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
index 7a53dd85fe54ff7cd1dacb532df0e4f83930e692..63243ba22d1dee938f19fdee002bca00e981ec31 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BioEntityField.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BioEntityField.java
@@ -10,22 +10,28 @@ import lcsb.mapviewer.model.map.BioEntity;
*
*/
public enum BioEntityField {
- ABBREVIATION,
- CHARGE,
- DESCRIPTION,
- FORMULA,
- FULL_NAME,
- INCHI,
- INCHI_KEY,
- NAME,
- MCS,
- PREVIOUS_SYMBOLS,
- SMILE,
- SYMBOL,
- SYNONYMS,
- SUBSYSTEM,
+ ABBREVIATION("Abbreviation"),
+ CHARGE("Charge"),
+ DESCRIPTION("Description"),
+ FORMULA("Formula"),
+ FULL_NAME("Full name"),
+ INCHI("InChi"),
+ INCHI_KEY("InChi Key"),
+ NAME("Name"),
+ MCS("Mechanical Confidence Score"),
+ PREVIOUS_SYMBOLS("Previous Symbols"),
+ SMILE("Smile"),
+ SYMBOL("Symbol"),
+ SYNONYMS("Synonyms"),
+ SUBSYSTEM("Subsystem"),
;
+ private String fieldName;
+
+ private BioEntityField(String fieldName) {
+ this.fieldName = fieldName;
+ }
+
public static String getFieldValueForBioEntity(BioEntity bioEntity, BioEntityField field) {
if (field.equals(ABBREVIATION)) {
return bioEntity.getAbbreviation();
@@ -36,4 +42,8 @@ public enum BioEntityField {
}
}
+ public String getFieldName() {
+ return fieldName;
+ }
+
}
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 67574765d2c64d419d785dc10396501a2184e8db..cb9d2b8aadae9869507dbef9b04da52b36bdacda 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
@@ -32,14 +32,17 @@ import lcsb.mapviewer.annotation.services.ExternalServiceStatusType;
import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.converter.model.celldesigner.annotation.NoteField;
import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
-import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.Species;
/**
* This class is responsible for connection to Vencata annotation service. The
@@ -305,14 +308,12 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
}
@Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
try {
String annotationString = getAnnotation(identifier);
if (annotationString != null) {
- if (element.getMiriamData().size() == 0) {
- element.addMiriamData(rap.getMiriamData(annotationString));
- }
+ element.addMiriamData(rap.getMiriamData(annotationString));
String annotations = "";
@@ -329,8 +330,14 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
remove = false;
}
}
- annotations = element.getNotes() + "\n" + annotations;
- rap.processNotes(annotations, element);
+ element.setDescription(rap.getDescription(annotations));
+ element.setSymbol(rap.getSymbol(annotations));
+ element.setSynonyms(rap.getSynonyms(annotations));
+ element.setAbbreviation(rap.getAbbreviation(annotations));
+ element.setFormula(rap.getFormula(annotations));
+ element.setFullName(rap.getFullName(annotations));
+ element.setFormerSymbols(rap.getFormerSymbols(annotations));
+
return true;
}
return false;
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 b9542602549caa0ce04d682d3d80c92e05921294..8a490ccda6d2568f00f9798f0bfc56d2916a2169 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
@@ -80,16 +80,11 @@ public class BrendaAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
List<MiriamData> mdUniprots = new ArrayList<>();
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- tairAnnotator.annotateElement(object);
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.UNIPROT)) {
- mdUniprots.add(md);
- }
- }
+ mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
} else if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
mdUniprots.add(identifier);
} else {
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 eea95ec57f6de637358fd108a50de56c49b072ec..23e1fe48b7dd03b36b399ae585693224db7b281a 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
@@ -82,16 +82,11 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
List<MiriamData> mdUniprots = new ArrayList<>();
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- tairAnnotator.annotateElement(object);
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.UNIPROT)) {
- mdUniprots.add(md);
- }
- }
+ mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
} else if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
mdUniprots.add(identifier);
} else {
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 0d778281f3868cf5f4197c9a3cf56d775014e1fb..7e7373937b6f5bff96ea8cd2a67adb08a09b6819 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
@@ -440,7 +440,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity element, String name, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, String name, AnnotationParameters parameters)
throws AnnotatorException {
try {
MiriamData chebi = getChebiForChebiName(name);
@@ -448,7 +448,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
element.addMiriamData(chebi);
return annotateElement(element, chebi, parameters);
} else {
- String warnPrefix = elementUtils.getElementTag(element, this);
+ String warnPrefix = element.getElementTag();
logger.warn(warnPrefix + "Chemical name cannot be found in chebi: " + name);
return false;
}
@@ -458,18 +458,17 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
try {
- String warnPrefix = elementUtils.getElementTag(element, this);
+ String warnPrefix = element.getElementTag();
Chebi chebi = getChebiElementForChebiId(identifier);
- Chemical species = (Chemical) element;
if (chebi != null) {
- setFullName(species, chebi.getName(), warnPrefix, parameters);
+ setFullName(element, chebi.getName(), warnPrefix, parameters);
- setInchi(species, chebi.getInchi(), warnPrefix, parameters);
- setInchiKey(species, chebi.getInchiKey(), warnPrefix, parameters);
- setSmile(species, chebi.getSmiles(), warnPrefix, parameters);
+ setInchi(element, chebi.getInchi(), warnPrefix, parameters);
+ setInchiKey(element, chebi.getInchiKey(), warnPrefix, parameters);
+ setSmile(element, chebi.getSmiles(), warnPrefix, parameters);
setSynonyms(element, chebi.getSynonyms(), warnPrefix, parameters);
return true;
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 73a0675dc772089b29c8e53dd7d70e92080dd162..5792038dc2c72960a04c2d5e1cb469f0599219e0 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
@@ -22,7 +22,9 @@ 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.map.species.field.UniprotRecord;
import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* Interface that allows to annotate {@link BioEntity elements} in the system.
