: "span",
+ className: "annotator-tooltip",
+ content: annotatorsClassMapping[annotatorClass].getDescription()
+ }));
+
+ descContainer.appendChild(tooltipContainer);
+ }
+ }
+ }
descContainer.className = "minerva-annotation-group-header";
if (!inline) groupContainer.className = "minerva-annotation-group";
groupContainer.appendChild(descContainer);
@@ -209,7 +242,7 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
groupContainer.appendChild(par);
}
- grouppedAnnotations[desc] = grouppedAnnotations[desc].sort(function(a, b) {
+ grouppedAnnotations[annotatorClass] = grouppedAnnotations[annotatorClass].sort(function(a, b) {
const aType = a.getType().toUpperCase();
const bType = b.getType().toUpperCase();
if (aType < bType) return -1;
@@ -217,11 +250,11 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
else return 0;
});
- for (var j = 0; j < grouppedAnnotations[desc].length; j++) {
+ for (var j = 0; j < grouppedAnnotations[annotatorClass].length; j++) {
cntAnnotations += 1;
- var element = grouppedAnnotations[desc][j];
+ var element = grouppedAnnotations[annotatorClass][j];
var link = self.createAnnotationLink(element, showType);
if (inline) {
if (j > 0) {
@@ -262,39 +295,7 @@ GuiUtils.prototype.createAnnotationList = function (annotations, options) {
result.appendChild(groupContainer);
});
-
- // for (var i = 0; i < annotations.length; i++) {
- // var element = annotations[i];
- // var link = self.createAnnotationLink(element, showType);
- // if (inline) {
- // if (i > 0) {
- // var coma = document.createElement("span");
- // coma.innerHTML = ", ";
- // result.appendChild(coma);
- // }
- // result.appendChild(link);
- // } else {
- //
- // var row = document.createElement("div");
- // row.style.height = "26px";
- // if (i % 2 === 0) {
- // row.className = "minerva-annotation-row-odd";
- // } else {
- // row.className = "minerva-annotation-row-even";
- // }
- // var header = document.createElement("div");
- // header.style.width = "24px";
- // header.style.float = "left";
- // header.innerHTML = "[" + (i + 1) + "]";
- // row.appendChild(header);
- //
- // var body = document.createElement("div");
- // body.style.float = "left";
- // body.appendChild(link);
- // row.appendChild(body);
- // result.appendChild(row);
- // }
- // }
+
return result;
};
diff --git a/frontend-js/src/main/js/map/data/Annotation.js b/frontend-js/src/main/js/map/data/Annotation.js
index 1496051649..489e4a3dc7 100644
--- a/frontend-js/src/main/js/map/data/Annotation.js
+++ b/frontend-js/src/main/js/map/data/Annotation.js
@@ -15,7 +15,9 @@ function Annotation(javaObject) {
}
this.setType(javaObject.getType());
this.setResource(javaObject.getResource());
- this.setDescription(javaObject.getDescription());
+ this.setAnnotatorClassName(javaObject.getAnnotatorClassName());
+ this.setDescriptionByType(javaObject.getDescriptionByType());
+ this.setDescriptionByTypeRelation(javaObject.getDescriptionByTypeRelation());
} else {
this.setLink(javaObject.link);
this.setId(javaObject.id);
@@ -24,7 +26,7 @@ function Annotation(javaObject) {
}
this.setType(javaObject.type);
this.setResource(javaObject.resource);
- this.setDescription(javaObject.description);
+ this.setAnnotatorClassName(javaObject.annotatorClassName);
}
}
@@ -74,12 +76,28 @@ Annotation.prototype.getArticle = function() {
return this._article;
};
-Annotation.prototype.setDescription = function(description) {
- this._description = description;
+Annotation.prototype.setAnnotatorClassName = function(annotatorClassName) {
+ this._annotatorClassName = annotatorClassName;
};
-Annotation.prototype.getDescription = function() {
- return this._description;
+Annotation.prototype.getAnnotatorClassName = function() {
+ return this._annotatorClassName;
+};
+
+Annotation.prototype.setDescriptionByType = function(descriptionByType) {
+ this._descriptionByType = descriptionByType;
+};
+
+Annotation.prototype.getDescriptionByType = function() {
+ return this.descriptionByType;
+};
+
+Annotation.prototype.setDescriptionByTypeRelation = function(descriptionByTypeRelation) {
+ this._descriptionByTypeRelation = descriptionByTypeRelation;
+};
+
+Annotation.prototype.getDescriptionByTypeRelation = function() {
+ return this.descriptionByTypeRelation;
};
module.exports = Annotation;
diff --git a/frontend-js/src/main/js/map/data/Annotator.js b/frontend-js/src/main/js/map/data/Annotator.js
index 74d342558a..4ab6dc69be 100644
--- a/frontend-js/src/main/js/map/data/Annotator.js
+++ b/frontend-js/src/main/js/map/data/Annotator.js
@@ -12,12 +12,14 @@ function Annotator(javaObject, configuration) {
self.setClassName(javaObject.getClassName());
this._elementTypes = javaObject.getElementTypes();
self.setName(javaObject.getName());
+ self.setDescription(javaObject.getDescription());
self.setParametersDefinitions(javaObject.getParametersDefinitions());
self.setUrl(javaObject.getUrl());
} else {
self.setClassName(javaObject.className);
self.setElementTypes(javaObject.elementClassNames, configuration);
self.setName(javaObject.name);
+ self.setDescription(javaObject.description);
self.setParametersDefinitions(javaObject.parametersDefinitions);
self.setUrl(javaObject.url);
}
@@ -39,6 +41,14 @@ Annotator.prototype.getName = function () {
return this._name;
};
+Annotator.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+Annotator.prototype.getDescription = function () {
+ return this._description;
+};
+
Annotator.prototype.setUrl = function (url) {
this._url = url;
};
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
index 6a53cd7b72..a42e0686b8 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/BaseRestImpl.java
@@ -110,17 +110,26 @@ public abstract class BaseRestImpl {
if (annotation.getAnnotator() != null) {
try {
- result.put("description",
- ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance()).getDescription(
- annotation.getDataType(),
- annotation.getRelationType())
- );
- }catch(Exception e) { //TODO
+ result.put("annotatorClassName", annotation.getAnnotator().getName());
+ result.put("descriptionByType",
+ ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance()).getDescription( annotation.getDataType())
+ );
+ result.put("descriptionByTypeRelation",
+ ((ElementAnnotator) annotation.getAnnotator().getConstructor().newInstance()).getDescription(
+ annotation.getDataType(),
+ annotation.getRelationType())
+ );
+
+ }catch(Exception e) {
logger.error("Problem with retrieving description from annotator", e);
- result.put("description", "");
+ result.put("annotatorClassName", "");
+ result.put("descriptionByType", "");
+ result.put("descriptionByTypeRelation", "");
}
} else {
- result.put("description", "");
+ result.put("annotatorClassName", "");
+ result.put("descriptionByType", "");
+ result.put("descriptionByTypeRelation", "");
}
return result;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
index 29a85d63d3..c6519c98fb 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/configuration/ConfigurationRestImpl.java
@@ -247,6 +247,7 @@ public class ConfigurationRestImpl {
Map<String, Object> result = new HashMap<>();
result.put("className", annotator.getClass().getName());
result.put("name", annotator.getCommonName());
+ result.put("description", annotator.getDescription());
result.put("url", annotator.getUrl());
result.put("elementClassNames", annotator.getValidClasses());
result.put("parametersDefinitions", annotator.getParametersDefinitions());
--
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