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 088c6eee2d084f3626756bd91ec2998ae912f0f3..529119fac3badd2aef3e36048596aa9352d62a3e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -14,7 +14,9 @@ import javax.annotation.PostConstruct;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+import lcsb.mapviewer.annotation.services.annotators.AnnotationParameters;
import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
import lcsb.mapviewer.annotation.services.annotators.BiocompendiumAnnotator;
import lcsb.mapviewer.annotation.services.annotators.BrendaAnnotator;
@@ -44,7 +46,6 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.UserAnnotatorsParam;
import lcsb.mapviewer.modelutils.map.ClassTreeNode;
import lcsb.mapviewer.modelutils.map.ElementUtils;
-import org.springframework.stereotype.Service;
/**
* This class annotates all elements in the model.
@@ -169,21 +170,21 @@ public class ModelAnnotator {
*/
@Autowired
public ModelAnnotator(MiriamConnector miriamConnector,
- BrendaAnnotator brendaAnnotator,
- BiocompendiumAnnotator biocompendiumAnnotator,
- CazyAnnotator cazyAnnotator,
- ChebiAnnotator chebiBackend,
- UniprotAnnotator uniprotAnnotator,
- PdbAnnotator pdbAnnotator,
- ReconAnnotator reconAnnotator,
- GoAnnotator goAnnotator,
- HgncAnnotator hgncAnnotator,
- KeggAnnotator keggAnnotator,
- EntrezAnnotator entrezAnnotator,
- EnsemblAnnotator ensemblAnnotator,
- StitchAnnotator stitchAnnotator,
- StringAnnotator stringAnnotator,
- TairAnnotator tairAnnotator) {
+ BrendaAnnotator brendaAnnotator,
+ BiocompendiumAnnotator biocompendiumAnnotator,
+ CazyAnnotator cazyAnnotator,
+ ChebiAnnotator chebiBackend,
+ UniprotAnnotator uniprotAnnotator,
+ PdbAnnotator pdbAnnotator,
+ ReconAnnotator reconAnnotator,
+ GoAnnotator goAnnotator,
+ HgncAnnotator hgncAnnotator,
+ KeggAnnotator keggAnnotator,
+ EntrezAnnotator entrezAnnotator,
+ EnsemblAnnotator ensemblAnnotator,
+ StitchAnnotator stitchAnnotator,
+ StringAnnotator stringAnnotator,
+ TairAnnotator tairAnnotator) {
this.miriamConnector = miriamConnector;
this.brendaAnnotator = brendaAnnotator;
this.biocompendiumAnnotator = biocompendiumAnnotator;
@@ -249,7 +250,7 @@ public class ModelAnnotator {
* @param progressUpdater
* callback function used for updating progress of the function
*/
- public void performAnnotations(Model model, final IProgressUpdater progressUpdater) {
+ public void performAnnotations(Model model, final IProgressUpdater progressUpdater) {
performAnnotations(model, progressUpdater, null, null);
}
@@ -265,7 +266,7 @@ public class ModelAnnotator {
* callback function used for updating progress of the function
*/
public void performAnnotations(Model model, final IProgressUpdater progressUpdater,
- Map<Class<?>, List<ElementAnnotator>> annotators, Map<Class<?>, List<UserAnnotatorsParam>> annotatorsParams) {
+ Map<Class<?>, List<ElementAnnotator>> annotators, Map<Class<?>, List<UserAnnotatorsParam>> annotatorsParams) {
progressUpdater.setProgress(0);
List<Model> models = new ArrayList<Model>();
models.add(model);
@@ -362,8 +363,8 @@ public class ModelAnnotator {
* callback function used to refresh progress of function execution
*/
protected void annotateModel(Model model, IProgressUpdater progressUpdater,
- Map<Class<?>, List<ElementAnnotator>> annotators, Map<Class<?>, List<UserAnnotatorsParam>> annotatorsParams) {
-
+ Map<Class<?>, List<ElementAnnotator>> annotators, Map<Class<?>, List<UserAnnotatorsParam>> annotatorsParams) {
+
ElementUtils elementUtils = new ElementUtils();
progressUpdater.setProgress(0);
@@ -380,19 +381,14 @@ public class ModelAnnotator {
if (list == null) {
list = getDefaultAnnotators();
}
-
- for (ElementAnnotator elementAnnotator : list) {
+
+ for (ElementAnnotator elementAnnotator : list) {
try {
+ AnnotationParameters parameters = new AnnotationParameters();
if (annotatorsParams != null) {
- List<UserAnnotatorsParam> params = annotatorsParams.get(elementAnnotator.getClass());
- if (params != null) {
- elementAnnotator.annotateElement(element, params);
- } else {
- elementAnnotator.annotateElement(element);
- }
- } else {
- elementAnnotator.annotateElement(element);
+ parameters.addAnnotatorParameters(annotatorsParams.get(elementAnnotator.getClass()));
}
+ elementAnnotator.annotateElement(element, parameters);
} catch (AnnotatorException e) {
logger.warn(elementUtils.getElementTag(element) + " " + elementAnnotator.getCommonName()
+ " annotation problem: " + e.getMessage());