@@ -56,6 +58,271 @@ public abstract class ElementAnnotator extends CachableInterface {
*/
protected List<AnnotatorParamDefinition> paramsDefs = new ArrayList<>();
+ class BioEntityProxy {
+ private BioEntity originalBioEntity;
+ private AnnotationParameters parameters;
+
+ public BioEntityProxy(BioEntity bioEntity, AnnotationParameters parameters) {
+ originalBioEntity = bioEntity;
+ this.parameters = parameters;
+
+ }
+
+ public void addMiriamData(Collection<MiriamData> annotations) {
+ for (MiriamData miriamData : annotations) {
+ addMiriamData(miriamData);
+ }
+ }
+
+ public void addMiriamData(MiriamData miriamData) {
+ if (!contains(miriamData)) {
+ originalBioEntity.addMiriamData(miriamData);
+ }
+ }
+
+ public boolean contains(MiriamData identifier) {
+ MiriamData copy = new MiriamData(identifier);
+ copy.setAnnotator(null);
+ return originalBioEntity.getMiriamData().contains(copy) || originalBioEntity.getMiriamData().contains(identifier);
+ }
+
+ public String getElementTag() {
+ return new ElementUtils().getElementTag(originalBioEntity, ElementAnnotator.this);
+ }
+
+ public boolean isElement() {
+ return originalBioEntity instanceof Element;
+ }
+
+ public void addUniprot(UniprotRecord ur) {
+ if (originalBioEntity instanceof Species) {
+ Species species = ((Species) originalBioEntity);
+ species.getUniprots().add(ur);
+ ur.setSpecies(species);
+ } else {
+ logger.warn("Cannot add uniprot object to: " + originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public boolean isReaction() {
+ return originalBioEntity instanceof Reaction;
+ }
+
+ public void setSynonyms(Collection<String> synonyms) {
+ if (canAssignStringSet(synonyms, originalBioEntity.getSynonyms(), BioEntityField.SYNONYMS)) {
+ List<String> sortedSynonyms = new ArrayList<>(synonyms);
+ Collections.sort(sortedSynonyms);
+
+ originalBioEntity.setSynonyms(sortedSynonyms);
+ }
+ }
+
+ private boolean canAssignStringSet(Collection<String> newCollection, Collection<String> oldCollection,
+ BioEntityField field) {
+ if (!parameters.hasOutputField(field)) {
+ return false;
+ }
+ if (oldCollection == null || oldCollection.size() == 0) {
+ return true;
+ } else if (newCollection == null || newCollection.size() == 0) {
+ return false;
+ } else {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+ Set<String> set1 = new HashSet<>();
+ Set<String> set2 = new HashSet<>();
+
+ set1.addAll(newCollection);
+ set2.addAll(oldCollection);
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.warn(getElementTag() + field.getFieldName() + " don't match: \"" + set1 + "\", \"" + set2 + "\"");
+ return false;
+ }
+ return true;
+ }
+ }
+
+ /**
+ * Sets symbol value to the element.
+ *
+ * @param symbol
+ * new symbol
+ */
+ public void setSymbol(String symbol) {
+ if (canAssign(symbol, originalBioEntity.getSymbol(), BioEntityField.SYMBOL)) {
+ originalBioEntity.setSymbol(symbol);
+ }
+ }
+
+ public void setName(String nam) {
+ if (canAssign(nam, originalBioEntity.getName(), BioEntityField.NAME)) {
+ originalBioEntity.setName(nam);
+ }
+ }
+
+ private boolean canAssign(String newValue, String oldValue, BioEntityField field) {
+ if (!parameters.hasOutputField(field)) {
+ return false;
+ }
+ if (oldValue == null || oldValue.trim().equals("") || oldValue.equals(newValue)) {
+ return true;
+ } else {
+ logger.warn(getElementTag(field) + " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
+ return false;
+ }
+ }
+
+ private boolean canAssign(String newValue, Integer oldValue, BioEntityField field) {
+ if (!parameters.hasOutputField(field)) {
+ return false;
+ }
+ if (newValue == null || newValue.isEmpty()) {
+ return false;
+ }
+ if (oldValue == null || oldValue == 0 || oldValue.toString().equals(newValue)) {
+ return true;
+ } else {
+ logger.warn(getElementTag(field) + " doesn't match: \"" + newValue + "\", \"" + oldValue + "\"");
+ return false;
+ }
+ }
+
+ private String getElementTag(BioEntityField field) {
+ return getElementTag() + " " + field.getFieldName();
+ }
+
+ public void setFormerSymbols(Collection<String> formerSymbols) {
+ if (originalBioEntity instanceof Element) {
+ Element element = (Element) originalBioEntity;
+ if (canAssignStringSet(formerSymbols, element.getFormerSymbols(), BioEntityField.SYMBOL)) {
+ List<String> sorted = new ArrayList<>(formerSymbols);
+ Collections.sort(sorted);
+ element.setFormerSymbols(sorted);
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.SYMBOL.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void setFullName(String name) {
+ if (originalBioEntity instanceof Element) {
+ Element element = (Element) originalBioEntity;
+ if (canAssign(name, element.getFullName(), BioEntityField.FULL_NAME)) {
+ element.setFullName(name);
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.FULL_NAME.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void setDescription(String description) {
+ if (originalBioEntity instanceof Element && description != null) {
+ Element element = (Element) originalBioEntity;
+ if (element.getNotes() == null || description.toLowerCase().contains(element.getNotes().toLowerCase())) {
+ element.setNotes(description);
+ } else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
+ element.setNotes(element.getNotes() + "\n" + description);
+ }
+ }
+ }
+
+ public void addMiriamData(String generalIdentifier) {
+ MiriamData md = null;
+ try {
+ md = MiriamType.getMiriamByUri(generalIdentifier);
+ } catch (InvalidArgumentException e) {
+ try {
+ md = MiriamType.getMiriamByUri("urn:miriam:" + generalIdentifier);
+ } catch (InvalidArgumentException e1) {
+ logger.warn(getElementTag() + "Unknown miriam uri: " + generalIdentifier);
+ }
+ }
+ addMiriamData(createMiriamData(md));
+ }
+
+ public void setInchi(String inchi) {
+ if (originalBioEntity instanceof Chemical) {
+ Chemical element = (Chemical) originalBioEntity;
+ if (canAssign(inchi, element.getInChI(), BioEntityField.INCHI)) {
+ element.setInChI(inchi);
+ }
+ } else {
+ logger.warn("Cannot assign inchi to " + originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void setInchiKey(String inchiKey) {
+ if (originalBioEntity instanceof Chemical) {
+ Chemical element = (Chemical) originalBioEntity;
+ if (canAssign(inchiKey, element.getInChIKey(), BioEntityField.INCHI_KEY)) {
+ element.setInChIKey(inchiKey);
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.INCHI_KEY.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void setSmile(String smile) {
+ if (originalBioEntity instanceof Chemical) {
+ Chemical element = (Chemical) originalBioEntity;
+ if (canAssign(smile, element.getSmiles(), BioEntityField.SMILE)) {
+ element.setSmiles(smile);
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.SMILE.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void addMiriamData(MiriamType miriamType, String resource) {
+ addMiriamData(createMiriamData(miriamType, resource));
+ }
+
+ public void setCharge(String charge) {
+ if (originalBioEntity instanceof Species) {
+ Species element = (Species) originalBioEntity;
+ if (canAssign(charge, element.getCharge(), BioEntityField.CHARGE)) {
+ element.setCharge(Integer.valueOf(charge));
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.CHARGE.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void setSubsystem(String subsystem) {
+ if (originalBioEntity instanceof Reaction) {
+ Reaction element = (Reaction) originalBioEntity;
+ if (canAssign(subsystem, element.getSubsystem(), BioEntityField.SUBSYSTEM)) {
+ element.setSubsystem(subsystem);
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.SUBSYSTEM.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+
+ public void setFormula(String formula) {
+ if (canAssign(formula, originalBioEntity.getFormula(), BioEntityField.FORMULA)) {
+ originalBioEntity.setFormula(formula);
+ }
+ }
+
+ public void setAbbreviation(String value) {
+ if (canAssign(value, originalBioEntity.getAbbreviation(), BioEntityField.ABBREVIATION)) {
+ originalBioEntity.setAbbreviation(value);
+ }
+ }
+
+ public void setMechanicalConfidenceScore(String value) {
+ if (originalBioEntity instanceof Reaction) {
+ Reaction element = (Reaction) originalBioEntity;
+ if (canAssign(value, element.getMechanicalConfidenceScore(), BioEntityField.MCS)) {
+ element.setMechanicalConfidenceScore(Integer.valueOf(value));
+ }
+ } else {
+ logger.warn("Cannot assign " + BioEntityField.MCS.getFieldName()+" to "+originalBioEntity.getClass().getSimpleName());
+ }
+ }
+ }
+
/**
* Default constructor.
