From 42d357fb260bb063b897eaf2c848348d1e3735db Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Thu, 5 Apr 2018 17:55:22 +0200
Subject: [PATCH] update on recon annotator after changes in API
---
.../services/annotators/ElementAnnotator.java | 1231 +++++++++--------
.../services/annotators/ReconAnnotator.java | 507 ++++---
.../annotators/ReconAnnotatorTest.java | 631 ++++-----
.../lcsb/mapviewer/model/map/MiriamType.java | 2 +-
4 files changed, 1238 insertions(+), 1133 deletions(-)
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 7be1c6bde1..520c32d4f3 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
@@ -30,598 +30,641 @@ import lcsb.mapviewer.model.user.UserAnnotatorsParam;
*/
public abstract class ElementAnnotator extends CachableInterface {
- /**
- * Default class logger.
- */
- private final Logger logger = Logger.getLogger(ElementAnnotator.class);
-
- /**
- * List of classes that can be annotated by this {@link IElementAnnotator
- * annotator}.
- */
- private final List<Class<? extends BioEntity>> validClasses = new ArrayList<>();
-
- /**
- * Should be this annotator used as a default annotator.
- */
- private boolean isDefault = false;
-
- /**
- * Parameters which this annotator can be provided. Should be set in constructor.
- */
- protected List<AnnotatorParamDefinition> paramsDefs = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param validClasses
- * list of classes for which this annotator is valid
- * @param isDefault
- * {@link #isDefault}
- * @param clazz
- * type that defines this interface
- */
- @SuppressWarnings("unchecked")
- public ElementAnnotator(Class<? extends CachableInterface> clazz, Class<?>[] validClasses, boolean isDefault) {
- super(clazz);
- for (Class<?> validClass : validClasses) {
- if (BioEntity.class.isAssignableFrom(validClass)) {
- addValidClass((Class<? extends BioEntity>) validClass);
- } else {
- throw new InvalidArgumentException("Cannot pass class of type: " + validClass + ". Only classes extending " + BioEntity.class + " are accepted.");
- }
- }
- this.isDefault = isDefault;
- }
-
- /**
- * Annotate element.
- *
- * @param element
- * object to be annotated
- * @throws AnnotatorException
- * thrown when there is a problem with annotating not related to
- * data
- */
- public abstract void annotateElement(BioEntity element) throws AnnotatorException;
-
- /**
- * Annotate element using parameters.
- *
- * @param element
- * object to be annotated
- * @param parameters
- * list of parameters passed to the annotator which is expected to
- * be in the same order as its {@link this#parameterDefs}
- * @throws AnnotatorException
- * thrown when there is a problem with annotating not related to
- * data
- */
- public void annotateElement(BioEntity element, List<UserAnnotatorsParam> parameters) throws AnnotatorException {
- annotateElement(element);
- }
-
- /**
- * Returns a list of all classes that can be annotated using this annotator.
- *
- * @return a list of all classes that can be annotated using this annotator
- */
- public List<Class<? extends BioEntity>> getValidClasses() {
- return validClasses;
- }
-
- /**
- * Returns <code>true</code> if this annotator can annotate the object given
- * in the parameter.
- *
- * @param object
- * object to be tested if can be annotated
- * @return <code>true</code> if object can be annotated by this annotator,
- * <code>false</code> otherwise
- */
- public boolean isAnnotatable(BioEntity object) {
- Class<?> clazz = object.getClass();
- for (Class<?> validClazz : getValidClasses()) {
- if (validClazz.isAssignableFrom(clazz)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Adds a class to list of classes that can be annotated by the annotator.
- *
- * @param clazz
- * class to add
- */
- private void addValidClass(Class<? extends BioEntity> clazz) {
- validClasses.add(clazz);
- }
-
- /**
- * Returns the common name that should be presented to user.
- *
- * @return the common name
- */
- public abstract String getCommonName();
-
- /**
- * Returns url to the external resource used for annotation.
- *
- * @return url
- */
- public abstract String getUrl();
-
- /**
- * Provides description of the extraction process
- * for {@link ElementAnnotator} to be used in the front end.
- * @return
- * the description
- */
- public String getDescription(){
- return "";
- }
-
- /**
- * Provides description for {@link ElementAnnotator} and {@link MiriamType} pair
- * to be used in the frontend.
- * @param mt
- * {@link MiriamType} annotated by this annotator.
- * @return
- * the description
- */
- public String getDescription(MiriamType mt){
- return "";
- }
-
- /**
- * Provides description for {@link ElementAnnotator}, {@link MiriamType} and
- * {@link MiriamRelationType} triplet to be used in the frontend.
- * @param mt
- * {@link MiriamType} annotated by this annotator
- * @param relationType
- * {@link MiriamRelationType} annotated by this annotator.
- * @return
- * the description
- */
- public String getDescription(MiriamType mt, MiriamRelationType relationType){
- return "";
- }
-
- /**
- * Returns list with definitions of the parameters available for this annotator.
- * @return the parameters {@link AnnotatorParamDefinition} list
- */
- public Collection<AnnotatorParamDefinition> getParametersDefinitions(){
- return paramsDefs;
- }
-
- /**
- * Returns <code>true</code> if this annotator can annotate the object of
- * given class type.
- *
- * @param clazz
- * class to be tested if can be annotated
- * @return <code>true</code> if class can be annotated by this annotator,
- * <code>false</code> otherwise
- */
- public boolean isAnnotatable(Class<?> clazz) {
- for (Class<?> clazz2 : validClasses) {
- if (clazz2.isAssignableFrom(clazz)) {
- return true;
- }
- }
- return false;
- }
-
- /**
- *
- * @return {@link #isDefault}
- */
- public boolean isDefault() {
- 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) {
- 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.
- *
- * @param element
- * element where we change data
- * @param synonyms
- * new synonyms list
- * @param prefix
- * prefix used in warnings
- */
- protected void setSynonyms(BioEntity element, Collection<String> synonyms, String prefix) {
- if (element.getSynonyms() == null || element.getSynonyms().size() == 0) {
- List<String> sortedSynonyms = new ArrayList<>();
- sortedSynonyms.addAll(synonyms);
- Collections.sort(sortedSynonyms);
-
- element.setSynonyms(sortedSynonyms);
- } else {
- logger.warn(prefix + "Synonyms don't match: \"" + synonyms + "\", \"" + element.getSynonyms() + "\"");
- }
- }
-
- /**
- * Sets name to the element.
