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 a95985e33938f17feadd1366c4d683bb82a491dd..99b71fdd1085e3955d2fd206b883390e3f8cd96a 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
@@ -1,5 +1,7 @@
package lcsb.mapviewer.annotation.services.annotators;
+import java.net.MalformedURLException;
+import java.net.URL;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedList;
@@ -7,6 +9,7 @@ import java.util.List;
import java.util.Queue;
import java.util.Set;
+import javax.xml.namespace.QName;
import javax.xml.ws.WebServiceException;
import org.apache.log4j.Logger;
@@ -44,464 +47,466 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.StarsCategory;
*/
public class ChebiAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * What is the maximum number of results that should be retrieved from chebi
- * API.
- */
- static final int MAX_SEARCH_RESULTS_FROM_CHEBI_API = 50;
-
- /**
- * Prefix used for entries identified by chebi id.
- */
- public static final String ID_PREFIX = "id: ";
-
- /**
- * Prefix used for ontology list for single chebi id.
- */
- static final String ONTOLOGY_PREFIX = "ontology: ";
-
- /**
- * Length of the prefix used for entries identified by chebi id.
- */
- private static final int ID_PREFIX_LENGTH = ID_PREFIX.length();
-
- /**
- * Prefix used for entries identified by name.
- */
- private static final String NAME_PREFIX = "name: ";
-
- /**
- * Length of the prefix used for entries identified by name.
- */
- private static final int NAME_PREFIX_LENGTH = NAME_PREFIX.length();
-
- /**
- * Class used for some simple operations on {@link BioEntity} elements.
- */
- private ElementUtils elementUtils = new ElementUtils();
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith(ID_PREFIX)) {
- String id = name.substring(ID_PREFIX_LENGTH);
- result = chebiSerializer.objectToString(getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, id)));
- } else if (name.startsWith(ONTOLOGY_PREFIX)) {
- String id = name.substring(ONTOLOGY_PREFIX.length());
- result = miriamListToStringList(getOntologyChebiIdsForChebi(new MiriamData(MiriamType.CHEBI, id)));
- } else if (name.startsWith(NAME_PREFIX)) {
- name = name.substring(NAME_PREFIX_LENGTH);
- MiriamData md = getChebiForChebiName(name);
- if (md != null) {
- result = md.getResource();
- }
- } 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());
- }
- } catch (ChebiSearchException e) {
- throw new SourceNotAvailable(e);
- }
-
- return result;
- }
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ChebiAnnotator.class);
-
- /**
- * Client to chebi API.
- */
- private ChebiWebServiceClient client = null;
-
- /**
- * Object that allows to serialize {@link Chebi} elements into xml string and
- * deserialize xml into {@link Chebi} objects.
- */
- private XmlSerializer<Chebi> chebiSerializer;
-
- /**
- * Default constructor. Initializes structures used for transforming
- * {@link Chebi} from/to xml.
- */
- public ChebiAnnotator() {
- super(ChebiAnnotator.class, new Class[] { Chemical.class }, true);
- chebiSerializer = new XmlSerializer<>(Chebi.class);
- }
-
- /**
- * Returns {@link MiriamData} for given chebi name.
- *
- * @param name
- * name of the entry in chebi database.
