From 2d1c00a6eea725a1f8e73461338f7ed5d0f1e14d Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Wed, 7 Feb 2018 14:12:36 +0100
Subject: [PATCH] Annotators params tooltip help.
Decription attribute renamed to description
---
.../annotation/services/ModelAnnotator.java | 3 ---
.../annotators/AnnotatorParamDefinition.java | 10 +++++-----
.../services/annotators/KeggAnnotator.java | 5 +++--
.../annotators/AnnotatorExceptionTest.java | 2 +-
.../annotators/KeggAnnotatorTest.java | 2 +-
frontend-js/src/main/css/global.css | 18 ++++++++++++++++++
.../js/gui/admin/ChooseAnnotatorsDialog.js | 19 +++++++++++++++----
7 files changed, 43 insertions(+), 16 deletions(-)
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 8328716508..8516fd4f6b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -348,9 +348,6 @@ public class ModelAnnotator {
double counter = 0;
double amount = model.getElements().size() + model.getReactions().size();
- logger.debug("annotatorsParams");
- logger.debug(annotatorsParams);
-
// annotate all elements
for (Element element : model.getElements()) {
List<ElementAnnotator> list = null;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java
index 3d13f4181e..9559952e60 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java
@@ -9,14 +9,14 @@ package lcsb.mapviewer.annotation.services.annotators;
public class AnnotatorParamDefinition {
private String name;
- private String decription;
+ private String description;
private Class<?> type;
- public AnnotatorParamDefinition(String name, Class<?> type, String decription) {
+ public AnnotatorParamDefinition(String name, Class<?> type, String description) {
super();
this.name = name;
- this.decription = decription;
+ this.description = description;
this.type = type;
}
@@ -24,8 +24,8 @@ public class AnnotatorParamDefinition {
return name;
}
- public String getDecription() {
- return decription;
+ public String getDescription() {
+ return description;
}
public Class<?> getType() {
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 cbf8cee52c..4f4238e70c 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
@@ -222,14 +222,15 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
if (params != null) {
String[] keggOrgnismCodes = params.get(0).getParamValue().trim().split(" +");
for (String code: keggOrgnismCodes) {
- if (code.toUpperCase() != "ATH") {
- logger.warn("KEGG annotator currently supports only ATH");
+ if (!code.equalsIgnoreCase("ATH")) {
+ logger.warn("KEGG annotator currently supports only ATH (" + code + " passed)" );
} else {
m = athOrthologMatcher.matcher(pageContent);
if (m.find()) {
String[] tairCodes = m.group(1).trim().split(" ");
for (String tairCode: tairCodes) {
tairCode = tairCode.split("\\(")[0]; //some codes are in the form AT1G08510(FATB)
+ logger.debug("Adding tair code " + tairCode);
result.add(createMiriamData(MiriamType.TAIR_LOCUS, tairCode));
}
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
index 05162124a4..629717e148 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
@@ -25,7 +25,7 @@ public class AnnotatorExceptionTest {
public void testConstructor() {
AnnotatorParamDefinition d = new AnnotatorParamDefinition("name", String.class, "description");
assertEquals(d.getName(), "name");
- assertEquals(d.getDecription(), "description");
+ assertEquals(d.getDescription(), "description");
assertEquals(d.getType(), String.class);
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
index 21e5e64b74..7228b8e6e4 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
@@ -148,7 +148,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
protein.setName("bla");
protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q42561"));
List<UserAnnotatorsParam> aps = new ArrayList<>();
- aps.add(new UserAnnotatorsParam(String.class, "KEGG organism identifier", "ATH XXX"));
+ aps.add(new UserAnnotatorsParam(String.class, "KEGG organism identifier", "ATH AAA"));
keggAnnotator.annotateElement(protein, aps);
int cntTairs = 0;
diff --git a/frontend-js/src/main/css/global.css b/frontend-js/src/main/css/global.css
index 04c3b36d73..3ad3f016a3 100644
--- a/frontend-js/src/main/css/global.css
+++ b/frontend-js/src/main/css/global.css
@@ -587,3 +587,21 @@ h1 {
font-weight: bold;
}
+.minerva-annotator-param-name .annotator-tooltip {
+ visibility: hidden;
+ width: 50%;
+ background-color: rgba(0, 0, 0, .5);
+ color: #fff;
+ text-align: left;
+ border-radius: 6px;
+ padding: 5px;
+
+ /* Position the tooltip */
+ position: absolute;
+ z-index: 1;
+}
+
+.minerva-annotator-param-name:hover .annotator-tooltip {
+ visibility: visible;
+}
+
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index 30e9ae6405..782de66346 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -106,6 +106,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var paramsDefs = annotator.getParametersDefinitions();
if (paramsDefs.length > 0) {
+ console.log('annotator', annotator);
annotatorsParams.appendChild(Functions.createElement({
type: "div",
@@ -132,11 +133,21 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
className: "minerva-annotator-param"
});
- paramElement.appendChild(Functions.createElement({
+ var paramName = Functions.createElement({
type: "div",
className: "minerva-annotator-param-name",
content: param.name
- }));
+ });
+
+ console.log('param', param);
+ var toolTip = Functions.createElement({
+ type: "span",
+ className: "annotator-tooltip",
+ content: param.description
+ });
+
+ paramName.appendChild(toolTip)
+ paramElement.appendChild(paramName);
var paramValue;
@@ -169,8 +180,8 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
paramValue.checked = (existingParamValue && existingParamValue === 'true');
} else {
throw new InvalidAlgorithmError("Unknown annotator parameter type");
- }
-
+ }
+
paramElement.appendChild(paramValue);
annotatorParams.appendChild(paramElement);
}
--
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