- *
- * @param element
- * element where we change data
- * @param name
- * new name
- * @param prefix
- * prefix used in warnings
- */
- protected void setFullName(Element element, String name, String prefix) {
- 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() + "\"");
- }
- }
-
- /**
- * Adds description to {@link BioEntity#getNotes()}.
- *
- * @param element
- * element where annotation should be added
- * @param description
- * value to set
- */
- protected void setDescription(BioEntity element, String 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);
- }
- }
- }
-
- /**
- * Adds {@link MiriamType#HMDB} annotation to element.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * annotation identifier
- */
- protected void addHmdbMiriam(BioEntity element, String value) {
- element.addMiriamData(createMiriamData(MiriamType.HMDB, value));
- }
-
- /**
- * Sets {@link CellDesignerChemical#inChI}.
- *
- * @param element
- * element where annotation should be added
- * @param prefix
- * prefix used in warnings
- * @param value
- * value to set
- */
- protected void setInchi(Chemical element, String value, String prefix) {
- 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);
- }
-
- }
-
- /**
- * Sets {@link CellDesignerChemical#inChIKey}.
- *
- * @param element
- * element where annotation should be added
- * @param prefix
- * prefix used in warnings
- * @param value
- * value to set
- */
- protected void setInchiKey(Chemical element, String value, String prefix) {
- 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);
- }
-
- }
-
- /**
- * Sets {@link CellDesignerChemical#smiles}.
- *
- * @param element
- * element where annotation should be added
- * @param prefix
- * prefix used in warnings
- * @param value
- * value to set
- */
- protected void setSmile(Chemical element, String value, String prefix) {
- 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);
- }
-
- }
-
- /**
- * Adds {@link MiriamType#CHEBI} annotation to element.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * annotation identifier
- */
- protected void addChebiMiriam(BioEntity element, String value) {
- if (!value.startsWith("CHEBI:")) {
- value = "CHEBI:" + value;
- }
- element.addMiriamData(createMiriamData(MiriamType.CHEBI, value));
- }
-
- /**
- * Sets {@link Species#charge}.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * value to set
- * @param prefix
- * prefix used in warnings
- */
- protected void setCharge(Species element, String value, String prefix) {
- 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);
- }
-
- }
-
- /**
- * Adds {@link MiriamType#PUBCHEM} annotation to element.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * annotation identifier
- */
- protected void addPubchemMiriam(BioEntity element, String value) {
- element.addMiriamData(createMiriamData(MiriamType.PUBCHEM, value));
- }
-
- /**
- * Adds {@link MiriamType#COG} annotation to element.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * annotation identifier
- */
- protected void addCogMiriam(BioEntity element, String value) {
- element.addMiriamData(createMiriamData(MiriamType.COG, value));
- }
-
- /**
- * Sets {@link Reaction#subsystem}.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * value to set
- * @param prefix
- * prefix used in warnings
- */
- protected void setSubsystem(Reaction element, String value, String prefix) {
- 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);
- }
- }
-
- /**
- * Adds {@link MiriamType#EC} annotation to element.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * annotation identifier
- */
- protected void addEcMiriam(BioEntity element, String value) {
- element.addMiriamData(createMiriamData(MiriamType.EC, value));
- }
-
- /**
- * Adds {@link MiriamType#KEGG_COMPOUND} or {@link MiriamType#KEGG_REACTION}
- * annotation to element.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * annotation identifier
- * @param prefix
- * prefix used in warnings
- */
- protected void addKeggMiriam(BioEntity element, String value, String prefix) {
- if (value.startsWith("C")) {
- MiriamData md = createMiriamData(MiriamType.KEGG_COMPOUND, value);
- element.addMiriamData(md);
- } else if (value.startsWith("R")) {
- MiriamData md = createMiriamData(MiriamType.KEGG_REACTION, value);
- element.addMiriamData(md);
- } else if (value.startsWith("K")) {
- MiriamData md = createMiriamData(MiriamType.KEGG_ORTHOLOGY, value);
- element.addMiriamData(md);
- } else {
- logger.warn(prefix + "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
- }
- }
-
- /**
- * Sets {@link BioEntity#getFormula()}.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * value to set
- * @param prefix
- * prefix used in warnings
- */
- protected void setFormula(BioEntity element, String value, String prefix) {
- 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 + "\"");
- }
- }
-
- /**
- * Sets {@link BioEntity#getAbbreviation()}.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * value to set
- * @param prefix
- * prefix used in warnings
- */
- protected void setAbbreviation(BioEntity element, String value, String prefix) {
- 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);
- }
- }
-
- /**
- * Sets {@link Reaction#getMechanicalConfidenceScore()}.
- *
- * @param element
- * element where annotation should be added
- * @param value
- * value to set
- * @param prefix
- * prefix used in warnings
- */
- protected void setMcs(Reaction element, String value, String prefix) {
- 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 + "\"");
- }
- }
-
- /**
- * Sets definitions of parameters for given annotator.
- * @param paramDefs
- * definitions to be set
- */
- public void setParametersDefinitions(List<AnnotatorParamDefinition> paramDefs){
- this.paramsDefs = paramDefs;
- }
-
- /**
- * Adds parameter definition to the definitions of parameters for given annotator
- * @param paramDef
- * parameter definition to be added
- */
- public void addParameterDefinition(AnnotatorParamDefinition paramDef){
- this.paramsDefs.add(paramDef);
- }
-
- /**
- * Sets MiriamData.annotator to this annotator
- *
- * @param md
- * data for which the annotator is to be set
- */
- private void setAnnotator(MiriamData md){
- md.setAnnotator(this.getClass());
- }
-
- /**
- * Creates {@link MiriamData} and sets its annotator to this annotator
- * @return
- * created {@link MiriamData}
- */
- protected MiriamData createMiriamData(){
- MiriamData md = new MiriamData();
- setAnnotator(md);
- return md;
- }
-
- /**
- * Creates {@link MiriamData} and sets its annotator to this annotator
- * @param _md
- * {@link MiriamData} based on which the new {@link MiriamData} should be created
- * @return
- * created {@link MiriamData}
- */
- protected MiriamData createMiriamData(MiriamData _md){
- MiriamData md = new MiriamData(_md);
- setAnnotator(md);
- return md;
- }
-
- /**
- * Creates {@link MiriamData} and sets its annotator to this annotator
- * @param mt
- * {@link MiriamType} to be set
- * @param resource
- * resource to be set
- * @return
- * created {@link MiriamData}
- */
- protected MiriamData createMiriamData(MiriamType mt, String resource){
- MiriamData md = new MiriamData(mt, resource);
- setAnnotator(md);
- return md;
- }
-
- /**
- * Creates {@link MiriamData} and sets its annotator to this annotator
- * @param relationType
- * {@link MiriamRelationType} to be set
- * @param mt
- * {@link MiriamType} to be set
- * @param resource
- * resource to be set
- * @return
- * created {@link MiriamData}
- */
- protected MiriamData createMiriamData(MiriamRelationType relationType, MiriamType mt, String resource){
- MiriamData md = new MiriamData(relationType, mt, resource);
- setAnnotator(md);
- return md;
- }
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = Logger.getLogger(ElementAnnotator.class);
+
+ /**
+ * List of classes that can be annotated by this {@link IElementAnnotator
+ * annotator}.
