From ddc14574feedbf9389c670e721c33ee0f849c41c Mon Sep 17 00:00:00 2001
From: David Hoksza <david.hoksza@uni.lu>
Date: Wed, 17 Jan 2018 16:18:29 +0100
Subject: [PATCH] Added associated annotator class to miriam data including
hibernate mapping + createMiriamData in element annotator. without unit tests
---
.../services/annotators/ElementAnnotator.java | 30 +++++++++
.../services/annotators/TairAnnotator.java | 4 +-
.../annotators/ElementAnnotatorTest.java | 33 ++++++++++
.../lcsb/mapviewer/model/map/MiriamData.java | 61 ++++++++++++++++++-
.../lcsb/mapviewer/model/map/MiriamType.java | 2 +-
persist/src/db/12.0.0/fix_db_20180117.sql | 2 +
6 files changed, 126 insertions(+), 6 deletions(-)
create mode 100644 persist/src/db/12.0.0/fix_db_20180117.sql
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 84761857a5..e71c85ce6a 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
@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerChemical;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
@@ -473,5 +474,34 @@ public abstract class ElementAnnotator extends CachableInterface {
logger.warn(prefix + "MCS in db different: \"" + element.getMechanicalConfidenceScore() + "\", \"" + value + "\"");
}
}
+
+ private void setAnnotator(MiriamData md){
+ md.setAnnotator(this.getClass());
+ }
+
+ protected MiriamData createMiriamData(){
+ MiriamData md = new MiriamData();
+ setAnnotator(md);
+ return md;
+ }
+
+ protected MiriamData createMiriamData(MiriamData _md){
+ MiriamData md = new MiriamData(_md);
+ setAnnotator(md);
+ return md;
+ }
+
+ protected MiriamData createMiriamData(MiriamType mt, String resource){
+ MiriamData md = new MiriamData(mt, resource);
+ setAnnotator(md);
+ return md;
+ }
+
+ 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/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index 0388293b12..9dcac43bcd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -58,7 +58,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- MiriamData md = tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+ MiriamData md = tairToUniprot(createMiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
status.setStatus(ExternalServiceStatusType.OK);
if (md == null || !md.getResource().equalsIgnoreCase("Q9MAN1")) {
@@ -122,7 +122,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
Collection<MiriamData> result = new HashSet<MiriamData>();
Matcher m = tairToUniprot.matcher(pageContent);
if (m.find()) {
- result.add(new MiriamData(MiriamType.UNIPROT, m.group(1)));
+ result.add(createMiriamData(MiriamType.UNIPROT, m.group(1)));
}
return result;
}
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 1dac8112d6..f4c613ca90 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
@@ -2,6 +2,7 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.assertNull;
import org.junit.After;
import org.junit.AfterClass;
@@ -12,6 +13,9 @@ import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Ion;
@@ -193,5 +197,34 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, getWarnings().size());
}
+
+ @Test
+ public void createMiriamData1() {
+ MiriamData md = annotator.createMiriamData();
+ assertEquals(md.getAnnotator(), annotator.getClass());
+ }
+
+ @Test
+ public void createMiriamData2() {
+ MiriamData md = annotator.createMiriamData(MiriamType.UNIPROT, "XXX");
+ assertEquals(md.getAnnotator(), annotator.getClass());
+ }
+
+ @Test
+ public void createMiriamData3() {
+ MiriamData md = annotator.createMiriamData(MiriamRelationType.BQ_BIOL_ENCODES, MiriamType.UNIPROT, "XXX");
+ assertEquals(md.getAnnotator(), annotator.getClass());
+ }
+
+ @Test
+ public void createMiriamData4() {
+ MiriamData md1 = new MiriamData(MiriamType.UNIPROT, "XXX");
+ assertNull(md1.getAnnotator());
+
+ MiriamData md2 = annotator.createMiriamData(md1);
+ assertEquals(md2.getAnnotator(), annotator.getClass());
+ }
+
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
index f6f3ba7142..12f8c4b232 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamData.java
@@ -64,6 +64,13 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
*/
@Column(name = "resource")
private String resource = "";
+
+ /**
+ * The annotator which created the miriam data or which
+ * should be associated with it.
+ */
+ @Column(name = "annotator")
+ private Class<?> annotator = null;
/**
* Default constructor.
@@ -82,8 +89,9 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
setRelationType(md.relationType);
setDataType(md.dataType);
setResource(md.resource);
+ setAnnotator(md.annotator);
}
-
+
/**
* Constructor that initialize the data by information from params.
*
@@ -93,8 +101,11 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
* type of the miriam data (see: {@link MiriamType})
* @param resource
* {@link #resource}
+ * @param annotator
+ * {@link #annotator}
+ *
*/
- public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
+ public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource, Class<?> annotator) {
if (mt == null) {
throw new InvalidArgumentException("MiriamType cannot be null");
}
@@ -104,8 +115,36 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
setRelationType(relationType);
setDataType(mt);
setResource(resource);
+ setAnnotator(annotator);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param relationType
+ * {@link #relationType}
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
+ this(relationType, mt, resource, null);
+ }
+
+ /**
+ * Constructor that initialize the data by information from params.
+ *
+ * @param mt
+ * type of the miriam data (see: {@link MiriamType})
+ * @param resource
+ * {@link #resource}
+ */
+ public MiriamData(MiriamType mt, String resource, Class<?> annotator) {
+ this(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, resource, annotator);
}
+
/**
* Constructor that initialize the data by information from params.
*
@@ -115,7 +154,7 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
* {@link #resource}
*/
public MiriamData(MiriamType mt, String resource) {
- this(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, mt, resource);
+ this(mt, resource, null);
}
/**
@@ -250,4 +289,20 @@ public class MiriamData implements Comparable<MiriamData>, Serializable {
}
}
+
+ /**
+ *
+ * @return {@link #annotator}
+ */
+ public Class<?> getAnnotator() {
+ return annotator;
+ }
+
+ /**
+ *
+ * @param {@link #annotator}
+ */
+ public void setAnnotator(Class<?> annotator) {
+ this.annotator = annotator;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 155ec768e4..338903c600 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -494,6 +494,7 @@ public enum MiriamType {
* then annotation of this type is valid.
*/
private List<Class<? extends BioEntity>> requiredClass = new ArrayList<>();
+
/**
* Constructor that initialize enum object.
@@ -700,5 +701,4 @@ public enum MiriamType {
}
throw new InvalidArgumentException("Invalid miriam uri: " + miriamUri);
}
-
}
diff --git a/persist/src/db/12.0.0/fix_db_20180117.sql b/persist/src/db/12.0.0/fix_db_20180117.sql
new file mode 100644
index 0000000000..af37bf7888
--- /dev/null
+++ b/persist/src/db/12.0.0/fix_db_20180117.sql
@@ -0,0 +1,2 @@
+-- column to store which annotator is responsible for given miriam data
+alter table miriam_data_table add column annotator varchar(256) default null;
--
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