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotationParameters.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotationParameters.java
new file mode 100644
index 0000000000000000000000000000000000000000..cc25744fe65a17b061c2747b68d2ef18735cc6b3
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotationParameters.java
@@ -0,0 +1,42 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
+import lcsb.mapviewer.model.user.UserAnnotatorsParam;
+
+public class AnnotationParameters {
+ private List<AnnotatorParameter> annotatorParameters = new ArrayList<>();
+
+ public AnnotationParameters addAnnotatorParameter(AnnotatorParamDefinition type, String value) {
+ annotatorParameters.add(new AnnotatorParameter(type, value));
+ return this;
+ }
+
+ public AnnotationParameters addAnnotatorParameter(AnnotatorParameter parameter) {
+ annotatorParameters.add(parameter);
+ return this;
+ }
+
+ public AnnotationParameters addAnnotatorParameters(List<?> parameters) {
+ for (Object object : parameters) {
+ if (object instanceof AnnotatorParameter) {
+ addAnnotatorParameter((AnnotatorParameter)object);
+ } else if (object instanceof UserAnnotatorsParam) {
+ addAnnotatorParameter(((UserAnnotatorsParam) object).getParameterType(),
+ ((UserAnnotatorsParam) object).getParamValue());
+ }
+ }
+ return this;
+ }
+
+ public String getValue(AnnotatorParamDefinition type) {
+ for (AnnotatorParameter annotatorParameter : annotatorParameters) {
+ if (annotatorParameter.getType().equals(type)) {
+ return annotatorParameter.getValue();
+ }
+ }
+ return null;
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorInput.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorInput.java
new file mode 100644
index 0000000000000000000000000000000000000000..4a25dd98a4166ff9f6a577cf11c8d4c530e21c6b
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorInput.java
@@ -0,0 +1,33 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import lcsb.mapviewer.model.map.MiriamType;
+
+/**
+ * Definition of annotator input. It describes which property/identifier should
+ * be used to identify element in the external database.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class AnnotatorInput{
+ private BioEntityField field;
+
+ private MiriamType identifierType;
+
+ public AnnotatorInput(BioEntityField field) {
+ this(field, null);
+ }
+
+ public AnnotatorInput(BioEntityField field, MiriamType identifierType) {
+ this.field = field;
+ this.identifierType = identifierType;
+ }
+
+ public BioEntityField getField() {
+ return field;
+ }
+
+ public MiriamType getIdentifierType() {
+ return identifierType;
+ }
+}
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
deleted file mode 100644
index 9559952e60378f012e6be87c251c6d5435ccb813..0000000000000000000000000000000000000000
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefinition.java
+++ /dev/null
@@ -1,35 +0,0 @@
-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 description;
-
- private Class<?> type;
-
- public AnnotatorParamDefinition(String name, Class<?> type, String description) {
- super();
- this.name = name;
- this.description = description;
- this.type = type;
- }
-
- public String getName() {
- return name;
- }
-
- public String getDescription() {
- return description;
- }
-
- public Class<?> getType() {
- return type;
- }
-
-}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParameter.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParameter.java
new file mode 100644
index 0000000000000000000000000000000000000000..258ca66252174fd4502f98cba60294abf25c6543
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParameter.java
@@ -0,0 +1,23 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
+
+public class AnnotatorParameter {
+
+ private String value;
+
+ private AnnotatorParamDefinition type;
+
+ public AnnotatorParameter(AnnotatorParamDefinition type, String value) {
+ this.type = type;
+ this.value = value;
+ }
+
+ public String getValue() {
+ return value;
+ }
+
+ public AnnotatorParamDefinition getType() {
+ return type;
+ }
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BioEntityField.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BioEntityField.java
new file mode 100644
index 0000000000000000000000000000000000000000..e2a7fa9ceee48d37578688e7b2753c0f2b86b6c9
--- /dev/null
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BioEntityField.java
@@ -0,0 +1,13 @@
+package lcsb.mapviewer.annotation.services.annotators;
+
+import lcsb.mapviewer.model.map.BioEntity;
+
+/**
+ * This enum identifies field of the {@link BioEntity}.
