From a5578611f5ebd2ad4eeb20e59ae14e4b50a2fe84 Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Tue, 23 Jan 2018 14:42:35 +0100
Subject: [PATCH] Implemented paramaters for all annotators + createMiriamData
for all annotators
---
.../annotators/AnnotatorParamDefinition.java | 35 +++++++
.../services/annotators/ChebiAnnotator.java | 8 +-
.../services/annotators/ElementAnnotator.java | 97 ++++++++++++++++++-
.../services/annotators/EnsemblAnnotator.java | 4 +-
.../services/annotators/HgncAnnotator.java | 2 +-
.../annotators/AllAnnotatorTests.java | 1 +
.../annotators/AnnotatorExceptionTest.java | 6 +-
.../annotators/AnnotatorParamDefTest.java | 30 ++++++
.../annotators/ElementAnnotatorTest.java | 5 +-
.../annotators/StitchAnnotatorTest.java | 2 -
.../configuration/ConfigurationRestImpl.java | 1 +
11 files changed, 177 insertions(+), 14 deletions(-)
create mode 100644 annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java
create mode 100644 annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefTest.java
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
new file mode 100644
index 0000000000..c3c3bda40c
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java
@@ -0,0 +1,35 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+/**
+ * Definition of a single parameter of an annotator.
+ *
+ * @author David Hoksza
+ *
+ */
+public class AnnotatorParamDefinition {
+ private String name;
+
+ private String decription;
+
+ private Class<?> type;
+
+ public AnnotatorParamDefinition(String name, String decription, Class<?> type) {
+ super();
+ this.name = name;
+ this.decription = decription;
+ this.type = type;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public String getDecription() {
+ return decription;
+ }
+
+ public Class<?> getType() {
+ return type;
+ }
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
index 224ea171fb..b526374026 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java
@@ -178,14 +178,14 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
String synonym = dataItem.getData();
if (synonym.trim().equalsIgnoreCase(name)) {
setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ return createMiriamData(MiriamType.CHEBI, entity.getChebiId());
}
}
for (DataItem dataItem : entity.getSynonyms()) {
String synonym = dataItem.getData();
if (synonym.trim().equalsIgnoreCase(name)) {
setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ return createMiriamData(MiriamType.CHEBI, entity.getChebiId());
}
}
}
@@ -197,14 +197,14 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
String formula = dataItem.getData();
if (formula.trim().equalsIgnoreCase(name)) {
setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ return createMiriamData(MiriamType.CHEBI, entity.getChebiId());
}
}
for (DataItem dataItem : entity.getSynonyms()) {
String synonym = dataItem.getData();
if (synonym.trim().equalsIgnoreCase(name)) {
setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ return createMiriamData(MiriamType.CHEBI, entity.getChebiId());
}
}
}
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 98da3ebf29..26a8389a2f 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
@@ -44,6 +44,11 @@ public abstract class ElementAnnotator extends CachableInterface {
* Should be this annotator used as a default annotator.
*/
private boolean isDefault = false;
+
+ /**
+ * Parameters which this annotator can be provided. Should be set in constructor.
+ */
+ protected List<AnnotatorParamDefinition> paramsDefs = new ArrayList<>();
/**
* Default constructor.
@@ -78,6 +83,22 @@ public abstract class ElementAnnotator extends CachableInterface {
* data
*/
public abstract void annotateElement(BioEntity element) throws AnnotatorException;
+
+ /**
+ * Annotate element using parameters.
+ *
+ * @param element
+ * object to be annotated
+ * @param parameters
+ * list of parameters passed to the annotator which is expected to
+ * be in the same order as its {@link this#parameterDefs}
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating not related to
+ * data
+ */
+ public void annotateElement(BioEntity element, List<Object> parameters) throws AnnotatorException {
+ annotateElement(element);
+ }
/**
* Returns a list of all classes that can be annotated using this annotator.
@@ -130,6 +151,42 @@ public abstract class ElementAnnotator extends CachableInterface {
* @return url
*/
public abstract String getUrl();
+
+
+ /**
+ * Provides description for {@link ElementAnnotator} and {@link MiriamType} pair
+ * to be used in the frontend.
+ * @param mt
+ * {@link MiriamType} annotated by this annotator.
+ * @return
+ * the description
+ */
+ public String getDescription(MiriamType mt){
+ return "";
+ }
+
+ /**
+ * Provides description for {@link ElementAnnotator}, {@link MiriamType} and
+ * {@link MiriamRelationType} triplet to be used in the frontend.
+ * @param mt
+ * {@link MiriamType} annotated by this annotator
+ * @param relationType
+ * {@link MiriamRelationType} annotated by this annotator.
+ * @return
+ * the description
+ */
+ public String getDescription(MiriamType mt, MiriamRelationType relationType){
+ return "";
+ }
+
+ /**
+ * Returns list with definitions of the parameters available for this annotator.