*
@@ -105,6 +372,7 @@ public abstract class ElementAnnotator extends CachableInterface {
*/
public final void annotateElement(BioEntity bioEntity, AnnotationParameters parameters) throws AnnotatorException {
if (isAnnotatable(bioEntity)) {
+ BioEntityProxy proxy = new BioEntityProxy(bioEntity, parameters);
List<AnnotatorInputParameter> inputParameters = parameters.getInputParameters();
if (inputParameters.size() == 0) {
inputParameters = getAvailableInputParameters();
@@ -117,11 +385,11 @@ public abstract class ElementAnnotator extends CachableInterface {
boolean annotated = false;
for (Object object : inputSet) {
if (object instanceof MiriamData) {
- if (annotateElement(bioEntity, (MiriamData) object, parameters)) {
+ if (annotateElement(proxy, (MiriamData) object, parameters)) {
annotated = true;
}
} else if (object instanceof String) {
- if (annotateElement(bioEntity, (String) object, parameters)) {
+ if (annotateElement(proxy, (String) object, parameters)) {
annotated = true;
}
} else {
@@ -135,10 +403,11 @@ public abstract class ElementAnnotator extends CachableInterface {
}
}
- public abstract boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ public abstract boolean annotateElement(BioEntityProxy element, MiriamData identifier,
+ AnnotationParameters parameters)
throws AnnotatorException;
- public boolean annotateElement(BioEntity element, String name, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, String name, AnnotationParameters parameters)
throws AnnotatorException {
throw new NotImplementedException();
};
@@ -266,29 +535,6 @@ public abstract class ElementAnnotator extends CachableInterface {
return isDefault;
}
- /**
- * Sets symbol value to the element.
- *
- * @param element
- * element where we change data
- * @param symbol
- * new symbol
- * @param prefix
- * prefix used in warnings
- */
- protected void setSymbol(BioEntity element, String symbol, String prefix, AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.SYMBOL)) {
- if (element.getSymbol() == null || element.getSymbol().equals("") || element.getSymbol().equals(symbol)) {
- element.setSymbol(symbol);
- } else {
- logger.warn(prefix + "Symbols doesn't match: \"" + symbol + "\", \"" + element.getSymbol() + "\"");
- }
- if (element.getName() == null || element.getName().equals("")) {
- element.setName(symbol);
- }
- }
- }
-
/**
* Sets synonyms to the element.
*
@@ -299,29 +545,14 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setSynonyms(BioEntity element, Collection<String> synonyms, String prefix,
+ protected void setSynonyms(BioEntityProxy element, Collection<String> synonyms, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.SYNONYMS)) {
- if (element.getSynonyms() == null || element.getSynonyms().size() == 0) {
- List<String> sortedSynonyms = new ArrayList<>();
- sortedSynonyms.addAll(synonyms);
- Collections.sort(sortedSynonyms);
-
- element.setSynonyms(sortedSynonyms);
- } else {
- StringSetComparator stringSetComparator = new StringSetComparator();
- Set<String> set1 = new HashSet<String>();
- Set<String> set2 = new HashSet<String>();
-
- set1.addAll(synonyms);
- set2.addAll(element.getSynonyms());
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.warn(prefix + "Synonyms don't match: \"" + synonyms + "\", \"" + element.getSynonyms() + "\"");
- }
+ element.setSynonyms(synonyms);
+ }
- }
- }
+ protected void setFormerSymbols(BioEntityProxy element, Collection<String> symbols, String prefix,
+ AnnotationParameters parameters) {
+ element.setFormerSymbols(symbols);
}
/**
@@ -334,16 +565,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setFullName(Element element, String name, String prefix,
+ protected void setFullName(BioEntityProxy element, String name, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.FULL_NAME)) {
- if (element.getFullName() == null || element.getFullName().equals("") || element.getFullName().equals(name)) {
- element.setFullName(name);
- } else {
- logger.warn(prefix + "Names doesn't match (" + getCommonName() + " annotator and current data): \"" + name
- + "\", \"" + element.getFullName() + "\"");
- }
- }
+ element.setFullName(name);
}
/**
@@ -354,17 +578,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param description
* value to set
*/
- protected void setDescription(BioEntity element, String description,
+ protected void setDescription(BioEntityProxy element, String description,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.DESCRIPTION)) {
- if (description != null) {
- if (element.getNotes() == null || element.getNotes().equals("") || element.getNotes().equals(description)) {
- element.setNotes(description);
- } else if (!element.getNotes().toLowerCase().contains(description.toLowerCase())) {
- element.setNotes(element.getNotes() + "\n" + description);
- }
- }
- }
+ element.setDescription(description);
}
/**
@@ -375,24 +591,12 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addHmdbMiriam(BioEntity element, String value) {
+ protected void addHmdbMiriam(BioEntityProxy element, String value) {
element.addMiriamData(createMiriamData(MiriamType.HMDB, value));
}
- protected void addMiriam(BioEntity element, String generalIdentifier, String prefix) {
- MiriamData md = null;
- try {
- md = MiriamType.getMiriamByUri(generalIdentifier);
- } catch (InvalidArgumentException e) {
- try {
- md = MiriamType.getMiriamByUri("urn:miriam:" + generalIdentifier);
- } catch (InvalidArgumentException e1) {
- logger.warn(prefix + "Unknown miriam uri: " + generalIdentifier);
- }
- }
- if (md != null && !element.getMiriamData().contains(md)) {
- element.addMiriamData(createMiriamData(md));
- }
+ protected void addMiriam(BioEntityProxy element, String generalIdentifier, String prefix) {
+ element.addMiriamData(generalIdentifier);
}
/**
@@ -405,15 +609,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* value to set
*/
- protected void setInchi(Chemical element, String value, String prefix,
+ protected void setInchi(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.INCHI)) {
- if (element.getInChI() == null || element.getInChI().isEmpty() || element.getInChI().equals(value)) {
- element.setInChI(value);
- } else {
- logger.warn(prefix + "InChI in db different: \"" + element.getInChI() + "\", " + value);
- }
- }
+ element.setInchi(value);
}
/**
@@ -426,16 +624,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* value to set
*/
- protected void setInchiKey(Chemical element, String value, String prefix,
+ protected void setInchiKey(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.INCHI_KEY)) {
- if (element.getInChIKey() == null || element.getInChIKey().equals("")) {
- element.setInChIKey(value);
- } else if (!element.getInChIKey().equalsIgnoreCase(value)) {
- logger.warn(prefix + "Different inchikey for chemical: " + element.getInChIKey() + ", " + value);
- }
- }
-
+ element.setInchiKey(value);
}
/**
@@ -448,15 +639,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* value to set
*/
- protected void setSmile(Chemical element, String value, String prefix,
+ protected void setSmile(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.SMILE)) {
- if (element.getSmiles() == null || element.getSmiles().isEmpty() || element.getSmiles().equals(value)) {
- element.setSmiles(value);
- } else {
- logger.warn(prefix + "InChI in db different: \"" + element.getSmiles() + "\", " + value);
- }
- }
+ element.setSmile(value);
}
/**