+ * @author Piotr Gawron
+ *
+ */
+public enum BioEntityField {
+ NAME,
+
+}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index 2e2478f7f2f8642123d095372c9fc38e1d0b8533..85dd092ed07b6a017f495c1a7d971864fcbdf68b 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -301,7 +301,7 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
}
@Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
+ public void annotateElement(BioEntity element, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(element)) {
try {
String annotationString = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, element.getName()));
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
index 403923f80bee148bbb92e976de5fa64b163dedfe..3dcac98d6ad61b3f0bb1f19c1f8ab3bdc2a66bc6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotator.java
@@ -81,7 +81,7 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
MiriamData mdTair = null;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index c9c4da932548b0cedb275b2cb579328b86b7b4dc..d88aa508c4e1bf2dc22b0b026815ba61ddc296d8 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
@@ -81,7 +81,7 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
MiriamData mdTair = null;
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 1d7aa61420d0d8791f479a26d77f2fb9d5cfbb26..72c89e1f29beb5e25bbbc6f2d1671356639fa6f8 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
@@ -439,7 +439,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
+ public void annotateElement(BioEntity element, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(element)) {
try {
String warnPrefix = elementUtils.getElementTag(element, this);
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 a3764c3c9ef6b96e57fa8924d5a379962e107209..f7fe0a423b151f5571674d0d93747774260f60ff 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
@@ -18,6 +18,7 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Chemical;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
import lcsb.mapviewer.model.user.UserAnnotatorsParam;
/**
@@ -84,7 +85,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @throws AnnotatorException
* thrown when there is a problem with annotating not related to data
*/
- public abstract void annotateElement(BioEntity element) throws AnnotatorException;
+ public final void annotateElement(BioEntity element) throws AnnotatorException {
+ annotateElement(element, new AnnotationParameters());
+ };
/**
* Annotate element using parameters.
@@ -97,9 +100,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @throws AnnotatorException
* thrown when there is a problem with annotating not related to data
*/
- public void annotateElement(BioEntity element, List<UserAnnotatorsParam> parameters) throws AnnotatorException {
- annotateElement(element);
- }
+ public abstract void annotateElement(BioEntity element, AnnotationParameters parameters) throws AnnotatorException;
/**
* Returns a list of all classes that can be annotated using this annotator.
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 fcd26ed5bf32ef26f7bb7c1c831ae7ff3d4f17c9..13199592294af41c76c39ecc90e0de57c124dc94 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
@@ -155,7 +155,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
+ public void annotateElement(BioEntity element, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(element)) {
ElementUtils eu = new ElementUtils();
String prefix = eu.getElementTag(element);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 5cbcfd99e74c8fc5bda5215008e14380019833fc..b80028ddbe85ae53f50f8d44988da9c9372cef26 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -156,7 +156,7 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
+ public void annotateElement(BioEntity element, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(element)) {
ElementUtils eu = new ElementUtils();
String prefix = eu.getElementTag(element);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
index 3991e7c9f44c0f337710ebaa018d0d9d1d4647d7..f09ba41b0a777c26198343e21c706bc4deb59149 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoAnnotator.java
@@ -97,7 +97,7 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
MiriamData goTerm = null;
for (MiriamData md : object.getMiriamData()) {
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 53ef651748eea2b3a1b901a723f8a49e07c9d4ec..627f94dc5d48f34bd905cbe1430a64ec21860164 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
@@ -119,7 +119,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
+ public void annotateElement(BioEntity element, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(element)) {
ElementUtils eu = new ElementUtils();
String prefix = eu.getElementTag(element);
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 0f92d1576d77d3018f8a96b588c3afdb7632a02d..a8929f06a07f55558e3a55e59edf8009b548b8bb 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
@@ -4,13 +4,12 @@ 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;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -28,8 +27,8 @@ 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.AnnotatorParamDefinition;
import lcsb.mapviewer.model.user.UserAnnotatorsParam;
-import org.springframework.stereotype.Service;
/**
* This is a class that implements KEGG annotator which extract from KEGG
@@ -73,13 +72,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
*/
public KeggAnnotator(TairAnnotator tairAnnotator, UniprotAnnotator uniprotAnnotator) {
super(KeggAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
- AnnotatorParamDefinition paramDef = new AnnotatorParamDefinition(
- "KEGG organism identifier",
- String.class,
- "Space-delimited list of organisms codes for which homologous genes"
- + " (GENE section in the KEGG enzyme record) should be imported."
