From 54a99a1712d6f743a7b49245ddf494ecd9827273 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Tue, 6 Feb 2018 19:28:30 +0100
Subject: [PATCH] Passing annotator parameters from client to server
---
.../annotation/services/ModelAnnotator.java | 4 +-
.../services/annotators/KeggAnnotator.java | 146 +++++++++++-------
.../annotators/BrendaAnnotatorTest.java | 8 -
.../annotators/KeggAnnotatorTest.java | 81 +++++++++-
.../js/gui/admin/ChooseAnnotatorsDialog.js | 6 +-
.../model/user/UserAnnotationSchema.java | 13 +-
.../services/impl/ProjectService.java | 11 +-
7 files changed, 186 insertions(+), 83 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 bc053783e1..8328716508 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -363,9 +363,7 @@ public class ModelAnnotator {
for (ElementAnnotator elementAnnotator : list) {
try {
- List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());
- logger.debug("params");
- logger.debug(params);
+ List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());
if (params != null) {
elementAnnotator.annotateElement(element, params);
} else {
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 51654c7b6b..cbf8cee52c 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
@@ -4,6 +4,7 @@ package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
import java.util.Collection;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -27,6 +28,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
/**
* This is a class that implements KEGG annotator which extract from KEGG
@@ -48,6 +50,11 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
*/
private Pattern pubmedMatcher = Pattern.compile("\\[PMID:(\\d+)\\]");
+ /**
+ * Pattern used for finding ATH orghologs in KEGG GENE sectionpage.
+ */
+ private Pattern athOrthologMatcher = Pattern.compile(" *ATH: (.*)");
+
/**
* Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS TAIR}.
@@ -73,14 +80,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
+ " (GENE section in the KEGG enzyme record) should be imported."
+ " Currently ATH (Arabidopsis Thaliana) is supported.");
this.addParameterDefinition(paramDef);
-
- this.addParameterDefinition(new AnnotatorParamDefinition("test string1", String.class, "test string1 comment"));
- this.addParameterDefinition(new AnnotatorParamDefinition("test int1", Integer.class, "int1 comment"));
- this.addParameterDefinition(new AnnotatorParamDefinition("test bool1", Boolean.class, "boolean comment"));
- this.addParameterDefinition(new AnnotatorParamDefinition("test bool2", Boolean.class, "boolean comment 2"));
- this.addParameterDefinition(new AnnotatorParamDefinition("test int2", Integer.class, "int2 comment"));
- this.addParameterDefinition(new AnnotatorParamDefinition("test int3", Integer.class, "int3 comment"));
- this.addParameterDefinition(new AnnotatorParamDefinition("test string2", String.class, "test string2 comment"));
}
@Override
@@ -122,61 +121,66 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
- if (isAnnotatable(object)) {
+ public void annotateElement(BioEntity object, List<UserAnnotatorsParam> params) throws AnnotatorException {
+
+ if (!isAnnotatable(object)) { return; }
- MiriamData mdTair = null;
- for (MiriamData md : object.getMiriamData()) {
- Class<?> annotator = md.getAnnotator();
- if (annotator == this.getClass()) {
- //this annotator was already used
- return;
- }
- else if (md.getDataType().equals(MiriamType.TAIR_LOCUS) &&
- (annotator == null ) ) {
- mdTair = md;
- }
+ MiriamData mdTair = null;
+ for (MiriamData md : object.getMiriamData()) {
+ Class<?> annotator = md.getAnnotator();
+ if (annotator == this.getClass()) {
+ //this annotator was already used
+ return;
}
-
- if (mdTair != null) tairAnnotator.annotateElement(object);
-
- MiriamData mdUniprot = null;
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.UNIPROT) ) {
- mdUniprot = md;
- }
+ else if (md.getDataType().equals(MiriamType.TAIR_LOCUS) &&
+ (annotator == null ) ) {
+ mdTair = md;
+ }
+ }
+
+ if (mdTair != null) tairAnnotator.annotateElement(object);
+
+ MiriamData mdUniprot = null;
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.UNIPROT) ) {
+ mdUniprot = md;
}
- if (mdUniprot != null) uniprotAnnotator.annotateElement(object);