+ */
+ private final List<Class<? extends BioEntity>> validClasses = new ArrayList<>();
+
+ /**
+ * Should be this annotator used as a default annotator.
+ */
+ private boolean isDefault = false;
+
+ /**
+ * Parameters which this annotator can be provided. Should be set in
+ * constructor.
+ */
+ protected List<AnnotatorParamDefinition> paramsDefs = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ *
+ * @param validClasses
+ * list of classes for which this annotator is valid
+ * @param isDefault
+ * {@link #isDefault}
+ * @param clazz
+ * type that defines this interface
+ */
+ @SuppressWarnings("unchecked")
+ public ElementAnnotator(Class<? extends CachableInterface> clazz, Class<?>[] validClasses, boolean isDefault) {
+ super(clazz);
+ for (Class<?> validClass : validClasses) {
+ if (BioEntity.class.isAssignableFrom(validClass)) {
+ addValidClass((Class<? extends BioEntity>) validClass);
+ } else {
+ throw new InvalidArgumentException("Cannot pass class of type: " + validClass + ". Only classes extending "
+ + BioEntity.class + " are accepted.");
+ }
+ }
+ this.isDefault = isDefault;
+ }
+
+ /**
+ * Annotate element.
+ *
+ * @param element
+ * object to be annotated
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating not related to data
+ */
+ public abstract void annotateElement(BioEntity element) throws AnnotatorException;
+
+ /**
+ * Annotate element using parameters.
+ *
+ * @param element
+ * object to be annotated
+ * @param parameters
+ * list of parameters passed to the annotator which is expected to be
+ * in the same order as its {@link this#parameterDefs}
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating not related to data
+ */
+ public void annotateElement(BioEntity element, List<UserAnnotatorsParam> parameters) throws AnnotatorException {
+ annotateElement(element);
+ }
+
+ /**
+ * Returns a list of all classes that can be annotated using this annotator.
+ *
+ * @return a list of all classes that can be annotated using this annotator
+ */
+ public List<Class<? extends BioEntity>> getValidClasses() {
+ return validClasses;
+ }
+
+ /**
+ * Returns <code>true</code> if this annotator can annotate the object given in
+ * the parameter.
+ *
+ * @param object
+ * object to be tested if can be annotated
+ * @return <code>true</code> if object can be annotated by this annotator,
+ * <code>false</code> otherwise
+ */
+ public boolean isAnnotatable(BioEntity object) {
+ Class<?> clazz = object.getClass();
+ for (Class<?> validClazz : getValidClasses()) {
+ if (validClazz.isAssignableFrom(clazz)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Adds a class to list of classes that can be annotated by the annotator.
+ *
+ * @param clazz
+ * class to add
+ */
+ private void addValidClass(Class<? extends BioEntity> clazz) {
+ validClasses.add(clazz);
+ }
+
+ /**
+ * Returns the common name that should be presented to user.
+ *
+ * @return the common name
+ */
+ public abstract String getCommonName();
+
+ /**
+ * Returns url to the external resource used for annotation.
+ *
+ * @return url
+ */
+ public abstract String getUrl();
+
+ /**
+ * Provides description of the extraction process for {@link ElementAnnotator}
+ * to be used in the front end.
+ *
+ * @return the description
+ */
+ public String getDescription() {
+ return "";
+ }
+
+ /**
+ * Provides description for {@link ElementAnnotator} and {@link MiriamType} pair
+ * to be used in the frontend.
+ *
+ * @param mt
+ * {@link MiriamType} annotated by this annotator.
+ * @return the description
+ */
+ public String getDescription(MiriamType mt) {
+ return "";
+ }
+
+ /**
+ * Provides description for {@link ElementAnnotator}, {@link MiriamType} and
+ * {@link MiriamRelationType} triplet to be used in the frontend.
+ *
+ * @param mt
+ * {@link MiriamType} annotated by this annotator
+ * @param relationType
+ * {@link MiriamRelationType} annotated by this annotator.
+ * @return the description
+ */
+ public String getDescription(MiriamType mt, MiriamRelationType relationType) {
+ return "";
+ }
+
+ /**
+ * Returns list with definitions of the parameters available for this annotator.
+ *
+ * @return the parameters {@link AnnotatorParamDefinition} list
+ */
+ public Collection<AnnotatorParamDefinition> getParametersDefinitions() {
+ return paramsDefs;
+ }
+
+ /**
+ * Returns <code>true</code> if this annotator can annotate the object of given
+ * class type.
+ *
+ * @param clazz
+ * class to be tested if can be annotated
+ * @return <code>true</code> if class can be annotated by this annotator,
+ * <code>false</code> otherwise
+ */
+ public boolean isAnnotatable(Class<?> clazz) {
+ for (Class<?> clazz2 : validClasses) {
+ if (clazz2.isAssignableFrom(clazz)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ *
+ * @return {@link #isDefault}
+ */
+ public boolean isDefault() {
+ 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) {
+ 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.
+ *
+ * @param element
+ * element where we change data
+ * @param synonyms
+ * new synonyms list
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setSynonyms(BioEntity element, Collection<String> synonyms, String prefix) {
+ if (element.getSynonyms() == null || element.getSynonyms().size() == 0) {
+ List<String> sortedSynonyms = new ArrayList<>();
+ sortedSynonyms.addAll(synonyms);
+ Collections.sort(sortedSynonyms);
+
+ element.setSynonyms(sortedSynonyms);
+ } else {
+ logger.warn(prefix + "Synonyms don't match: \"" + synonyms + "\", \"" + element.getSynonyms() + "\"");
+ }
+ }
+
+ /**
+ * Sets name to the element.