- * @return {@link MiriamData} entry for given chebi name
- * @throws ChebiSearchException
- * thrown when there is aproblem with accessing data from external
- * chebi database
- */
- public MiriamData getChebiForChebiName(String name) throws ChebiSearchException {
- if (name == null) {
- return null;
- }
- // Japanese people use strange dash symbol
- name = name.replace("−", "-").toLowerCase().trim();
-
- String id = getCacheValue("name: " + name);
- if (id != null) {
- return new MiriamData(MiriamType.CHEBI, id);
- }
- try {
- ChebiWebServiceClient client = getClient();
-
- LiteEntityList entities = client.getLiteEntity(name, SearchCategory.CHEBI_NAME, MAX_SEARCH_RESULTS_FROM_CHEBI_API, StarsCategory.ALL);
- List<LiteEntity> resultList = entities.getListElement();
-
- for (LiteEntity liteEntity : resultList) {
- Entity entity = client.getCompleteEntity(liteEntity.getChebiId());
- String chebiName = entity.getChebiAsciiName();
- if (chebiName.trim().equalsIgnoreCase(name)) {
- setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
- }
- for (DataItem dataItem : entity.getFormulae()) {
- String synonym = dataItem.getData();
- if (synonym.trim().equalsIgnoreCase(name)) {
- setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
- }
- }
- for (DataItem dataItem : entity.getSynonyms()) {
- String synonym = dataItem.getData();
- if (synonym.trim().equalsIgnoreCase(name)) {
- setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
- }
- }
- }
- entities = client.getLiteEntity(name, SearchCategory.ALL, MAX_SEARCH_RESULTS_FROM_CHEBI_API, StarsCategory.ALL);
- resultList = entities.getListElement();
- for (LiteEntity liteEntity : resultList) {
- Entity entity = client.getCompleteEntity(liteEntity.getChebiId());
- for (DataItem dataItem : entity.getFormulae()) {
- String formula = dataItem.getData();
- if (formula.trim().equalsIgnoreCase(name)) {
- setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
- }
- }
- for (DataItem dataItem : entity.getSynonyms()) {
- String synonym = dataItem.getData();
- if (synonym.trim().equalsIgnoreCase(name)) {
- setCacheValue("name: " + name, entity.getChebiId());
- return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
- }
- }
- }
- } catch (ChebiWebServiceFault_Exception e) {
- throw new ChebiSearchException("Problem with chebi connection", e);
- }
- return null;
- }
-
- /**
- * This method returns list of ChEBI identifiers that correspond to the whole
- * chebi tree for a given chemical name.
- *
- * @param name
- * - name of chemical
- * @return - list of ChEBI identifiers
- * @throws ChebiSearchException
- * thrown when there is aproblem with accessing data from external
- * chebi database
- */
- public List<MiriamData> getOntologyChebiIdsForChebiName(String name) throws ChebiSearchException {
- // Japanese people use strange dash symbol
- name = name.replace("−", "-").toLowerCase().trim();
-
- MiriamData md = getChebiForChebiName(name);
- return getOntologyChebiIdsForChebi(md);
- }
-
- /**
- * This method returns list of ChEBI identifiers that correspond to the whole
- * chebi tree for a given chebi identifier.
- *
- * @param md
- * - chebi identifier
- * @return - list of ChEBI identifiers
- * @throws ChebiSearchException
- * thrown when there is a problemw ith accessing information from
- * external chebi database
- */
- public List<MiriamData> getOntologyChebiIdsForChebi(MiriamData md) throws ChebiSearchException {
- if (md == null) {
- return new ArrayList<>();
- }
- String query = ONTOLOGY_PREFIX + md.getResource();
-
- String res = getCacheValue(query);
- if (res != null) {
- return chebiStringListToMiriam(res);
- }
-
- List<MiriamData> result = new ArrayList<MiriamData>();
- try {
- ChebiWebServiceClient client = getClient();
-
- Set<String> children = new HashSet<String>();
- children.add(md.getResource());
- Queue<String> queue = new LinkedList<String>();
- queue.add(md.getResource());
- while (!queue.isEmpty()) {
- String element = queue.poll();
- result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, element));
- Entity entity = client.getCompleteEntity(element);
- for (OntologyDataItem di : entity.getOntologyChildren()) {
- if (!children.contains(di.getChebiId()) && "is a".equals(di.getType())) {
- children.add(di.getChebiId());
- queue.add(di.getChebiId());
- }
- }
- }
-
- Set<String> parents = new HashSet<String>();
- parents.add(md.getResource());
- queue = new LinkedList<String>();
- queue.add(md.getResource());
- while (!queue.isEmpty()) {
- String element = queue.poll();
- Entity entity = client.getCompleteEntity(element);
- for (OntologyDataItem di : entity.getOntologyParents()) {
- if (!parents.contains(di.getChebiId()) && "is a".equals(di.getType())) {
- result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, di.getChebiId()));
- parents.add(di.getChebiId());
- queue.add(di.getChebiId());
- }
- }
- }
- String value = miriamListToStringList(result);
-
- setCacheValue(query, value);
- } catch (ChebiWebServiceFault_Exception e) {
- throw new ChebiSearchException("Problem with chebi", e);
- }
- return result;
- }
-
- /**
- * Serialize list of chebi identifiers.