-
- Set<String> ecs = new HashSet<String>();
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.EC)) {
- ecs.add(md.getResource());
- }
+ }
+ if (mdUniprot != null) uniprotAnnotator.annotateElement(object);
+
+ Set<String> ecs = new HashSet<String>();
+ for (MiriamData md : object.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.EC)) {
+ ecs.add(md.getResource());
}
+ }
+
+ if (ecs.size() == 0) {
+ return;
+ }
+
+ //annotate from KEGG
+ Set<MiriamData> annotations = new HashSet<MiriamData>();
+ for (String ec: ecs) {
- if (ecs.size() == 0) {
- return;
- }
-
- //annotate from KEGG
- Set<MiriamData> annotations = new HashSet<MiriamData>();
- for (String ec: ecs) {
-
- String accessUrl = getKeggUrl(ec);
-
- try {
- String pageContent = getWebPageContent(accessUrl);
- annotations.addAll(parseKegg(pageContent));
-
- } catch (WrongResponseCodeIOException exception) {
- logger.warn("Cannot find kegg data for id: " + ec);
- } catch (IOException exception) {
- throw new AnnotatorException(exception);
- }
+ String accessUrl = getKeggUrl(ec);
+
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ annotations.addAll(parseKegg(pageContent, params));
+
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Cannot find kegg data for id: " + ec);
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
}
- object.addMiriamData(annotations);
- }
+ }
+ object.addMiriamData(annotations);
+ }
+
+ @Override
+ public void annotateElement(BioEntity object) throws AnnotatorException {
+ this.annotateElement(object, null);
}
/**
@@ -196,9 +200,16 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
*
* @param pageContent
* Kegg page
- * @return {@link MiriamType#PUBMED}s found on the page
+ * @param params
+ * List of {@link UserAnnotatorsParam} to be used
+ * for parameterization. Should contain only at most
+ * one record with space separated KEGG organisms names.
+ * If the value has not been set by the user,
+ * null will be passed.
+ * @return
+ * {@link MiriamType#PUBMED}s found on the page
*/
- private Collection<MiriamData> parseKegg(String pageContent) {
+ private Collection<MiriamData> parseKegg(String pageContent, List<UserAnnotatorsParam> params) {
//Retrieve Pubmeds
Collection<MiriamData> result = new HashSet<MiriamData>();
@@ -208,6 +219,23 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
}
//Retrieve homologous organisms based on parameterization
+ 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");
+ } 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)
+ result.add(createMiriamData(MiriamType.TAIR_LOCUS, tairCode));
+ }
+ }
+ }
+ }
+ }
return result;
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
index a6db99a245..b26e1a87ca 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
@@ -2,23 +2,15 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import static org.mockito.Matchers.anyString;
-import static org.mockito.Mockito.when;
-
-import java.util.Collection;
-import java.io.IOException;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
-import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
-import lcsb.mapviewer.annotation.cache.WebPageDownloader;
import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.map.MiriamData;
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 a5a98a3a34..21e5e64b74 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
@@ -11,6 +11,7 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
+import java.util.List;
import java.util.Set;
import org.junit.After;
@@ -27,6 +28,7 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
public class KeggAnnotatorTest extends AnnotationTestFunctions {
@@ -71,7 +73,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
@Test
- public void testAnnotateFromUniprot() throws Exception {
+ public void testAnnotateFromUniprotWithoutParams() throws Exception {
try {
Species protein = new GenericProtein("id");
@@ -89,6 +91,82 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
}
}
+ @Test
+ public void testAnnotateFromUniprotWithParams() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q42561"));
+
+ UserAnnotatorsParam ap = new UserAnnotatorsParam(String.class, "KEGG organism identifier", "ATH");