- + " Currently only ATH (Arabidopsis Thaliana) is supported.");
- this.addParameterDefinition(paramDef);
+ this.addParameterDefinition(AnnotatorParamDefinition .KEGG_ORGANISM_IDENTIFIER);
this.tairAnnotator = tairAnnotator;
this.uniprotAnnotator = uniprotAnnotator;
}
@@ -123,7 +116,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
@Override
- public void annotateElement(BioEntity object, List<UserAnnotatorsParam> params) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters params) throws AnnotatorException {
if (!isAnnotatable(object)) { return; }
@@ -180,11 +173,6 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
object.addMiriamData(annotations);
}
- @Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
- this.annotateElement(object, null);
- }
-
/**
* Returns url to KEGG restful API about enzyme classification.
*
@@ -211,7 +199,7 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
* @return
* {@link MiriamType#PUBMED}s found on the page
*/
- private Collection<MiriamData> parseKegg(String pageContent, List<UserAnnotatorsParam> params) {
+ private Collection<MiriamData> parseKegg(String pageContent, AnnotationParameters params) {
//Retrieve Pubmeds
Collection<MiriamData> result = new HashSet<MiriamData>();
@@ -220,9 +208,10 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
result.add(createMiriamData(MiriamType.PUBMED, m.group(1)));
}
+ String organismParameter = params.getValue(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER);
//Retrieve homologous organisms based on parameterization
- if (params != null) {
- String[] keggOrgnismCodes = params.get(0).getParamValue().trim().split(" +");
+ if (organismParameter != null) {
+ String[] keggOrgnismCodes = organismParameter.trim().split(" +");
for (String code: keggOrgnismCodes) {
if (!code.equalsIgnoreCase("ATH")) {
logger.warn("KEGG annotator currently supports only ATH (" + code + " passed)" );
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index 0b9e8500275f6debfbbae765b6fd850ed6752b32..db62422078e18566bf888a42e5684578a2080bed 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -109,7 +109,7 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
}
@Override
- public void annotateElement(BioEntity bioEntity) throws AnnotatorException {
+ public void annotateElement(BioEntity bioEntity, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(bioEntity)) {
Set<MiriamData> mds = getUnitProts(bioEntity);
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index b41ee984effc76035b637aa4cb5a80f3b1deb11c..7db2b7b84b89fb9f31bc05aeb189ce28ca6bd5ae 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
@@ -114,7 +114,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
+ public void annotateElement(BioEntity annotatedObject, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(annotatedObject)) {
String id = annotatedObject.getAbbreviation();
if (id == null || id.isEmpty()) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
index a5eaa3ffe96afa1d09763348e529482ee072e90c..1f76633264037f7e6fbeaca70f04c55c6f557988 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
@@ -58,7 +58,7 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
MiriamData mdChebi = null;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
index 3893a948b9e24f06fc4cd51f8236359e373ad9f2..b331dc036870189d1e9fde6fce5b274e8383c3b7 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
@@ -46,7 +46,7 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
MiriamData mdTair = null;
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 66a49c98ed069145ee0d575e8beef7cdbcf193dd..89efd6e01ab1aa54701399c22dd5b8e1914d9062 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
@@ -75,7 +75,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
// boolean uniprotFound = false;
List<MiriamData> mdUniProts = new ArrayList<MiriamData>(); //keeps record of existing UniProt annotations which can differ from those retrieved using TAIR
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 7eede10e1ad917b5c3ed8b2380e283ada3989335..15144d49cacdf5248e0c59acbe4e0c644c632b4e 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -93,7 +93,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- public void annotateElement(BioEntity object) throws AnnotatorException {
+ public void annotateElement(BioEntity object, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(object)) {
String uniprotId = object.getName();
boolean uniprotFound = false;
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 b343f67f1db7df65a5a46d67d28dcc489d090d83..7467c92caa46534d503b52a55d8cffcd3fbebd8a 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/ModelAnnotatorTest.java