+ *
+ * @param element
+ * element where we change data
+ * @param name
+ * new name
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setFullName(Element element, String name, String prefix) {
+ 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() + "\"");
+ }
+ }
+
+ /**
+ * Adds description to {@link BioEntity#getNotes()}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param description
+ * value to set
+ */
+ protected void setDescription(BioEntity element, String 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);
+ }
+ }
+ }
+
+ /**
+ * Adds {@link MiriamType#HMDB} annotation to element.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * annotation identifier
+ */
+ protected void addHmdbMiriam(BioEntity 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));
+ }
+ }
+
+ /**
+ * Sets {@link CellDesignerChemical#inChI}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param prefix
+ * prefix used in warnings
+ * @param value
+ * value to set
+ */
+ protected void setInchi(Chemical element, String value, String prefix) {
+ 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);
+ }
+
+ }
+
+ /**
+ * Sets {@link CellDesignerChemical#inChIKey}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param prefix
+ * prefix used in warnings
+ * @param value
+ * value to set
+ */
+ protected void setInchiKey(Chemical element, String value, String prefix) {
+ 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);
+ }
+
+ }
+
+ /**
+ * Sets {@link CellDesignerChemical#smiles}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param prefix
+ * prefix used in warnings
+ * @param value
+ * value to set
+ */
+ protected void setSmile(Chemical element, String value, String prefix) {
+ 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);
+ }
+
+ }
+
+ /**
+ * Adds {@link MiriamType#CHEBI} annotation to element.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * annotation identifier
+ */
+ protected void addChebiMiriam(BioEntity 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));
+ }
+ }
+
+ /**
+ * Sets {@link Species#charge}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * value to set
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setCharge(Species element, String value, String prefix) {
+ 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);
+ }
+
+ }
+
+ /**
+ * Adds {@link MiriamType#PUBCHEM} annotation to element.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * annotation identifier
+ */
+ protected void addPubchemMiriam(BioEntity element, String value) {
+ element.addMiriamData(createMiriamData(MiriamType.PUBCHEM, value));
+ }
+
+ /**
+ * Adds {@link MiriamType#COG} annotation to element.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * annotation identifier
+ */
+ protected void addCogMiriam(BioEntity element, String value) {
+ element.addMiriamData(createMiriamData(MiriamType.COG, value));
+ }
+
+ /**
+ * Sets {@link Reaction#subsystem}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * value to set
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setSubsystem(Reaction element, String value, String prefix) {
+ 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);
+ }
+ }
+
+ /**
+ * Adds {@link MiriamType#EC} annotation to element.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * annotation identifier
+ */
+ protected void addEcMiriam(BioEntity element, String value) {
+ element.addMiriamData(createMiriamData(MiriamType.EC, value));
+ }
+
+ /**
+ * Adds {@link MiriamType#KEGG_COMPOUND} or {@link MiriamType#KEGG_REACTION}
+ * annotation to element.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * annotation identifier
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void addKeggMiriam(BioEntity element, String value, String prefix) {
+ if (value.startsWith("C")) {
+ MiriamData md = createMiriamData(MiriamType.KEGG_COMPOUND, value);
+ element.addMiriamData(md);
+ } else if (value.startsWith("R")) {
+ MiriamData md = createMiriamData(MiriamType.KEGG_REACTION, value);
+ element.addMiriamData(md);
+ } else if (value.startsWith("K")) {
+ MiriamData md = createMiriamData(MiriamType.KEGG_ORTHOLOGY, value);
+ element.addMiriamData(md);
+ } else {
+ logger.warn(
+ prefix + "Unknown Kegg identifier type (only Kegg compounds and reactions are supported): \"" + value + "\"");
+ }
+ }
+
+ protected void addChemspider(BioEntity element, String value) {
+ MiriamData md = createMiriamData(MiriamType.CHEMSPIDER, value);
+ element.addMiriamData(md);
+ }
+
+ protected void addWikipedia(BioEntity element, String value) {
+ MiriamData md = createMiriamData(MiriamType.WIKIPEDIA, value);
+ element.addMiriamData(md);
+ }
+
+ protected void addCas(BioEntity element, String value) {
+ MiriamData md = createMiriamData(MiriamType.CAS, value);
+ element.addMiriamData(md);
+ }
+
+ /**
+ * Sets {@link BioEntity#getFormula()}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * value to set
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setFormula(BioEntity element, String value, String prefix) {
+ 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 + "\"");
+ }
+ }
+
+ /**
+ * Sets {@link BioEntity#getAbbreviation()}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * value to set
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setAbbreviation(BioEntity element, String value, String prefix) {
+ 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);
+ }
+ }
+
+ /**
+ * Sets {@link Reaction#getMechanicalConfidenceScore()}.
+ *
+ * @param element
+ * element where annotation should be added
+ * @param value
+ * value to set
+ * @param prefix
+ * prefix used in warnings
+ */
+ protected void setMcs(Reaction element, String value, String prefix) {
+ 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 + "\"");
+ }
+ }
+
+ /**
+ * Sets definitions of parameters for given annotator.