+ List<UserAnnotatorsParam> aps = new ArrayList<>();
+ aps.add(ap);
+ keggAnnotator.annotateElement(protein, aps);
+
+ int cntTairs = 0;
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+ cntTairs++;
+ }
+ }
+
+ assertTrue("Invalid number of TAIR annotators from KEGG", cntTairs == 3);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateFromUniprotWithWrongParams1() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "Q42561"));
+
+ UserAnnotatorsParam ap = new UserAnnotatorsParam(String.class, "XXX", "XXX");
+ List<UserAnnotatorsParam> aps = new ArrayList<>();
+ aps.add(ap);
+ keggAnnotator.annotateElement(protein, aps);
+
+ assertEquals("There should be warning about unsupported parameter", 1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateFromUniprotWithWrongParams2() throws Exception {
+ try {
+
+ Species protein = new GenericProtein("id");
+ 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"));
+ keggAnnotator.annotateElement(protein, aps);
+
+ int cntTairs = 0;
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+ cntTairs++;
+ }
+ }
+
+ assertTrue("Invalid number of TAIR annotators from KEGG", cntTairs == 3);
+ assertEquals("There should be warning about unsupported parameter", 1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testAnnotateFromEc() throws Exception {
try {
@@ -101,7 +179,6 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
Evaluate_3_1_2_14(protein);
-
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index b5c8cd9563..30e9ae6405 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -65,7 +65,8 @@ function onChangeParameterValue(element, user){
var annotatorsParams = {};
annotatorsParams[annotatorClassName] = {};
- annotatorsParams[annotatorClassName][name] = element.value;
+ if (element.type == 'checkbox') annotatorsParams[annotatorClassName][name] = element.checked.toString();
+ else annotatorsParams[annotatorClassName][name] = element.value;
data.setAnnotatorsParameters(annotatorsParams);
return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
@@ -95,6 +96,7 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
+
for (var i = 0; i < annotators.length; i++) {
var annotator = annotators[i];
var selected = false;
@@ -157,12 +159,14 @@ ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
inputType: "number",
onchange: function(){return onChangeParameterValue(this, user);}
});
+ if (existingParamValue) paramValue.value = existingParamValue;
} else if (param.type.indexOf("Boolean") >= 0) {
paramValue = Functions.createElement({
type: "input",
inputType: "checkbox",
onchange: function(){return onChangeParameterValue(this, user);}
});
+ paramValue.checked = (existingParamValue && existingParamValue === 'true');
} else {
throw new InvalidAlgorithmError("Unknown annotator parameter type");
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
index 398f339169..40c1fec0c2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
@@ -248,17 +248,12 @@ public class UserAnnotationSchema implements Serializable {
if (params.getAnnotatorClassName().equals(ap.getAnnotatorClassName()) &&
params.getParamName().equals(ap.getParamName())) {
this.annotatorsParams.get(i).setParamValue(ap.getParamValue());
- } else {
- ap.setAnnotationSchema(this);
- this.annotatorsParams.add(ap);
+ return;
}
}
-
- if (this.annotatorsParams.size() == 0) {
- ap.setAnnotationSchema(this);
- this.annotatorsParams.add(ap);
- }
-
+
+ ap.setAnnotationSchema(this);
+ this.annotatorsParams.add(ap);
}
/**
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index c8409f670f..8d7ff171de 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -1469,7 +1469,16 @@ public class ProjectService implements IProjectService {
dbUser.setAnnotationSchema(annotationSchema);
}
- return annotationSchema.getAnnotatorsParams();
+ /*
+ * Hibernate lazy loads collections so each element needs to be accessed
+ * to be loaded now or otherwise the data might not be available
+ * when accessed because the session might not be available at that time.
+ */
+ List<UserAnnotatorsParam> aps = new ArrayList<>();
+ for (UserAnnotatorsParam ap: annotationSchema.getAnnotatorsParams()){
+ aps.add(ap);
+ }
+ return aps;
}
/**
--
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