@@ -98,7 +98,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- public void testAnnotateModelWithGivenAnnotators() {
+ public void testAnnotateModelWithGivenAnnotators() throws Exception {
try {
Model model = new ModelFullIndexed(null);
GenericProtein species = new GenericProtein("id1");
@@ -117,8 +117,8 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
annotators.put(Reaction.class, annotatorList);
annotators.put(GenericProtein.class, new ArrayList<>());
- ReconAnnotator reconMock = Mockito.mock(ReconAnnotator.class);
- Mockito.doThrow(new AnnotatorException("")).when(reconMock).annotateElement(any());
+ ReconAnnotator reconMock = Mockito.mock(ReconAnnotator.class, Mockito.CALLS_REAL_METHODS);
+ Mockito.doThrow(AnnotatorException.class).when(reconMock).annotateElement(any(),any());
annotators.get(Reaction.class).add(reconMock);
modelAnnotator.annotateModel(model, updater, annotators);
@@ -127,7 +127,7 @@ public class ModelAnnotatorTest extends AnnotationTestFunctions {
} catch (Exception e) {
e.printStackTrace();
- fail("Unknown exception");
+ throw e;
}
}
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 ad8a63731459a40aedc769e86387edd3d43fc779..d30e43ae11d147a1020494813b00cdf72a0a520b 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
@@ -6,7 +6,7 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ AnnotatorExceptionTest.class,
- AnnotatorParamDefTest.class,
+ AnnotatorExceptionTest.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 3001461019e5c2d007f7ecc8568b0155e0527c93..68f6a0176587ab7f5e5bdd4b25ba536c77c9b7ad 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
@@ -23,10 +23,8 @@ public class AnnotatorExceptionTest {
@Test
public void testConstructor() {
- AnnotatorParamDefinition d = new AnnotatorParamDefinition("name", String.class, "description");
- assertEquals(d.getName(), "name");
- assertEquals(d.getDescription(), "description");
- assertEquals(d.getType(), String.class);
+ AnnotatorException e = new AnnotatorException("messss");
+ assertEquals("messss",e.getMessage());
}
}
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
deleted file mode 100644
index 90682ba6e3188646ab0fd3ec5a29f45775fbdac2..0000000000000000000000000000000000000000
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorParamDefTest.java
+++ /dev/null
@@ -1,30 +0,0 @@
-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/KeggAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
index 5856154b2ee33753469ac6405ab3becd57b11d8c..7d97f4585b9600991e89e860ab4380f428b18207 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
@@ -32,6 +32,7 @@ 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.AnnotatorParamDefinition;
import lcsb.mapviewer.model.user.UserAnnotatorsParam;
public class KeggAnnotatorTest extends AnnotationTestFunctions {
@@ -102,10 +103,9 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
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);
+ AnnotationParameters parameters = new AnnotationParameters()
+ .addAnnotatorParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "ATH");
+ keggAnnotator.annotateElement(protein, parameters);
int cntTairs = 0;
for (MiriamData md : protein.getMiriamData()) {
@@ -130,10 +130,9 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
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);
+ AnnotationParameters parameters = new AnnotationParameters()
+ .addAnnotatorParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "XXX");
+ keggAnnotator.annotateElement(protein, parameters);
assertEquals("There should be warning about unsupported parameter", 1, getWarnings().size());
@@ -150,9 +149,9 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
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 AAA"));
- keggAnnotator.annotateElement(protein, aps);
+ AnnotationParameters parameters = new AnnotationParameters()
+ .addAnnotatorParameter(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER, "ATH AAA");
+ keggAnnotator.annotateElement(protein, parameters);
int cntTairs = 0;
for (MiriamData md : protein.getMiriamData()) {
@@ -365,7 +364,8 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = keggAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
keggAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, keggAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
index c54e225ed7bbb125f4430ce8436b5b9a643359c4..ef6138383b8ff2e866f5e8cdfe6551343a8f3574 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/genome/UcscReferenceGenomeConnectorTest.java