- *
- * @param list
- * list of chebi identfiers
- * @return string with identifiers
- */
- private String miriamListToStringList(List<MiriamData> list) {
- StringBuilder result = new StringBuilder("");
- boolean first = true;
- for (MiriamData miriamData : list) {
- if (!first) {
- result.append(",");
- }
- first = false;
- result.append(miriamData.getResource());
- }
-
- return result.toString();
- }
-
- /**
- * Deserialize list of chebi identifiers.
- *
- * @param res
- * text with list of chebi identifeirs
- * @return list with chebi identifiers
- */
- private List<MiriamData> chebiStringListToMiriam(String res) {
- String[] tmp = res.split(",");
- List<MiriamData> result = new ArrayList<MiriamData>();
- for (String string : tmp) {
- result.add(new MiriamData(MiriamType.CHEBI, string));
- }
- return result;
- }
-
- /**
- * This method returns ChEBI structure for identifier given as a parameter.
- *
- * @param md
- * {@link MiriamData} with ChEBI identifier
- * @return - ChEBI structure
- * @throws ChebiSearchException
- * thrown when there is a problemw ith accessing information from
- * external chebi database
- */
- public Chebi getChebiElementForChebiId(MiriamData md) throws ChebiSearchException {
- if (!MiriamType.CHEBI.equals(md.getDataType())) {
- throw new InvalidArgumentException(MiriamType.CHEBI + " expected");
- }
- String id = md.getResource().toLowerCase().trim();
- if (!id.contains("chebi")) {
- id = "chebi:" + id;
- }
- Chebi result = chebiSerializer.xmlToObject(getCacheNode("id: " + id));
- if (result != null) {
- return result;
- }
- try {
- ChebiWebServiceClient client = getClient();
-
- LiteEntityList entities = client.getLiteEntity(id, SearchCategory.CHEBI_ID, MAX_SEARCH_RESULTS_FROM_CHEBI_API, StarsCategory.ALL);
- List<LiteEntity> resultList = entities.getListElement();
-
- for (LiteEntity liteEntity : resultList) {
- Entity entity = client.getCompleteEntity(liteEntity.getChebiId());
-
- if (entity.getChebiId().trim().equalsIgnoreCase(id)) {
- result = new Chebi(entity);
- }
- }
-
- if (result != null) {
- setCacheValue("id: " + id, chebiSerializer.objectToString(result));
- }
- return result;
- } catch (ChebiWebServiceFault_Exception e) {
- throw new ChebiSearchException("Problem with chebi", e);
- }
- }
-
- /**
- * This method returns common name for chemical identified by chebi id.
- *
- * @param id
- * - chebi identifier in format (XXXXX represents numerical
- * identifier): "CHEBI:XXXXX" or "XXXXX"
- * @return common name of chemical
- * @throws ChebiSearchException
- * thrown when there is a problemw ith accessing information from
- * external chebi database
- */
- protected String getChebiNameForChebiId(MiriamData id) throws ChebiSearchException {
- if (id == null) {
- return null;
- }
- Chebi chebi = getChebiElementForChebiId(id);
- if (chebi == null) {
- return null;
- }
- return chebi.getName();
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
- try {
- MiriamData data = getChebiForChebiName("water");
- status.setStatus(ExternalServiceStatusType.OK);
- if (data == null || !data.getResource().equals("CHEBI:15377")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- *
- * @return {@link #client}
- * @throws ChebiSearchException
- * thrown when there is a problemw ith accessing information from
- * external chebi database
- */
- private ChebiWebServiceClient getClient() throws ChebiSearchException {
- if (client == null) {
- try {
- client = new ChebiWebServiceClient();
- } catch (WebServiceException exception) {
- throw new ChebiSearchException("Cannot initialize chebi connector", exception);
- }
- }
- return client;
- }
-
- @Override
- public void annotateElement(BioEntity element) throws AnnotatorException {
- if (isAnnotatable(element)) {
- try {
- String warnPrefix = elementUtils.getElementTag(element, this);