+ * @return the parameters {@link AnnotatorParamDefinition} list
+ */
+
+ public Collection<AnnotatorParamDefinition> getParametersDefinitions(){
+ return paramsDefs;
+ }
/**
* Returns <code>true</code> if this annotator can annotate the object of
@@ -475,33 +532,69 @@ public abstract class ElementAnnotator extends CachableInterface {
}
}
+ /**
+ * Sets MiriamData.annotator to this annotator
+ *
+ * @param md
+ * data for which the annotator is to be set
+ */
private void setAnnotator(MiriamData md){
md.setAnnotator(this.getClass());
}
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ * @return
+ * created {@link MiriamData}
+ */
protected MiriamData createMiriamData(){
MiriamData md = new MiriamData();
setAnnotator(md);
return md;
}
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ * @param _md
+ * {@link MiriamData} based on which the new {@link MiriamData} should be created
+ * @return
+ * created {@link MiriamData}
+ */
protected MiriamData createMiriamData(MiriamData _md){
MiriamData md = new MiriamData(_md);
setAnnotator(md);
return md;
}
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ * @param mt
+ * {@link MiriamType} to be set
+ * @param resource
+ * resource to be set
+ * @return
+ * created {@link MiriamData}
+ */
protected MiriamData createMiriamData(MiriamType mt, String resource){
MiriamData md = new MiriamData(mt, resource);
setAnnotator(md);
return md;
}
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ * @param relationType
+ * {@link MiriamRelationType} to be set
+ * @param mt
+ * {@link MiriamType} to be set
+ * @param resource
+ * resource to be set
+ * @return
+ * created {@link MiriamData}
+ */
protected MiriamData createMiriamData(MiriamRelationType relationType, MiriamType mt, String resource){
MiriamData md = new MiriamData(relationType, mt, resource);
setAnnotator(md);
return md;
}
-
-
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index 2a680742e7..65d3eebe51 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -230,11 +230,11 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
String hgncId = super.getNodeAttr("primary_id", node);
if (hgncId != null && !hgncId.isEmpty()) {
hgncId = hgncId.replaceAll("HGNC:", "");
- annotatedObject.addMiriamData(new MiriamData(MiriamType.HGNC, hgncId));
+ annotatedObject.addMiriamData(createMiriamData(MiriamType.HGNC, hgncId));
}
String hgncSymbol = super.getNodeAttr("display_id", node);
if (hgncSymbol != null && !hgncSymbol.isEmpty()) {
- annotatedObject.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, hgncSymbol));
+ annotatedObject.addMiriamData(createMiriamData(MiriamType.HGNC_SYMBOL, hgncSymbol));
}
NodeList synonymNodeList = node.getChildNodes();
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index b1b4678ce8..a8b5d0184f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -232,7 +232,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
for (int j = 0; j < sublist.getLength(); j++) {
Node subnode = sublist.item(j);
if (subnode.getNodeType() == Node.ELEMENT_NODE) {
- element.addMiriamData(new MiriamData(MiriamType.UNIPROT, getNodeValue(subnode)));
+ element.addMiriamData(createMiriamData(MiriamType.UNIPROT, getNodeValue(subnode)));
}
}
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index 0bd9c6f3f8..8490ffda2b 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -6,6 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ AnnotatorExceptionTest.class, //
+ AnnotatorParamDefTest.class, //
BrendaAnnotatorTest.class, //
BiocompendiumAnnotatorTest.class, //
CazyAnnotatorTest.class, //
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 c8ecdc1029..a18773f47d 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
@@ -23,8 +23,10 @@ public class AnnotatorExceptionTest {
@Test
public void testConstructor() {
- AnnotatorException e = new AnnotatorException("messss");
- assertEquals("messss",e.getMessage());
+ AnnotatorParamDefinition d = new AnnotatorParamDefinition("name", "description", String.class);
+ assertEquals(d.getName(), "name");
+ assertEquals(d.getDecription(), "description");
+ assertEquals(d.getType(), String.class);
}
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefTest.java
new file mode 100644
index 0000000000..90682ba6e3
--- /dev/null
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefTest.java
@@ -0,0 +1,30 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import static org.junit.Assert.*;
+
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+
+public class AnnotatorParamDefTest {
+
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testConstructor() {
+ AnnotatorException e = new AnnotatorException("messss");
+ assertEquals("messss",e.getMessage());
+ }
+
+}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
index f4c613ca90..bf0e806a68 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ElementAnnotatorTest.java
@@ -225,6 +225,9 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
assertEquals(md2.getAnnotator(), annotator.getClass());
}
-
+ @Test
+ public void testEmptyParamsDefs() {
+ assertEquals(annotator.getParametersDefinitions().size(), 0);
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
index 2016f4875e..b3d3e31e77 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
@@ -87,8 +87,6 @@ public class StitchAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, bioEntity.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
} catch (Exception e) {
e.printStackTrace();
throw e;
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 581b00bb73..0ca63135b5 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 extends BaseRestImpl {
result.put("name", annotator.getCommonName());
result.put("url", annotator.getUrl());
result.put("elementClassNames", annotator.getValidClasses());
+ result.put("parametersDefinitions", annotator.getParametersDefinitions());
return result;
}
--
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