@@ -467,14 +652,11 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addChebiMiriam(BioEntity element, String value) {
+ protected void addChebiMiriam(BioEntityProxy element, String value) {
if (!value.startsWith("CHEBI:")) {
value = "CHEBI:" + value;
}
- MiriamData md = createMiriamData(MiriamType.CHEBI, value);
- if (md != null && !element.getMiriamData().contains(md)) {
- element.addMiriamData(createMiriamData(md));
- }
+ element.addMiriamData(MiriamType.CHEBI, value);
}
/**
@@ -487,17 +669,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setCharge(Species element, String value, String prefix,
+ protected void setCharge(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.CHARGE)) {
- Integer charge = Integer.parseInt(value);
- if (element.getCharge() == null || element.getCharge() == 0 || element.getCharge().equals(charge)) {
- element.setCharge(Integer.valueOf(charge));
- } else {
- logger.warn(prefix + "Charge in db different: \"" + element.getCharge() + "\", " + charge);
- }
- }
-
+ element.setCharge(value);
}
/**
@@ -508,7 +682,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addPubchemMiriam(BioEntity element, String value) {
+ protected void addPubchemMiriam(BioEntityProxy element, String value) {
element.addMiriamData(createMiriamData(MiriamType.PUBCHEM, value));
}
@@ -520,7 +694,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addCogMiriam(BioEntity element, String value) {
+ protected void addCogMiriam(BioEntityProxy element, String value) {
element.addMiriamData(createMiriamData(MiriamType.COG, value));
}
@@ -534,15 +708,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setSubsystem(Reaction element, String value, String prefix,
+ protected void setSubsystem(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.SUBSYSTEM)) {
- if (element.getSubsystem() == null || element.getSubsystem().isEmpty() || element.getSubsystem().equals(value)) {
- element.setSubsystem(value);
- } else {
- logger.warn(prefix + "Subsystem in db different: \"" + element.getSubsystem() + "\", " + value);
- }
- }
+ element.setSubsystem(value);
}
/**
@@ -553,7 +721,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param value
* annotation identifier
*/
- protected void addEcMiriam(BioEntity element, String value) {
+ protected void addEcMiriam(BioEntityProxy element, String value) {
element.addMiriamData(createMiriamData(MiriamType.EC, value));
}
@@ -568,7 +736,7 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void addKeggMiriam(BioEntity element, String value, String prefix) {
+ protected void addKeggMiriam(BioEntityProxy element, String value, String prefix) {
if (value.startsWith("C")) {
MiriamData md = createMiriamData(MiriamType.KEGG_COMPOUND, value);
element.addMiriamData(md);
@@ -584,42 +752,42 @@ public abstract class ElementAnnotator extends CachableInterface {
}
}
- protected void addChemspider(BioEntity element, String value) {
+ protected void addChemspider(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.CHEMSPIDER, value);
element.addMiriamData(md);
}
- protected void addWikipedia(BioEntity element, String value) {
+ protected void addWikipedia(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.WIKIPEDIA, value);
element.addMiriamData(md);
}
- protected void addCas(BioEntity element, String value) {
+ protected void addCas(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.CAS, value);
element.addMiriamData(md);
}
- protected void addHgnc(BioEntity element, String value) {
+ protected void addHgnc(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.HGNC, value);
element.addMiriamData(md);
}
- protected void addHgncSymbol(BioEntity element, String value) {
+ protected void addHgncSymbol(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.HGNC_SYMBOL, value);
element.addMiriamData(md);
}
- protected void addMesh(BioEntity element, String value) {
+ protected void addMesh(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.MESH_2012, value);
element.addMiriamData(md);
}
- protected void addChemblCompound(BioEntity element, String value) {
+ protected void addChemblCompound(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.CHEMBL_COMPOUND, value);
element.addMiriamData(md);
}
- protected void addRhea(BioEntity element, String value) {
+ protected void addRhea(BioEntityProxy element, String value) {
MiriamData md = createMiriamData(MiriamType.RHEA, value);
element.addMiriamData(md);
}
@@ -634,15 +802,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setFormula(BioEntity element, String value, String prefix,
+ protected void setFormula(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.FORMULA)) {
- if (element.getFormula() == null || element.getFormula().isEmpty() || element.getFormula().equals(value)) {
- element.setFormula(value);
- } else {
- logger.warn(prefix + "Formula in db different: \"" + element.getFormula() + "\", \"" + value + "\"");
- }
- }
+ element.setFormula(value);
}
/**
@@ -655,16 +817,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setAbbreviation(BioEntity element, String value, String prefix,
+ protected void setAbbreviation(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.ABBREVIATION)) {
- if (element.getAbbreviation() == null || element.getAbbreviation().isEmpty()
- || element.getAbbreviation().equals(value)) {
- element.setAbbreviation(value);
- } else if (!element.getAbbreviation().contains(value)) {
- logger.warn(prefix + "Abbreviation in db different: \"" + element.getAbbreviation() + "\", " + value);
- }
- }
+ element.setAbbreviation(value);
}
/**
@@ -677,17 +832,9 @@ public abstract class ElementAnnotator extends CachableInterface {
* @param prefix
* prefix used in warnings
*/
- protected void setMcs(Reaction element, String value, String prefix,
+ protected void setMcs(BioEntityProxy element, String value, String prefix,
AnnotationParameters parameters) {
- if (parameters.hasOutputField(BioEntityField.MCS)) {
- if (element.getMechanicalConfidenceScore() == null || element.getMechanicalConfidenceScore() == 0
- || element.getMechanicalConfidenceScore().toString().equals(value)) {
- element.setMechanicalConfidenceScore(Integer.valueOf(value));
- } else {
- logger.warn(
- prefix + "MCS in db different: \"" + element.getMechanicalConfidenceScore() + "\", \"" + value + "\"");
- }
- }
+ element.setMechanicalConfidenceScore(value);
}
/**
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 cd1899de2061e615f2ed9e5ea8c7ca8c71746258..9355ef063aa47a9a9d91c5614288f71993d82980 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
@@ -138,11 +138,10 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.ENSEMBL)) {
- ElementUtils eu = new ElementUtils();
- String prefix = eu.getElementTag(element);
+ String prefix = element.getElementTag();
return annotateElement(element, identifier, prefix, parameters);
} else {
throw new NotImplementedException();
@@ -161,7 +160,7 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
* @throws AnnotatorException
* thrown when there is a problem with annotating element
*/
- private boolean annotateElement(BioEntity annotatedObject, MiriamData entrezMiriamData, String prefix, AnnotationParameters parameters)
+ private boolean annotateElement(BioEntityProxy annotatedObject, MiriamData entrezMiriamData, String prefix, AnnotationParameters parameters)
throws AnnotatorException {
String query = REST_SERVICE_URL + entrezMiriamData.getResource() + URL_SUFFIX;
try {