- if (element.getMiriamData().size() == 0) {
-
- MiriamData chebi = getChebiForChebiName(element.getName());
- if (chebi != null) {
- element.addMiriamData(chebi);
- } else {
- logger.warn(warnPrefix + "Chemical name cannot be found in chebi: " + element.getName());
- }
- }
- Chebi chebi = null;
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.CHEBI.equals(md.getDataType())) {
- chebi = getChebiElementForChebiId(md);
- }
- }
- Chemical species = (Chemical) element;
- if (chebi != null) {
- super.setFullName(species, chebi.getName(), warnPrefix);
-
- setInchi(species, chebi.getInchi(), warnPrefix);
- setInchiKey(species, chebi.getInchiKey(), warnPrefix);
- setSmile(species, chebi.getSmiles(), warnPrefix);
-
- if (species.getSynonyms().size() == 0) {
- species.addSynonyms(chebi.getSynonyms());
- } else {
- StringSetComparator stringSetComparator = new StringSetComparator();
- Set<String> set1 = new HashSet<String>();
- Set<String> set2 = new HashSet<String>();
-
- set1.addAll(species.getSynonyms());
- set2.addAll(chebi.getSynonyms());
-
- if (stringSetComparator.compare(set1, set2) != 0) {
- logger.warn(warnPrefix + "Different set of synonyms: " + species.getFullName() + ", " + chebi.getName());
- }
- }
- }
- } catch (ChebiSearchException e) {
- throw new AnnotatorException("Problem with getting information about chebi", e);
- }
- }
- }
-
- @Override
- public String getCommonName() {
- return MiriamType.CHEBI.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.CHEBI.getDbHomepage();
- }
-
- /**
- * @param client
- * the client to set
- * @see #client
- */
- void setClient(ChebiWebServiceClient client) {
- this.client = client;
- }
+ /**
+ * What is the maximum number of results that should be retrieved from chebi
+ * API.
+ */
+ static final int MAX_SEARCH_RESULTS_FROM_CHEBI_API = 50;
+
+ /**
+ * Prefix used for entries identified by chebi id.
+ */
+ public static final String ID_PREFIX = "id: ";
+
+ /**
+ * Prefix used for ontology list for single chebi id.
+ */
+ static final String ONTOLOGY_PREFIX = "ontology: ";
+
+ /**
+ * Length of the prefix used for entries identified by chebi id.
+ */
+ private static final int ID_PREFIX_LENGTH = ID_PREFIX.length();
+
+ /**
+ * Prefix used for entries identified by name.
+ */
+ private static final String NAME_PREFIX = "name: ";
+
+ /**
+ * Length of the prefix used for entries identified by name.
+ */
+ private static final int NAME_PREFIX_LENGTH = NAME_PREFIX.length();
+
+ /**
+ * Class used for some simple operations on {@link BioEntity} elements.
+ */
+ private ElementUtils elementUtils = new ElementUtils();
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith(ID_PREFIX)) {
+ String id = name.substring(ID_PREFIX_LENGTH);
+ result = chebiSerializer.objectToString(getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, id)));
+ } else if (name.startsWith(ONTOLOGY_PREFIX)) {
+ String id = name.substring(ONTOLOGY_PREFIX.length());
+ result = miriamListToStringList(getOntologyChebiIdsForChebi(new MiriamData(MiriamType.CHEBI, id)));
+ } else if (name.startsWith(NAME_PREFIX)) {
+ name = name.substring(NAME_PREFIX_LENGTH);
+ MiriamData md = getChebiForChebiName(name);
+ if (md != null) {
+ result = md.getResource();
+ }
+ } 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());
+ }
+ } catch (ChebiSearchException e) {
+ throw new SourceNotAvailable(e);
+ }
+
+ return result;
+ }
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ChebiAnnotator.class);
+
+ /**
+ * Client to chebi API.
+ */
+ private ChebiWebServiceClient client = null;
+
+ /**
+ * Object that allows to serialize {@link Chebi} elements into xml string and
+ * deserialize xml into {@link Chebi} objects.
+ */
+ private XmlSerializer<Chebi> chebiSerializer;
+
+ /**
+ * Default constructor. Initializes structures used for transforming
+ * {@link Chebi} from/to xml.