+ *
+ * @param paramDefs
+ * definitions to be set
+ */
+ public void setParametersDefinitions(List<AnnotatorParamDefinition> paramDefs) {
+ this.paramsDefs = paramDefs;
+ }
+
+ /**
+ * Adds parameter definition to the definitions of parameters for given
+ * annotator
+ *
+ * @param paramDef
+ * parameter definition to be added
+ */
+ public void addParameterDefinition(AnnotatorParamDefinition paramDef) {
+ this.paramsDefs.add(paramDef);
+ }
+
+ /**
+ * Sets MiriamData.annotator to this annotator
+ *
+ * @param md
+ * data for which the annotator is to be set
+ */
+ private void setAnnotator(MiriamData md) {
+ md.setAnnotator(this.getClass());
+ }
+
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ *
+ * @return created {@link MiriamData}
+ */
+ protected MiriamData createMiriamData() {
+ MiriamData md = new MiriamData();
+ setAnnotator(md);
+ return md;
+ }
+
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ *
+ * @param _md
+ * {@link MiriamData} based on which the new {@link MiriamData} should
+ * be created
+ * @return created {@link MiriamData}
+ */
+ protected MiriamData createMiriamData(MiriamData _md) {
+ MiriamData md = new MiriamData(_md);
+ setAnnotator(md);
+ return md;
+ }
+
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ *
+ * @param mt
+ * {@link MiriamType} to be set
+ * @param resource
+ * resource to be set
+ * @return created {@link MiriamData}
+ */
+ protected MiriamData createMiriamData(MiriamType mt, String resource) {
+ MiriamData md = new MiriamData(mt, resource);
+ setAnnotator(md);
+ return md;
+ }
+
+ /**
+ * Creates {@link MiriamData} and sets its annotator to this annotator
+ *
+ * @param relationType
+ * {@link MiriamRelationType} to be set
+ * @param mt
+ * {@link MiriamType} to be set
+ * @param resource
+ * resource to be set
+ * @return created {@link MiriamData}
+ */
+ protected MiriamData createMiriamData(MiriamRelationType relationType, MiriamType mt, String resource) {
+ MiriamData md = new MiriamData(relationType, mt, resource);
+ setAnnotator(md);
+ return md;
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
index c006d49ed4..8cf0fd072e 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
@@ -35,244 +35,305 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class ReconAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Address of annotation rest service for elements.
- */
- private static final String ELEMENT_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/metabolites/?page_size=10000&format=json&search=";
+ /**
+ * Address of annotation rest service for elements.
+ */
+ private static final String ELEMENT_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/metabolites/?page_size=10000&format=json&search=";
- /**
- * Address of annotation rest service for reactions.
- */
- private static final String REACTION_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
+ /**
+ * Address of annotation rest service for reactions.
+ */
+ private static final String REACTION_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
- /**
- * Class used for some simple operations on {@link BioEntity} elements.
- */
- private ElementUtils elementUtils = new ElementUtils();
+ /**
+ * Class used for some simple operations on {@link BioEntity} elements.
+ */
+ private ElementUtils elementUtils = new ElementUtils();
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String name;
- String result = null;
- if (query instanceof String) {
- name = (String) query;
- if (name.startsWith("http")) {
- try {
- result = getWebPageContent(name);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- return result;
- }
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String name;
+ String result = null;
+ if (query instanceof String) {
+ name = (String) query;
+ if (name.startsWith("http")) {
+ try {
+ result = getWebPageContent(name);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ReconAnnotator.class);
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ReconAnnotator.class);
- /**
- * Default constructor.
- */
- public ReconAnnotator() {
- super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false);
- }
+ /**
+ * Default constructor.
+ */
+ public ReconAnnotator() {
+ super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false);
+ }
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
- EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
- Logger.getRootLogger().addAppender(appender);
- try {
- SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id");
- smallMoleculeAlias.setName("h2o");
- annotateElement(smallMoleculeAlias);
- status.setStatus(ExternalServiceStatusType.OK);
- if (smallMoleculeAlias.getMiriamData().size() == 0) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else if (appender.getWarnings().size() > 0) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- Logger.getRootLogger().removeAppender(appender);
- this.setCache(cacheCopy);
- return status;
- }
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ Logger.getRootLogger().addAppender(appender);
+ try {
+ SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id");
+ smallMoleculeAlias.setName("h2o");
+ annotateElement(smallMoleculeAlias);
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (smallMoleculeAlias.getMiriamData().size() == 0) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else if (appender.getWarnings().size() > 0) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ Logger.getRootLogger().removeAppender(appender);
+ this.setCache(cacheCopy);
+ return status;
+ }
- @Override
- public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
- if (isAnnotatable(annotatedObject)) {
- String id = annotatedObject.getAbbreviation();
- if (id == null || id.isEmpty()) {
- id = annotatedObject.getName();
- }
- if (id.indexOf("[") > 0) {
- id = id.substring(0, id.indexOf("["));
- }
- if (id.indexOf(" ") >= 0) {
- String[] tmp = id.split(" ");
- id = tmp[tmp.length - 1];
- }
- String url = null;
- if (annotatedObject instanceof Element) {
- url = ELEMENT_ANNOTATION_URL_PREFIX + id;
- } else if (annotatedObject instanceof Reaction) {
- url = REACTION_ANNOTATION_URL_PREFIX + id;
- } else {
- logger.warn("Unknown class type: " + annotatedObject.getClass());
- return;
- }
- try {
- String content = getWebPageContent(url);
+ @Override
+ public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
+ if (isAnnotatable(annotatedObject)) {
+ String id = annotatedObject.getAbbreviation();
+ if (id == null || id.isEmpty()) {
+ id = annotatedObject.getName();
+ }
+ if (id.indexOf("[") > 0) {
+ id = id.substring(0, id.indexOf("["));
+ }
+ if (id.indexOf(" ") >= 0) {
+ String[] tmp = id.split(" ");
+ id = tmp[tmp.length - 1];
+ }
+ String url = null;
+ if (annotatedObject instanceof Element) {
+ url = ELEMENT_ANNOTATION_URL_PREFIX + id;
+ } else if (annotatedObject instanceof Reaction) {
+ url = REACTION_ANNOTATION_URL_PREFIX + id;
+ } else {