@@ -188,11 +187,11 @@ public class EnsemblAnnotator extends ElementAnnotator implements IExternalServi
}
String symbol = super.getNodeAttr("display_id", node);
if (symbol != null) {
- setSymbol(annotatedObject, symbol, prefix, parameters);
+ annotatedObject.setSymbol(symbol);
}
String fullName = super.getNodeAttr("description", node);
if (fullName != null) {
- setFullName((Element) annotatedObject, fullName, prefix, parameters);
+ setFullName( annotatedObject, fullName, prefix, parameters);
}
NodeList synonymNodeList = node.getChildNodes();
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 486ab08516b5192c22f0b5b18c3dc46922221972..011c5a2e98d1c1acfc5e09b04dba8643a3c641ae 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
@@ -142,11 +142,11 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.ENTREZ)) {
ElementUtils eu = new ElementUtils();
- String prefix = eu.getElementTag(element);
+ String prefix = element.getElementTag();
return annotateElement(element, identifier, prefix, parameters);
} else {
throw new NotImplementedException();
@@ -165,13 +165,13 @@ public class EntrezAnnotator extends ElementAnnotator implements IExternalServic
* @throws AnnotatorException
* thrown when there is a problem with annotating element
*/
- private boolean annotateElement(BioEntity element, MiriamData entrezMiriamData, String prefix, AnnotationParameters parameters)
+ private boolean annotateElement(BioEntityProxy element, MiriamData entrezMiriamData, String prefix, AnnotationParameters parameters)
throws AnnotatorException {
EntrezData data = getEntrezForMiriamData(entrezMiriamData, prefix);
if (data != null) {
- setSymbol(element, data.getSymbol(), prefix, parameters);
+ element.setSymbol(data.getSymbol());
- setFullName((Element) element, data.getFullName(), prefix, parameters);
+ setFullName(element, data.getFullName(), prefix, parameters);
element.addMiriamData(data.getMiriamData());
setSynonyms(element, data.getSynonyms(), prefix, parameters);
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 c375146db725f2dcc59a3a4dfe203bf0044af5d8..b9ad300d0eb1f64b780ab311ce09957ed7d25779 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
@@ -99,13 +99,13 @@ public class GoAnnotator extends ElementAnnotator implements IExternalService {
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.GO)) {
try {
Go go = getGoElement(identifier);
if (go != null) {
- setFullName((Element) object, go.getCommonName(), new ElementUtils().getElementTag(object, this), parameters);
+ setFullName(object, go.getCommonName(), object.getElementTag(), parameters);
setDescription(object, go.getDescription(), parameters);
return true;
}
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 d9399fdfa3f1584b9933c99dab3154a45dd461b4..56bb125ca3ef0ac102756b1c1342b69e7f18d29d 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
@@ -20,16 +20,13 @@ import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-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.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This class is responsible for connecting to
@@ -100,10 +97,9 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy element, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
- ElementUtils eu = new ElementUtils();
- String prefix = eu.getElementTag(element);
+ String prefix = element.getElementTag();
String query;
if (identifier.getDataType().equals(MiriamType.HGNC_SYMBOL)) {
@@ -144,15 +140,15 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
} else if (type.equals("entrez_id")) {
element.addMiriamData(createMiriamData(MiriamType.ENTREZ, getNodeValue(node)));
} else if (type.equals("symbol")) {
- if (!identifier.getDataType().equals(MiriamType.HGNC_SYMBOL)
- || !element.getMiriamData().contains(identifier)) {
+ if (!identifier.getDataType().equals(MiriamType.HGNC_SYMBOL) || !element.contains(identifier)) {
// add hgnc symbol annnotation only when there was no
// hgnc_symbol in the element
element.addMiriamData(createMiriamData(MiriamType.HGNC_SYMBOL, getNodeValue(node)));
}
- setSymbol(element, getNodeValue(node), prefix, parameters);
+ element.setSymbol(getNodeValue(node));
+ element.setName(getNodeValue(node));
} else if (type.equals("name")) {
- setFullName((Element) element, getNodeValue(node), prefix, parameters);
+ setFullName(element, getNodeValue(node), prefix, parameters);
}
} else if (node.getNodeName().equals("arr")) {
String type = getNodeAttr("name", node);
@@ -173,7 +169,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
strings.add(getNodeValue(subnode));
}
}
- ((Element) element).setFormerSymbols(strings);
+ setFormerSymbols(element, strings, prefix, parameters);
} else if (type.equals("alias_symbol")) {
List<String> strings = new ArrayList<>();
NodeList sublist = node.getChildNodes();
@@ -445,6 +441,7 @@ public class HgncAnnotator extends ElementAnnotator implements IExternalService
new AnnotatorOutputParameter(MiriamType.UNIPROT),
new AnnotatorOutputParameter(BioEntityField.SYMBOL),
new AnnotatorOutputParameter(BioEntityField.SYNONYMS),
+ new AnnotatorOutputParameter(BioEntityField.NAME),
new AnnotatorOutputParameter(BioEntityField.FULL_NAME));
}
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 0ee5bdb5d9c5325f421cc201d8e8f51a6fa9ef3f..4934cc07c4e143e3ab5bc70356a391215d1cf2e7 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
@@ -115,25 +115,25 @@ public class KeggAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
Set<MiriamData> ecIdentifiers = new HashSet<>();
+ try {
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- tairAnnotator.annotateElement(object);
- uniprotAnnotator.annotateElement(object);
+ for (MiriamData uniprotId: tairAnnotator.tairToUniprot(identifier)) {
+ ecIdentifiers.addAll(uniprotAnnotator.uniProtToEC(uniprotId));
+ }
} else if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
- uniprotAnnotator.annotateElement(object);
+ ecIdentifiers.addAll(uniprotAnnotator.uniProtToEC(identifier));
} else if (identifier.getDataType().equals(MiriamType.EC)) {
ecIdentifiers.add(identifier);
} else {
throw new NotImplementedException();
}
- if (ecIdentifiers.size() == 0) {
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.EC)) {
- ecIdentifiers.add(md);
- }
- }
+ } catch (UniprotSearchException e) {
+ e.printStackTrace();
+ logger.warn(e);
+ return false;
}
if (ecIdentifiers.size() == 0) {
logger.warn("Cannot find kegg data for id: " + identifier);
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 cd973d7665cc8bfbc0498850c32501a3ec54ad76..58b60aa03dd7c42a4ac713c9edc248c370b576fc 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
@@ -101,14 +101,13 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
}
@Override
- public boolean annotateElement(BioEntity bioEntity, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy bioEntity, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
try {
Collection<Structure> structures = uniProtToPdb(identifier);
if (structures.size() == 0) {
- logger.warn(
- elementUtils.getElementTag(bioEntity) + " No PDB mapping for UniProt ID: " + identifier.getResource());
+ logger.warn(bioEntity.getElementTag() + " No PDB mapping for UniProt ID: " + identifier.getResource());
return false;
} else {
// add the annotations to the set of annotation irrespective on
@@ -121,17 +120,17 @@ public class PdbAnnotator extends ElementAnnotator implements IExternalService {
}
bioEntity.addMiriamData(annotations);
+
// insert the full information directly into species, .i.e.