@@ -128,7 +128,7 @@ public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
MiriamData human = new MiriamData(MiriamType.TAXONOMY, "9606");
MiriamData chicken = new MiriamData(MiriamType.TAXONOMY, "9031");
List<MiriamData> list = connector.getAvailableOrganisms();
- assertTrue(list.size() > 40);
+ assertTrue("At least 40 different organism were expected but found: " + list.size(), list.size() > 40);
assertTrue(list.contains(human));
assertTrue(list.contains(chicken));
@@ -148,7 +148,8 @@ public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
connector.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
connector.setWebPageDownloader(mockDownloader);
connector.getAvailableOrganisms();
fail("Exception expected");
@@ -765,7 +766,8 @@ public class UcscReferenceGenomeConnectorTest extends AnnotationTestFunctions {
// exclude first cached value
connector.setCache(null);
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
connector.setWebPageDownloader(mockDownloader);
connector.refreshCacheQuery("http://google.pl/");
fail("Exception expected");
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/AnnotatorParamDefinition.java b/model/src/main/java/lcsb/mapviewer/model/user/AnnotatorParamDefinition.java
new file mode 100644
index 0000000000000000000000000000000000000000..7377a7bfdda574209afa2a62e73a4361e43143c6
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/user/AnnotatorParamDefinition.java
@@ -0,0 +1,39 @@
+package lcsb.mapviewer.model.user;
+
+/**
+ * Definition of a single parameter of an annotator.
+ *
+ * @author David Hoksza
+ *
+ */
+public enum AnnotatorParamDefinition {
+ KEGG_ORGANISM_IDENTIFIER("KEGG organism identifier",
+ String.class,
+ "Space-delimited list of organisms codes for which homologous genes"
+ + " (GENE section in the KEGG enzyme record) should be imported."
+ + " Currently only ATH (Arabidopsis Thaliana) is supported.");
+ private String name;
+
+ private String description;
+
+ private Class<?> type;
+
+ AnnotatorParamDefinition(String name, Class<?> type, String description) {
+ this.name = name;
+ this.description = description;
+ this.type = type;
+ }
+
+ public String getName() {
+ return name;
+ }
+
+ public String getDescription() {
+ return description;
+ }
+
+ public Class<?> getType() {
+ return 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 603eeb8d58c0ce8d1f7e72a0c23bb3bc4ef71fc7..cc1f2905218c8b9a8206457cf2d22ea1a189fd5b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotationSchema.java
@@ -238,7 +238,7 @@ public class UserAnnotationSchema implements Serializable {
if (ap.getAnnotatorClassName() == null) {
throw new InvalidArgumentException("Class name cannot be null");
}
- if (ap.getParamName() == null) {
+ if (ap.getParameterType() == null) {
throw new InvalidArgumentException("Parameter name cannot be null");
}
if (ap.getParamValue() == null) {
@@ -248,7 +248,7 @@ public class UserAnnotationSchema implements Serializable {
for (int i = 0; i < this.annotatorsParams.size(); i++) {
UserAnnotatorsParam params = this.annotatorsParams.get(i);
if (params.getAnnotatorClassName().equals(ap.getAnnotatorClassName())
- && params.getParamName().equals(ap.getParamName())) {
+ && params.getParameterType().equals(ap.getParameterType())) {
this.annotatorsParams.get(i).setParamValue(ap.getParamValue());
return;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java
index 787ba75e919dfcc69df14b13f4bb4111c9153276..1cd9d1986c9c26e34299dcfa99e2906f99f9350c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java
+++ b/model/src/main/java/lcsb/mapviewer/model/user/UserAnnotatorsParam.java
@@ -4,6 +4,8 @@ import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
+import javax.persistence.EnumType;
+import javax.persistence.Enumerated;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
@@ -38,8 +40,8 @@ public class UserAnnotatorsParam implements Serializable {
private UserAnnotationSchema annotationSchema;
/**
- * Class name of the annotator {@link #paramName parameter} of which is being
- * set to the {@link #paramValue value}.
+ * Class name of the annotator {@link #parameterType parameter} of which is
+ * being set to the {@link #paramValue value}.
*/
@Column(nullable = false)
private Class<?> annotatorClassName;
@@ -48,7 +50,8 @@ public class UserAnnotatorsParam implements Serializable {
* Parameter name to be set.
*/
@Column(nullable = false)
- private String paramName;
+ @Enumerated(EnumType.STRING)
+ private AnnotatorParamDefinition parameterType;
/**
* Parameter value to be set.