+ */
+ public ChebiAnnotator() {
+ super(ChebiAnnotator.class, new Class[] { Chemical.class }, true);
+ chebiSerializer = new XmlSerializer<>(Chebi.class);
+ }
+
+ /**
+ * Returns {@link MiriamData} for given chebi name.
+ *
+ * @param name
+ * name of the entry in chebi database.
+ * @return {@link MiriamData} entry for given chebi name
+ * @throws ChebiSearchException
+ * thrown when there is aproblem with accessing data from external
+ * chebi database
+ */
+ public MiriamData getChebiForChebiName(String name) throws ChebiSearchException {
+ if (name == null) {
+ return null;
+ }
+ // Japanese people use strange dash symbol
+ name = name.replace("−", "-").toLowerCase().trim();
+
+ String id = getCacheValue("name: " + name);
+ if (id != null) {
+ return new MiriamData(MiriamType.CHEBI, id);
+ }
+ try {
+ ChebiWebServiceClient client = getClient();
+
+ LiteEntityList entities = client.getLiteEntity(name, SearchCategory.CHEBI_NAME, MAX_SEARCH_RESULTS_FROM_CHEBI_API,
+ StarsCategory.ALL);
+ List<LiteEntity> resultList = entities.getListElement();
+
+ for (LiteEntity liteEntity : resultList) {
+ Entity entity = client.getCompleteEntity(liteEntity.getChebiId());
+ String chebiName = entity.getChebiAsciiName();
+ if (chebiName.trim().equalsIgnoreCase(name)) {
+ setCacheValue("name: " + name, entity.getChebiId());
+ return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ }
+ for (DataItem dataItem : entity.getFormulae()) {
+ String synonym = dataItem.getData();
+ if (synonym.trim().equalsIgnoreCase(name)) {
+ setCacheValue("name: " + name, entity.getChebiId());
+ return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ }
+ }
+ for (DataItem dataItem : entity.getSynonyms()) {
+ String synonym = dataItem.getData();
+ if (synonym.trim().equalsIgnoreCase(name)) {
+ setCacheValue("name: " + name, entity.getChebiId());
+ return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ }
+ }
+ }
+ entities = client.getLiteEntity(name, SearchCategory.ALL, MAX_SEARCH_RESULTS_FROM_CHEBI_API, StarsCategory.ALL);
+ resultList = entities.getListElement();
+ for (LiteEntity liteEntity : resultList) {
+ Entity entity = client.getCompleteEntity(liteEntity.getChebiId());
+ for (DataItem dataItem : entity.getFormulae()) {
+ String formula = dataItem.getData();
+ if (formula.trim().equalsIgnoreCase(name)) {
+ setCacheValue("name: " + name, entity.getChebiId());
+ return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ }
+ }
+ for (DataItem dataItem : entity.getSynonyms()) {
+ String synonym = dataItem.getData();
+ if (synonym.trim().equalsIgnoreCase(name)) {
+ setCacheValue("name: " + name, entity.getChebiId());
+ return new MiriamData(MiriamType.CHEBI, entity.getChebiId());
+ }
+ }
+ }
+ } catch (ChebiWebServiceFault_Exception e) {
+ throw new ChebiSearchException("Problem with chebi connection", e);
+ }
+ return null;
+ }
+
+ /**
+ * This method returns list of ChEBI identifiers that correspond to the whole
+ * chebi tree for a given chemical name.
+ *
+ * @param name
+ * - name of chemical
+ * @return - list of ChEBI identifiers
+ * @throws ChebiSearchException
+ * thrown when there is aproblem with accessing data from external
+ * chebi database
+ */
+ public List<MiriamData> getOntologyChebiIdsForChebiName(String name) throws ChebiSearchException {
+ // Japanese people use strange dash symbol
+ name = name.replace("−", "-").toLowerCase().trim();
+
+ MiriamData md = getChebiForChebiName(name);
+ return getOntologyChebiIdsForChebi(md);
+ }
+
+ /**
+ * This method returns list of ChEBI identifiers that correspond to the whole
+ * chebi tree for a given chebi identifier.