// create new uniprot record which includes the mapped structures
// and add it to the species (bioentity)
UniprotRecord ur = new UniprotRecord();
ur.setUniprotId(identifier.getResource());
- ur.setSpecies((Species) bioEntity);
for (Structure s : structures) {
s.setUniprot(ur);
}
ur.addStructures(structures);
- ((Species) bioEntity).getUniprots().add(ur);
+ bioEntity.addUniprot(ur);
return true;
}
} catch (WrongResponseCodeIOException exception) {
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 fbdc13b3703ddbe1954ea6023f155a9a3be37ccd..444f481e72038ce6ad99970439a0fd72bed61fac 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
@@ -26,9 +26,7 @@ import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
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.SimpleMolecule;
-import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
@@ -95,13 +93,13 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity annotatedObject, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy annotatedObject, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.VMH_METABOLITE)) {
String url = null;
- if (annotatedObject instanceof Element) {
+ if (annotatedObject.isElement()) {
url = ELEMENT_ANNOTATION_URL_PREFIX + identifier.getResource();
- } else if (annotatedObject instanceof Reaction) {
+ } else if (annotatedObject.isReaction()) {
url = REACTION_ANNOTATION_URL_PREFIX + identifier.getResource();
} else {
logger.warn("Unknown class type: " + annotatedObject.getClass());
@@ -110,7 +108,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
try {
String content = getWebPageContent(url);
- String prefix = elementUtils.getElementTag(annotatedObject, this);
+ String prefix = annotatedObject.getElementTag();
if (!content.isEmpty()) {
JsonElement jelement = new JsonParser().parse(content);
@@ -143,11 +141,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
} else if (key.equals("reversible")) {
continue;
} else if (key.equals("mcs")) {
- if (annotatedObject instanceof Reaction) {
- setMcs((Reaction) annotatedObject, value, prefix, parameters);
- } else {
- unknown = true;
- }
+ setMcs(annotatedObject, value, prefix, parameters);
} else if (key.equals("notes")) {
setDescription(annotatedObject, value, parameters);
} else if (key.equals("ecnumber")) {
@@ -155,33 +149,17 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
} else if (key.equals("chargedFormula")) {
setFormula(annotatedObject, value, prefix, parameters);
} else if (key.equals("charge")) {
- if (annotatedObject instanceof Species) {
- setCharge((Species) annotatedObject, value, prefix, parameters);
- } else {
- unknown = true;
- }
+ setCharge(annotatedObject, value, prefix, parameters);
} else if (key.equals("inchiString")) {
- if (annotatedObject instanceof Chemical) {
- setInchi((Chemical) annotatedObject, value, prefix, parameters);
- } else {
- unknown = true;
- }
+ setInchi(annotatedObject, value, prefix, parameters);
} else if (key.equals("cheBlId")) {
addChebiMiriam(annotatedObject, value);
} else if (key.equals("subsystem")) {
- if (annotatedObject instanceof Reaction) {
- setSubsystem((Reaction) annotatedObject, value, prefix, parameters);
- } else {
- unknown = true;
- }
+ setSubsystem(annotatedObject, value, prefix, parameters);
} else if (key.equals("keggId")) {
addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("fullName")) {
- if (annotatedObject instanceof Element) {
- setFullName((Element) annotatedObject, value, prefix, parameters);
- } else {
- unknown = true;
- }
+ setFullName(annotatedObject, value, prefix, parameters);
} else if (key.equals("keggorthology")) {
addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("pubChemId")) {
@@ -199,13 +177,9 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
} else if (key.equals("miriam")) {
addMiriam(annotatedObject, value, prefix);
} else if (key.equals("inchiKey")) {
- if (annotatedObject instanceof Chemical) {
- setInchiKey((Chemical) annotatedObject, value, prefix, parameters);
- }
+ setInchiKey(annotatedObject, value, prefix, parameters);
} else if (key.equals("smile")) {
- if (annotatedObject instanceof Chemical) {
- setSmile((Chemical) annotatedObject, value, prefix, parameters);
- }
+ setSmile(annotatedObject, value, prefix, parameters);
} else if (key.equals("chemspider")) {
addChemspider(annotatedObject, value);
} else if (key.equals("wikipedia")) {
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 95be1a8e000e3b445e7323ae63ef54d670df3421..5efb7a658d052a7ef001d4c92459533f88526e3b 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
@@ -64,7 +64,7 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.CHEBI)) {
try {
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 dbbf4aae7ff9efd11b590afbb480b106006f0bd3..56c186015c9b7a41d042c75e8ac74c0074a3ef8b 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
@@ -48,16 +48,11 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
List<MiriamData> mdUniprots = new ArrayList<>();
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- tairAnnotator.annotateElement(object);
- for (MiriamData md : object.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.UNIPROT)) {
- mdUniprots.add(md);
- }
- }
+ mdUniprots.addAll(tairAnnotator.tairToUniprot(identifier));
} else if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
mdUniprots.add(identifier);
} else {
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 28ec47a55bfebe420f475f9adf071ef8183d533d..6d15ec8184a57e1d293385f6dc5aa883daf90edb 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
@@ -1,7 +1,6 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
@@ -20,8 +19,6 @@ import lcsb.mapviewer.annotation.services.IExternalService;
import lcsb.mapviewer.annotation.services.WrongResponseCodeIOException;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.NoteField;
-import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Gene;
@@ -62,10 +59,12 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
this.setCache(null);
try {
- MiriamData md = tairToUniprot(createMiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+ Collection<MiriamData> collection = tairToUniprot(createMiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
status.setStatus(ExternalServiceStatusType.OK);
- if (md == null || !md.getResource().equalsIgnoreCase("Q9MAN1")) {
+ if (collection.size() == 0) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (!collection.iterator().next().getResource().equalsIgnoreCase("Q9MAN1")) {
status.setStatus(ExternalServiceStatusType.CHANGED);
}
} catch (Exception e) {
@@ -77,15 +76,17 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- MiriamData mdUniprot = tairToUniprot(identifier);
- if (mdUniprot != null) {
- object.addMiriamData(mdUniprot);
+ Collection<MiriamData> collection = tairToUniprot(identifier);
+ if (collection.size() > 0) {
+ object.addMiriamData(collection);
return true;
+ } else {
+ logger.warn("Cannot find uniprot data for id: " + identifier.getResource() + " in the tair page");
+ return false;
}
- return false;
} else {
throw new NotImplementedException();
}
@@ -163,7 +164,7 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
* @throws AnnotatorException
* thrown when there is a problem with accessing external database
*/
- public MiriamData tairToUniprot(MiriamData tair) throws AnnotatorException {
+ public Collection<MiriamData> tairToUniprot(MiriamData tair) throws AnnotatorException {
if (tair == null) {
return null;
}
@@ -172,18 +173,12 @@ public class TairAnnotator extends ElementAnnotator implements IExternalService
throw new InvalidArgumentException(MiriamType.TAIR_LOCUS + " expected.");
}
- // String accessUrl = getTairUrl(tair.getResource());
- String accessUrl = getUniProtUrl(tair.getResource());
try {
+ // String accessUrl = getTairUrl(tair.getResource());
+ String accessUrl = getUniProtUrl(tair.getResource());
String pageContent = getWebPageContent(accessUrl);
// Collection<MiriamData> collection = parseUniprot(pageContent);
- Collection<MiriamData> collection = parseUniprotUniprot(pageContent);
- if (collection.size() > 0) {
- return collection.iterator().next();
- } else {
- logger.warn("Cannot find uniprot data for id: " + tair.getResource() + " in the tair page");
- return null;
- }
+ return parseUniprotUniprot(pageContent);
} catch (WrongResponseCodeIOException exception) {
logger.warn("Wrong reponse code when accessing tair data with id: " + tair.getResource());
return null;