@@ -71,9 +74,9 @@ public class UserAnnotatorsParam implements Serializable {
* @param annotators
* {@link #annotators}
*/
- public UserAnnotatorsParam(Class<?> annotatorClassName, String paramName, String paramValue) {
+ public UserAnnotatorsParam(Class<?> annotatorClassName, AnnotatorParamDefinition parameterType, String paramValue) {
setAnnotatorClassName(annotatorClassName);
- setParamName(paramName);
+ setParameterType(parameterType);
setParamValue(paramValue);
}
@@ -129,19 +132,19 @@ public class UserAnnotatorsParam implements Serializable {
}
/**
- * @return the parameter name
- * @see #paramName
+ * @return the parameter type
+ * @see #parameterType
*/
- public String getParamName() {
- return paramName;
+ public AnnotatorParamDefinition getParameterType() {
+ return parameterType;
}
/**
* @param paramName
- * the {@link UserAnnotatorsParam#paramName} to set
+ * the {@link UserAnnotatorsParam#parameterType} to set
*/
- public void setParamName(String paramName) {
- this.paramName = paramName;
+ public void setParameterType(AnnotatorParamDefinition paramName) {
+ this.parameterType = paramName;
}
/**
diff --git a/persist/src/main/resources/db/migration/12.3.0~alpha.0/V12.3.0.20190124__annotation_paramteres_refactor.sql b/persist/src/main/resources/db/migration/12.3.0~alpha.0/V12.3.0.20190124__annotation_paramteres_refactor.sql
new file mode 100644
index 0000000000000000000000000000000000000000..c54fc9a12d69291a8cc03a7630903a7b2f94436b
--- /dev/null
+++ b/persist/src/main/resources/db/migration/12.3.0~alpha.0/V12.3.0.20190124__annotation_paramteres_refactor.sql
@@ -0,0 +1,3 @@
+--create font color
+update user_annotators_param_table set param_name = 'KEGG_ORGANISM_IDENTIFIER' where param_name='KEGG organism identifier';
+alter table user_annotators_param_table rename column param_name to parameter_type;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
index e35c3001917c347644e50d998bd9c764d46ab07d..8d996cb52e7c272d1df7096b047c79d5feb14160 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/user/UserDaoTest.java
@@ -19,6 +19,7 @@ import org.springframework.security.crypto.password.PasswordEncoder;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
import lcsb.mapviewer.model.user.Privilege;
import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.model.user.User;
@@ -275,7 +276,7 @@ public class UserDaoTest extends PersistTestFunctions {
user.setAnnotationSchema(uas);
UserAnnotatorsParam param = new UserAnnotatorsParam();
param.setAnnotatorClassName(String.class);
- param.setParamName("nam");
+ param.setParameterType(AnnotatorParamDefinition.KEGG_ORGANISM_IDENTIFIER);
param.setParamValue("val");
uas.addAnnotatorParam(param);
userDao.add(user);
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
index d1c3f427d40e41ca5755eab3a7668fa1387d3478..32f89462a3a5d1e0d8c3352256dc73de1e355336 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/users/UserRestImpl.java
@@ -21,6 +21,7 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
import lcsb.mapviewer.model.user.ConfigurationOption;
import lcsb.mapviewer.model.user.ObjectPrivilege;
import lcsb.mapviewer.model.user.Privilege;
@@ -188,7 +189,7 @@ public class UserRestImpl extends BaseRestImpl {
annotatorParams = new TreeMap<>();
result.put(className, annotatorParams);
}
- annotatorParams.put(param.getParamName(), param.getParamValue());
+ annotatorParams.put(param.getParameterType().name(), param.getParamValue());
}
return result;
}
@@ -227,7 +228,7 @@ public class UserRestImpl extends BaseRestImpl {
for (String name : nameValueS.keySet()) {
String value = (String) nameValueS.get(name);
try {
- UserAnnotatorsParam param = new UserAnnotatorsParam(Class.forName(annotatorClassname), name, value);
+ UserAnnotatorsParam param = new UserAnnotatorsParam(Class.forName(annotatorClassname), AnnotatorParamDefinition.valueOf(name), value);
schema.addAnnotatorParam(param);
} catch (ClassNotFoundException e) {
throw new QueryException("Unknown annotator class name: " + annotatorClassname);