+ logger.warn("Unknown class type: " + annotatedObject.getClass());
+ return;
+ }
+ try {
+ String content = getWebPageContent(url);
- String prefix = elementUtils.getElementTag(annotatedObject, this);
- if (!content.isEmpty()) {
+ String prefix = elementUtils.getElementTag(annotatedObject, this);
+ if (!content.isEmpty()) {
- JsonElement jelement = new JsonParser().parse(content);
- JsonObject jobject = jelement.getAsJsonObject();
- if (jobject.get("results").getAsJsonArray().size() > 0) {
- jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject();
+ JsonElement jelement = new JsonParser().parse(content);
+ JsonObject jobject = jelement.getAsJsonObject();
+ if (jobject.get("results").getAsJsonArray().size() > 0) {
+ jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject();
- for (Entry<String, JsonElement> entry : jobject.entrySet()) {
- String key = entry.getKey();
- String value = null;
- if (!entry.getValue().isJsonNull()) {
- // if (entry.getValue().isJsonPrimitive()) {
- value = entry.getValue().getAsString().trim();
- }
- if (value == null || value.isEmpty()) {
- continue;
- }
+ for (Entry<String, JsonElement> entry : jobject.entrySet()) {
+ String key = entry.getKey();
+ String value = null;
+ if (!entry.getValue().isJsonNull()) {
+ // if (entry.getValue().isJsonPrimitive()) {
+ value = entry.getValue().getAsString().trim();
+ }
+ if (value == null || value.isEmpty()) {
+ continue;
+ }
- boolean unknown = false;
- if (key.equals("url")) {
- continue;
- } else if (key.equals("rxn_id")) {
- continue;
- } else if (key.equals("abbreviation")) {
- setAbbreviation(annotatedObject, value, prefix);
- } else if (key.equals("description")) {
- setDescription(annotatedObject, value);
- } else if (key.equals("formula")) {
- setFormula(annotatedObject, value, prefix);
- } else if (key.equals("reversible")) {
- continue;
- } else if (key.equals("mcs")) {
- if (annotatedObject instanceof Reaction) {
- setMcs((Reaction) annotatedObject, value, prefix);
- } else {
- unknown = true;
- }
- } else if (key.equals("notes")) {
- setDescription(annotatedObject, value);
- } else if (key.equals("ecnumber")) {
- addEcMiriam(annotatedObject, value);
- } else if (key.equals("ref")) {
- continue;
- } else if (key.equals("lastModified")) {
- continue;
- } else if (key.equals("met_id")) {
- continue;
- } else if (key.equals("csecoida")) {
- continue;
- } else if (key.equals("chargedFormula")) {
- setFormula(annotatedObject, value, prefix);
- } else if (key.equals("charge")) {
- if (annotatedObject instanceof Species) {
- setCharge((Species) annotatedObject, value, prefix);
- } else {
- unknown = true;
- }
- } else if (key.equals("inchiString")) {
- if (annotatedObject instanceof Chemical) {
- setInchi((Chemical) annotatedObject, value, prefix);
- } else {
- unknown = true;
- }
- } else if (key.equals("cheBlId")) {
- addChebiMiriam(annotatedObject, value);
- } else if (key.equals("subsystem")) {
- if (annotatedObject instanceof Reaction) {
- setSubsystem((Reaction) annotatedObject, value, prefix);
- } else {
- unknown = true;
- }
- } else if (key.equals("keggId")) {
- addKeggMiriam(annotatedObject, value, prefix);
- } else if (key.equals("fullName")) {
- if (annotatedObject instanceof Element) {
- setFullName((Element) annotatedObject, value, prefix);
- } else {
- unknown = true;
- }
- } else if (key.equals("keggorthology")) {
- addKeggMiriam(annotatedObject, value, prefix);
- } else if (key.equals("pubChemId")) {
- addPubchemMiriam(annotatedObject, value);
- } else if (key.equals("hmdb")) {
- addHmdbMiriam(annotatedObject, value);
- } else if (key.equals("cog")) {
- addCogMiriam(annotatedObject, value);
- } else if (key.equals("synonyms")) {
- List<String> synonyms = new ArrayList<>();
- for (String str : value.split(",")) {
- synonyms.add(str);
- }
- setSynonyms(annotatedObject, synonyms, prefix);
- } else if (key.equals("pdmapName")) {
- // for now we skip it...
- continue;
- } else if (key.equals("reconMap")) {
- // for now we don't handle it
- continue;
- } else {
- unknown = true;
- }
- if (unknown) {
- logger.warn(prefix + "Unknown field in recon annotation: \"" + key + "\" (value: " + value + ")");
- }
- }
- } else {
- logger.warn(prefix + "No recon annotations \"" + id + "\"");
- }
- } else {
- logger.warn(prefix + "No recon annotations \"" + id + "\"");
- }
- } catch (IOException e) {
- throw new AnnotatorException(e);
- }
- }
- }
+ boolean unknown = false;
+ if (key.equals("url")) {
+ continue;
+ } else if (key.equals("rxn_id")) {
+ continue;
+ } else if (key.equals("abbreviation")) {
+ setAbbreviation(annotatedObject, value, prefix);
+ } else if (key.equals("description")) {
+ setDescription(annotatedObject, value);
+ } else if (key.equals("formula")) {
+ setFormula(annotatedObject, value, prefix);
+ } else if (key.equals("reversible")) {
+ continue;
+ } else if (key.equals("mcs")) {
+ if (annotatedObject instanceof Reaction) {
+ setMcs((Reaction) annotatedObject, value, prefix);
+ } else {
+ unknown = true;
+ }
+ } else if (key.equals("notes")) {
+ setDescription(annotatedObject, value);
+ } else if (key.equals("ecnumber")) {
+ addEcMiriam(annotatedObject, value);
+ } else if (key.equals("ref")) {
+ continue;
+ } else if (key.equals("lastModified")) {
+ continue;
+ } else if (key.equals("met_id")) {
+ continue;
+ } else if (key.equals("csecoida")) {
+ continue;
+ } else if (key.equals("chargedFormula")) {
+ setFormula(annotatedObject, value, prefix);
+ } else if (key.equals("charge")) {
+ if (annotatedObject instanceof Species) {
+ setCharge((Species) annotatedObject, value, prefix);
+ } else {
+ unknown = true;
+ }
+ } else if (key.equals("inchiString")) {
+ if (annotatedObject instanceof Chemical) {
+ setInchi((Chemical) annotatedObject, value, prefix);
+ } else {
+ unknown = true;
+ }
+ } else if (key.equals("cheBlId")) {
+ addChebiMiriam(annotatedObject, value);
+ } else if (key.equals("subsystem")) {
+ if (annotatedObject instanceof Reaction) {
+ setSubsystem((Reaction) annotatedObject, value, prefix);
+ } else {
+ unknown = true;
+ }
+ } else if (key.equals("keggId")) {
+ addKeggMiriam(annotatedObject, value, prefix);
+ } else if (key.equals("fullName")) {
+ if (annotatedObject instanceof Element) {
+ setFullName((Element) annotatedObject, value, prefix);
+ } else {
+ unknown = true;
+ }
+ } else if (key.equals("keggorthology")) {
+ addKeggMiriam(annotatedObject, value, prefix);
+ } else if (key.equals("pubChemId")) {
+ addPubchemMiriam(annotatedObject, value);
+ } else if (key.equals("hmdb")) {
+ addHmdbMiriam(annotatedObject, value);
+ } else if (key.equals("cog")) {
+ addCogMiriam(annotatedObject, value);
+ } else if (key.equals("synonyms")) {
+ List<String> synonyms = new ArrayList<>();
+ for (String str : value.split(",")) {
+ synonyms.add(str);
+ }
+ setSynonyms(annotatedObject, synonyms, prefix);
+ } else if (key.equals("pdmapName")) {
+ // for now we skip it...