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 03d047276b400a13a1a470782cef950daa5c5a38..9309addb9099effea69043554f502bfe2f81e009 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
@@ -95,7 +95,7 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
}
@Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ public boolean annotateElement(BioEntityProxy object, MiriamData identifier, AnnotationParameters parameters)
throws AnnotatorException {
if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
@@ -108,15 +108,13 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
annotations.addAll(parseHgnc(pageContent));
annotations.addAll(parseEntrez(pageContent));
annotations.addAll(parseEC(pageContent));
- if (!object.getMiriamData().contains(identifier)) {
- annotations.add(createMiriamData(MiriamType.UNIPROT, identifier.getResource()));
- }
+ object.addMiriamData(createMiriamData(MiriamType.UNIPROT, identifier.getResource()));
object.addMiriamData(annotations);
return true;
} else {
// this means that entry with a given uniprot id doesn't exist
- if (object.getMiriamData().contains(identifier)) {
- logger.warn(elementUtils.getElementTag(object) + " Invalid uniprot id: " + identifier);
+ if (object.contains(identifier)) {
+ logger.warn(object.getElementTag() + " Invalid uniprot id: " + identifier);
}
return false;
}
@@ -247,12 +245,9 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
String accessUrl = getUniprotUrl(uniprot.getResource());
try {
String pageContent = getWebPageContent(accessUrl);
- Collection<MiriamData> collection = parseEC(pageContent);
- if (collection.size() > 0) {
- return collection;
- } else {
- return null;
- }
+ return parseEC(pageContent);
+ } catch (WrongResponseCodeIOException e) {
+ return new HashSet<>();
} catch (IOException e) {
throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
}
@@ -292,5 +287,4 @@ public class UniprotAnnotator extends ElementAnnotator implements IExternalServi
new AnnotatorOutputParameter(MiriamType.EC),
new AnnotatorOutputParameter(MiriamType.ENTREZ));
}
-
}
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 4e1fa2ccb4552d7695da44170dfdc74827d9c3bb..60c55a1e9fde82e6ffe095c1120534ca8874274f 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
@@ -188,8 +188,6 @@ public class BrendaAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, protein.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
index 92f2d0e4bc0489a2296c3cc64ab02b61fa869fbf..081648349144c8a0e49811fc80544a8b716161c9 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
@@ -173,9 +173,6 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
cazyAnnotator.annotateElement(protein);
assertEquals(1, protein.getMiriamData().size());
-
- assertEquals(1, getWarnings().size());
-
} catch (Exception e) {
e.printStackTrace();
throw e;
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 301fcebca8a631748fbb4df95bfbead9cd8ee90e..c0ca85955993f6fefbf4744077438c129c0ff49d 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
@@ -64,7 +64,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingSymbol() {
GenericProtein species = new GenericProtein("id");
species.setSymbol("X");
- annotator.setSymbol(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setSymbol("Y");
assertEquals(1, getWarnings().size());
}
@@ -73,7 +74,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingFullname() {
GenericProtein species = new GenericProtein("id");
species.setFullName("X");
- annotator.setFullName(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setFullName("Y");
assertEquals(1, getWarnings().size());
}
@@ -82,7 +84,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingNotes() {
GenericProtein species = new GenericProtein("id");
species.setNotes("X");
- annotator.setDescription(species, "Y", allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setDescription("Y");
assertEquals(0, getWarnings().size());
}
@@ -91,7 +94,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetEmptyDescription() {
GenericProtein species = new GenericProtein("id");
species.setNotes("X");
- annotator.setDescription(species, null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setDescription(null);
assertEquals("X", species.getNotes());
}
@@ -99,7 +103,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingIchi() {
Ion species = new Ion("id");
species.setInChI("X");
- annotator.setInchi(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setInchi("Y");
assertEquals(1, getWarnings().size());
}
@@ -107,8 +112,9 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testSetNotMatchingSmile() {
Ion species = new Ion("id");
- annotator.setSmile(species, "X", null, allOutputFieldsAndAnnotations);
- annotator.setSmile(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setSmile("X");
+ proxy.setSmile("Y");
assertEquals(1, getWarnings().size());
}
@@ -117,7 +123,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingCharge() {
Ion species = new Ion("id");
species.setCharge(2);
- annotator.setCharge(species, "3", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setCharge("3");
assertEquals(1, getWarnings().size());
}
@@ -126,7 +133,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingSubsystem() {
Reaction species = new Reaction();
species.setSubsystem("X");
- annotator.setSubsystem(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setSubsystem("Y");
assertEquals(1, getWarnings().size());
}
@@ -135,7 +143,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingFormula() {
Reaction species = new Reaction();
species.setFormula("X");
- annotator.setFormula(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setFormula("Y");
assertEquals(1, getWarnings().size());
}
@@ -144,7 +153,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingAbbreviation() {
Reaction species = new Reaction();
species.setAbbreviation("X");
- annotator.setAbbreviation(species, "Y", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setAbbreviation("Y");
assertEquals(1, getWarnings().size());
}
@@ -153,7 +163,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetNotMatchingMCS() {
Reaction species = new Reaction();
species.setMechanicalConfidenceScore(1);
- annotator.setMcs(species, "2", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setMechanicalConfidenceScore("2");
assertEquals(1, getWarnings().size());
}
@@ -163,7 +174,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
try {
Reaction reaction = new Reaction();
reaction.setMechanicalConfidenceScore(4);
- annotator.setMcs(reaction, "4", null, allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(reaction, allOutputFieldsAndAnnotations);
+ proxy.setMechanicalConfidenceScore( "4");
assertEquals(0, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
@@ -173,26 +185,10 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testAddKegg() {
- Reaction species = new Reaction();
- annotator.addKeggMiriam(species, "R123", null);
- assertEquals(1, species.getMiriamData().size());
- }
-
- @Test
- public void testAddChebi() {
- Reaction species = new Reaction();
- annotator.addChebiMiriam(species, "123");
- assertEquals(1, species.getMiriamData().size());
- assertTrue(species.getMiriamData().iterator().next().getResource().contains("CHEBI"));
- }
-
- @Test
- public void testAddInvalidKegg() {
- Reaction species = new Reaction();
- annotator.addKeggMiriam(species, "unk_id", null);
- assertEquals(0, species.getMiriamData().size());
-
- assertEquals(1, getWarnings().size());
+ Reaction reaction = new Reaction();
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(reaction, allOutputFieldsAndAnnotations);
+ proxy.addMiriamData(new MiriamData(MiriamType.KEGG_COMPOUND, "R123"));
+ assertEquals(1, reaction.getMiriamData().size());
}
@Test
@@ -226,7 +222,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
public void testSetSynonymsWarning() {
GenericProtein species = new GenericProtein("1");
species.addSynonym("X");
- annotator.setSynonyms(species, Arrays.asList("Y"), "warn", allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setSynonyms(Arrays.asList("Y"));
assertEquals(1, getWarnings().size());
}
@@ -236,7 +233,8 @@ public class ElementAnnotatorTest extends AnnotationTestFunctions {
GenericProtein species = new GenericProtein("1");
species.addSynonym("X");
species.addSynonym("Y");
- annotator.setSynonyms(species, Arrays.asList("Y", "X"), "warn", allOutputFieldsAndAnnotations);
+ ElementAnnotator.BioEntityProxy proxy = annotator.new BioEntityProxy(species, allOutputFieldsAndAnnotations);
+ proxy.setSynonyms(Arrays.asList("Y", "X"));
assertEquals(0, getWarnings().size());
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index e2fbc6310c98dcc521b1de084b1c7f4020b199e9..946fbda815c484b56f63a907a749b1da89b55e2f 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -104,11 +104,12 @@ public class HgncAnnotatorTest extends AnnotationTestFunctions {
MiriamData snca = new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA");
MiriamData park7 = new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7");
GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias.setName("SNCA");
proteinAlias.addMiriamData(snca);
proteinAlias.addMiriamData(park7);
hgncAnnotator.annotateElement(proteinAlias);
- assertEquals(3, getWarnings().size());
+ assertEquals(4, getWarnings().size());
} catch (Exception e) {
e.printStackTrace();
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 cf9319218e2c93ffdba5b05c87d1353221b08c81..a9d38923e6e38b1c0a0b7146966399a24d9ad0fb 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
@@ -243,7 +243,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
}
}
- assertEquals("Wrong number of publications extracted from KEGG annotator", 11, mdPubmed.size());
+ assertTrue("Wrong number of publications extracted from KEGG annotator", mdPubmed.size() >= 9);
} catch (Exception e) {
e.printStackTrace();
@@ -280,7 +280,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, protein.getMiriamData().size());
- assertEquals(3, getWarnings().size());
+ assertTrue(getWarnings().size() > 0);
} catch (Exception e) {
e.printStackTrace();
@@ -299,7 +299,7 @@ public class KeggAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, protein.getMiriamData().size());
- assertEquals(3, getWarnings().size());
+ assertTrue(getWarnings().size() > 0);
} catch (Exception e) {
e.printStackTrace();
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
index 573089f79a6ed37204405a6588bae092ae7104e0..a16ebc551fd01655d4e6345dd55a09762fc5592d 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotatorTest.java
@@ -114,8 +114,6 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
reconAnnotator.annotateElement(ion);
assertEquals(2, getWarnings().size());
- assertTrue(getWarnings().get(0).getMessage().toString().contains("Unknown field"));
- assertTrue(getWarnings().get(1).getMessage().toString().contains("Unknown field"));
} catch (Exception e) {
e.printStackTrace();
throw e;
@@ -144,8 +142,6 @@ public class ReconAnnotatorTest extends AnnotationTestFunctions {
reconAnnotator.annotateElement(reaction);
assertEquals(2, getWarnings().size());
- assertTrue(getWarnings().get(0).getMessage().toString().contains("Unknown field"));
- assertTrue(getWarnings().get(1).getMessage().toString().contains("Unknown field"));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
index bdf2a45fdef7d52f81b01c75e32a16c59d958cac..4c1f91dd1fc7a3938e5cf8299be28f4d200095ee 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotatorTest.java
@@ -105,8 +105,6 @@ public class StringAnnotatorTest extends AnnotationTestFunctions {
assertEquals(1, bioEntity.getMiriamData().size());
- assertEquals(1, getWarnings().size());
-
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
index 22b97fc09addbb69c508a66dfe19b7046eb24bff..cf3e9b9d7da2699fbd8e479e51e84fd93ccbca11 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -156,8 +156,8 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
// @Ignore("TAIR DB restricts queries by IP")
public void testTairToUniprot() throws Exception {
try {
- assertEquals(new MiriamData(MiriamType.UNIPROT, "Q9MAN1", TairAnnotator.class),
- tairAnnotator.tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030")));
+ assertTrue(tairAnnotator.tairToUniprot(new MiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"))
+ .contains(new MiriamData(MiriamType.UNIPROT, "Q9MAN1", TairAnnotator.class)));
} catch (Exception e) {
e.printStackTrace();
throw e;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
index fdb539dc60edc3c3c4e016229128e1999e860f9c..24f7e3b02404053d2c3aa97b35fd2f20e9205663 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
@@ -234,7 +234,7 @@ public class RestAnnotationParser extends XmlParser {
* annotation string
* @return list of symbol
*/
- protected List<String> getSynonyms(String annotationString) {
+ public List<String> getSynonyms(String annotationString) {
List<String> result = new ArrayList<String>();
String synonyms = getParamByPrefix(annotationString, NoteField.SYNONYMS.getCommonName() + ":");
if (synonyms != null) {
@@ -254,7 +254,7 @@ public class RestAnnotationParser extends XmlParser {
* annotation string
* @return list of former symbol
*/
- protected List<String> getFormerSymbols(String annotationString) {
+ public List<String> getFormerSymbols(String annotationString) {
List<String> result = new ArrayList<String>();
String formerSymbols = getParamByPrefix(annotationString, NoteField.PREVIOUS_SYMBOLS.getCommonName() + ":");
if (formerSymbols != null) {
@@ -419,7 +419,7 @@ public class RestAnnotationParser extends XmlParser {
*/
private void setFullNameToSpecies(Element element, String annotationString) {
StringComparator stringComparator = new StringComparator();
- String fullName = getParamByPrefix(annotationString, NoteField.NAME.getCommonName() + ":");
+ String fullName = getFullName(annotationString);
if (fullName == null) {
return;
}
@@ -431,6 +431,10 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ public String getFullName(String annotationString) {
+ return getParamByPrefix(annotationString, NoteField.NAME.getCommonName() + ":");
+ }
+
/**
* Assigns abbreviation to the element from notes string.
*
@@ -441,7 +445,7 @@ public class RestAnnotationParser extends XmlParser {
*/
private void setAbbreviation(BioEntity element, String annotationString) {
StringComparator stringComparator = new StringComparator();
- String abbreviation = getParamByPrefix(annotationString, NoteField.ABBREVIATION.getCommonName() + ":");
+ String abbreviation = getAbbreviation(annotationString);
if (abbreviation == null) {
return;
}
@@ -453,6 +457,10 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ public String getAbbreviation(String annotationString) {
+ return getParamByPrefix(annotationString, NoteField.ABBREVIATION.getCommonName() + ":");
+ }
+
/**
* Assigns subsystem to the reaction from notes string.
*
@@ -507,7 +515,7 @@ public class RestAnnotationParser extends XmlParser {
*/
private void setFormula(BioEntity element, String annotationString) {
StringComparator stringComparator = new StringComparator();
- String formula = getParamByPrefix(annotationString, NoteField.FORMULA.getCommonName() + ":");
+ String formula = getFormula(annotationString);
if (formula == null) {
formula = getParamByPrefix(annotationString, NoteField.CHARGED_FORMULA.getCommonName() + ":");
if (formula == null) {
@@ -522,6 +530,10 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ public String getFormula(String annotationString) {
+ return getParamByPrefix(annotationString, NoteField.FORMULA.getCommonName() + ":");
+ }
+
/**
* Assigns mechanical confidence score to the reaction from notes string.
*
@@ -628,7 +640,7 @@ public class RestAnnotationParser extends XmlParser {
* notes string
*/
private void setSymbol(BioEntity element, String annotationString) {
- String symbol = getParamByPrefix(annotationString, NoteField.SYMBOL.getCommonName() + ":");
+ String symbol = getSymbol(annotationString);
if (symbol == null) {
return;
}
@@ -640,6 +652,10 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ public String getSymbol(String annotationString) {
+ return getParamByPrefix(annotationString, NoteField.SYMBOL.getCommonName() + ":");
+ }
+
/**
* Assigns semanticZoomingLevel to the element from notes string.
*
@@ -690,7 +706,7 @@ public class RestAnnotationParser extends XmlParser {
* notes string
*/
private void setNotes(BioEntity element, String annotationString) {
- String description = getParamByPrefix(annotationString, NoteField.DESCRIPTION.getCommonName() + ":");
+ String description = getDescription(annotationString);
if (description == null) {
return;
}
@@ -703,6 +719,10 @@ public class RestAnnotationParser extends XmlParser {
}
}
+ public String getDescription(String annotationString) {
+ return getParamByPrefix(annotationString, NoteField.DESCRIPTION.getCommonName() + ":");
+ }
+
/**
* Process notes and assign structural information from it.
*