+ continue;
+ } else if (key.equals("reconMap")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("reconMap3")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("massbalance")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("isHuman")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("isMicrobe")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("iupac")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("avgmolweight")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("monoisotopicweight")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("miriam")) {
+ addMiriam(annotatedObject, value, prefix);
+ } else if (key.equals("biggId")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("lmId")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("hepatonetId")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("inchiKey")) {
+ if (annotatedObject instanceof Chemical) {
+ setInchiKey((Chemical) annotatedObject, value, prefix);
+ }
+ } else if (key.equals("smile")) {
+ if (annotatedObject instanceof Chemical) {
+ setSmile((Chemical) annotatedObject, value, prefix);
+ }
+ } else if (key.equals("metanetx")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("seed")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("food_db")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("chemspider")) {
+ addChemspider(annotatedObject, value);
+ } else if (key.equals("wikipedia")) {
+ addWikipedia(annotatedObject, value);
+ } else if (key.equals("metlin")) {
+ // for now we don't handle it
+ continue;
+ } else if (key.equals("casRegistry")) {
+ addCas(annotatedObject, value);
+ } else if (key.equals("epa_id")) {
+ // for now we don't handle it
+ continue;
+ } else {
+ unknown = true;
+ }
+ if (unknown) {
+ logger.warn(prefix + "Unknown field in recon annotation: \"" + key + "\" (value: " + value + ")");
+ }
+ }
+ } else {
+ logger.warn(prefix + "No recon annotations \"" + id + "\"");
+ }
+ } else {
+ logger.warn(prefix + "No recon annotations \"" + id + "\"");
+ }
+ } catch (IOException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ }
- @Override
- public String getCommonName() {
- return "Recon annotator";
- }
+ @Override
+ public String getCommonName() {
+ return "Recon annotator";
+ }
- @Override
- public String getUrl() {
- return "http://humanmetabolism.org/";
- }
+ @Override
+ public String getUrl() {
+ return "http://humanmetabolism.org/";
+ }
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
}
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 b70fe82bdf..3fe3c8a56a 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
@@ -32,320 +32,321 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
public class ReconAnnotatorTest extends AnnotationTestFunctions {
- Logger logger = Logger.getLogger(ReconAnnotatorTest.class);
- @Autowired
- ReconAnnotator reconAnnotator;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAnnotateReaction() throws Exception {
- try {
- Reaction reaction = new Reaction();
- reaction.setAbbreviation("P5CRm");
- reconAnnotator.annotateElement(reaction);
- assertTrue("No new annotations from recon db imported", reaction.getMiriamData().size() > 0);
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotating_O16G2e_Reaction() throws Exception {
- try {
- Reaction reaction = new Reaction();
- reaction.setName("O16G2e");
- reconAnnotator.annotateElement(reaction);
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSpeciesAnnotationWithInvalidResponse() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = reconAnnotator.getCache();
- try {
- Ion ion = new Ion("id");
- ion.setName("O16G2e");
-
- // exclude first cached value
- reconAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- reconAnnotator.setWebPageDownloader(mockDownloader);
-
- reconAnnotator.annotateElement(ion);
- assertEquals(1, getWarnings().size());
- assertTrue(getWarnings().get(0).getMessage().toString().contains("No recon annotations"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- reconAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testSpeciesAnnotationWithReactionResponse() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = reconAnnotator.getCache();
- try {
- Ion ion = new Ion("id");
- ion.setName("O16G2e");
-
- // exclude first cached value
- reconAnnotator.setCache(null);
-
- String response = super.readFile("testFiles/annotation/recon_reaction_response.json");
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
- reconAnnotator.setWebPageDownloader(mockDownloader);
-
- 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;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- reconAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testReactionAnnotationWithChemicalResponse() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = reconAnnotator.getCache();
- try {
- Reaction reaction = new Reaction();
- reaction.setName("nad[m]");
-
- // exclude first cached value
- reconAnnotator.setCache(null);
-
- String response = super.readFile("testFiles/annotation/recon_chemical_response.json");
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
- reconAnnotator.setWebPageDownloader(mockDownloader);
-
- 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;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- reconAnnotator.setCache(originalCache);
- }
- }
-
- @Test
- public void testAnnotateUnknownElement() throws Exception {
- try {
- BioEntity obj = Mockito.mock(BioEntity.class);
- when(obj.getName()).thenReturn("O16G2e");
-
- ReconAnnotator tweakedReconAnnotator = Mockito.spy(reconAnnotator);
- doReturn(true).when(tweakedReconAnnotator).isAnnotatable(any(BioEntity.class));
-
- tweakedReconAnnotator.annotateElement(obj);
- assertEquals(1, getWarnings().size());
- assertTrue(getWarnings().get(0).getMessage().toString().contains("Unknown class type"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotatingWithParentehesis() throws Exception {
- try {
- Reaction reaction = new Reaction();
- reaction.setName("gm2_hs[g]");
- reconAnnotator.annotateElement(reaction);
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotatingWithWhitespace() throws Exception {
- try {
- Reaction reaction = new Reaction();
- reaction.setName("NDPK4m ");
- reconAnnotator.annotateElement(reaction);
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateElement() throws Exception {
- try {
- SimpleMolecule smallMolecule = new SimpleMolecule("id");
- smallMolecule.setAbbreviation("h2o");
- reconAnnotator.annotateElement(smallMolecule);
- assertTrue("No new annotations from recon db imported", smallMolecule.getMiriamData().size() > 0);
- assertEquals(0, getWarnings().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateElement2() throws Exception {
- try {
- Species smallMolecule = new SimpleMolecule("id");
- smallMolecule.setAbbreviation("P5CRm");
- reconAnnotator.annotateElement(smallMolecule);
- assertEquals(0, smallMolecule.getMiriamData().size());
- assertFalse(getWarnings().size() == 0);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery() throws Exception {
- try {
- reconAnnotator.refreshCacheQuery("invalid_query");
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshInvalidCacheQuery2() throws Exception {
- try {
- reconAnnotator.refreshCacheQuery(new Object());
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- assertTrue(e.getMessage().contains("Don't know what to do"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshCacheQuery() throws Exception {
- try {
- String res = reconAnnotator.refreshCacheQuery("http://google.pl/");
- assertNotNull(res);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, reconAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- reconAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, reconAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangeStatus() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("{\"results\":[{}]}");
- reconAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, reconAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangeStatus2() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("{\"results\":[{\"keggId\":\"C00001\",\"xxx\":\"yyy\"}]}");
- reconAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, reconAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testRefreshCacheQueryNotAvailable() throws Exception {
- WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
- GeneralCacheInterface originalCache = reconAnnotator.getCache();
- try {
- // exclude first cached value
- reconAnnotator.setCache(null);
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
- reconAnnotator.setWebPageDownloader(mockDownloader);
- reconAnnotator.refreshCacheQuery("http://google.pl/");
- fail("Exception expected");
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- reconAnnotator.setWebPageDownloader(downloader);
- reconAnnotator.setCache(originalCache);
- }
- }
+ Logger logger = Logger.getLogger(ReconAnnotatorTest.class);
+ @Autowired
+ ReconAnnotator reconAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotateReaction() throws Exception {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.setAbbreviation("P5CRm");
+ reconAnnotator.annotateElement(reaction);
+ assertTrue("No new annotations from recon db imported", reaction.getMiriamData().size() > 0);
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotating_O16G2e_Reaction() throws Exception {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.setName("O16G2e");
+ reconAnnotator.annotateElement(reaction);
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSpeciesAnnotationWithInvalidResponse() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = reconAnnotator.getCache();
+ try {
+ Ion ion = new Ion("id");
+ ion.setName("O16G2e");
+
+ // exclude first cached value
+ reconAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+
+ reconAnnotator.annotateElement(ion);
+ assertEquals(1, getWarnings().size());
+ assertTrue(getWarnings().get(0).getMessage().toString().contains("No recon annotations"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ reconAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testSpeciesAnnotationWithReactionResponse() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = reconAnnotator.getCache();
+ try {
+ Ion ion = new Ion("id");
+ ion.setName("O16G2e");
+
+ // exclude first cached value
+ reconAnnotator.setCache(null);
+
+ String response = super.readFile("testFiles/annotation/recon_reaction_response.json");
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+
+ 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;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ reconAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testReactionAnnotationWithChemicalResponse() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = reconAnnotator.getCache();
+ try {
+ Reaction reaction = new Reaction();
+ reaction.setName("nad[m]");
+
+ // exclude first cached value
+ reconAnnotator.setCache(null);
+
+ String response = super.readFile("testFiles/annotation/recon_chemical_response.json");
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn(response);
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+
+ 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;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ reconAnnotator.setCache(originalCache);
+ }
+ }
+
+ @Test
+ public void testAnnotateUnknownElement() throws Exception {
+ try {
+ BioEntity obj = Mockito.mock(BioEntity.class);
+ when(obj.getName()).thenReturn("O16G2e");
+
+ ReconAnnotator tweakedReconAnnotator = Mockito.spy(reconAnnotator);
+ doReturn(true).when(tweakedReconAnnotator).isAnnotatable(any(BioEntity.class));
+
+ tweakedReconAnnotator.annotateElement(obj);
+ assertEquals(1, getWarnings().size());
+ assertTrue(getWarnings().get(0).getMessage().toString().contains("Unknown class type"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotatingWithParentehesis() throws Exception {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.setName("gm2_hs[g]");
+ reconAnnotator.annotateElement(reaction);
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotatingWithWhitespace() throws Exception {
+ try {
+ Reaction reaction = new Reaction();
+ reaction.setName("NDPK4m ");
+ reconAnnotator.annotateElement(reaction);
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateElement() throws Exception {
+ try {
+ SimpleMolecule smallMolecule = new SimpleMolecule("id");
+ smallMolecule.setAbbreviation("h2o");
+ reconAnnotator.annotateElement(smallMolecule);
+ assertTrue("No new annotations from recon db imported", smallMolecule.getMiriamData().size() > 0);
+ assertEquals(0, getWarnings().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateElement2() throws Exception {
+ try {
+ Species smallMolecule = new SimpleMolecule("id");
+ smallMolecule.setAbbreviation("P5CRm");
+ reconAnnotator.annotateElement(smallMolecule);
+ assertEquals(0, smallMolecule.getMiriamData().size());
+ assertFalse(getWarnings().size() == 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery() throws Exception {
+ try {
+ reconAnnotator.refreshCacheQuery("invalid_query");
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidCacheQuery2() throws Exception {
+ try {
+ reconAnnotator.refreshCacheQuery(new Object());
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ assertTrue(e.getMessage().contains("Don't know what to do"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQuery() throws Exception {
+ try {
+ String res = reconAnnotator.refreshCacheQuery("http://google.pl/");
+ assertNotNull(res);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, reconAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, reconAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangeStatus() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("{\"results\":[{}]}");
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, reconAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangeStatus2() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("{\"results\":[{\"keggId\":\"C00001\",\"xxx\":\"yyy\"}]}");
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, reconAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testRefreshCacheQueryNotAvailable() throws Exception {
+ WebPageDownloader downloader = reconAnnotator.getWebPageDownloader();
+ GeneralCacheInterface originalCache = reconAnnotator.getCache();
+ try {
+ // exclude first cached value
+ reconAnnotator.setCache(null);
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenThrow(new IOException());
+ reconAnnotator.setWebPageDownloader(mockDownloader);
+ reconAnnotator.refreshCacheQuery("http://google.pl/");
+ fail("Exception expected");
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ reconAnnotator.setWebPageDownloader(downloader);
+ reconAnnotator.setCache(originalCache);
+ }
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index b39394717c..df27800781 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -674,7 +674,7 @@ public enum MiriamType {
*
* @param generalIdentifier
* identifier in the format NAME:IDENTIFIER. Where NAME is the name
- * from {@link MiriamType#commonName} and IDENTIFIER is reasource
+ * from {@link MiriamType#commonName} and IDENTIFIER is resource
* identifier.
* @return {@link MiriamData} representing generalIdentifier, when identifier is
* invalid InvalidArgumentException is thrown
--
GitLab