+ *
+ * @param md
+ * - chebi identifier
+ * @return - list of ChEBI identifiers
+ * @throws ChebiSearchException
+ * thrown when there is a problemw ith accessing information from
+ * external chebi database
+ */
+ public List<MiriamData> getOntologyChebiIdsForChebi(MiriamData md) throws ChebiSearchException {
+ if (md == null) {
+ return new ArrayList<>();
+ }
+ String query = ONTOLOGY_PREFIX + md.getResource();
+
+ String res = getCacheValue(query);
+ if (res != null) {
+ return chebiStringListToMiriam(res);
+ }
+
+ List<MiriamData> result = new ArrayList<MiriamData>();
+ try {
+ ChebiWebServiceClient client = getClient();
+
+ Set<String> children = new HashSet<String>();
+ children.add(md.getResource());
+ Queue<String> queue = new LinkedList<String>();
+ queue.add(md.getResource());
+ while (!queue.isEmpty()) {
+ String element = queue.poll();
+ result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, element));
+ Entity entity = client.getCompleteEntity(element);
+ for (OntologyDataItem di : entity.getOntologyChildren()) {
+ if (!children.contains(di.getChebiId()) && "is a".equals(di.getType())) {
+ children.add(di.getChebiId());
+ queue.add(di.getChebiId());
+ }
+ }
+ }
+
+ Set<String> parents = new HashSet<String>();
+ parents.add(md.getResource());
+ queue = new LinkedList<String>();
+ queue.add(md.getResource());
+ while (!queue.isEmpty()) {
+ String element = queue.poll();
+ Entity entity = client.getCompleteEntity(element);
+ for (OntologyDataItem di : entity.getOntologyParents()) {
+ if (!parents.contains(di.getChebiId()) && "is a".equals(di.getType())) {
+ result.add(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, di.getChebiId()));
+ parents.add(di.getChebiId());
+ queue.add(di.getChebiId());
+ }
+ }
+ }
+ String value = miriamListToStringList(result);
+
+ setCacheValue(query, value);
+ } catch (ChebiWebServiceFault_Exception e) {
+ throw new ChebiSearchException("Problem with chebi", e);
+ }
+ return result;
+ }
+
+ /**
+ * Serialize list of chebi identifiers.
+ *
+ * @param list
+ * list of chebi identfiers
+ * @return string with identifiers
+ */
+ private String miriamListToStringList(List<MiriamData> list) {
+ StringBuilder result = new StringBuilder("");
+ boolean first = true;
+ for (MiriamData miriamData : list) {
+ if (!first) {
+ result.append(",");
+ }
+ first = false;
+ result.append(miriamData.getResource());
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * Deserialize list of chebi identifiers.
+ *
+ * @param res
+ * text with list of chebi identifeirs
+ * @return list with chebi identifiers
+ */
+ private List<MiriamData> chebiStringListToMiriam(String res) {
+ String[] tmp = res.split(",");
+ List<MiriamData> result = new ArrayList<MiriamData>();
+ for (String string : tmp) {
+ result.add(new MiriamData(MiriamType.CHEBI, string));
+ }
+ return result;
+ }
+
+ /**
+ * This method returns ChEBI structure for identifier given as a parameter.
+ *
+ * @param md
+ * {@link MiriamData} with ChEBI identifier
+ * @return - ChEBI structure
+ * @throws ChebiSearchException
+ * thrown when there is a problemw ith accessing information from
+ * external chebi database
+ */
+ public Chebi getChebiElementForChebiId(MiriamData md) throws ChebiSearchException {
+ if (!MiriamType.CHEBI.equals(md.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.CHEBI + " expected");
+ }
+ String id = md.getResource().toLowerCase().trim();
+ if (!id.contains("chebi")) {
+ id = "chebi:" + id;
+ }
+ Chebi result = chebiSerializer.xmlToObject(getCacheNode("id: " + id));
+ if (result != null) {
+ return result;
+ }
+ try {
+ ChebiWebServiceClient client = getClient();
+
+ LiteEntityList entities = client.getLiteEntity(id, SearchCategory.CHEBI_ID, MAX_SEARCH_RESULTS_FROM_CHEBI_API,
+ StarsCategory.ALL);
+ List<LiteEntity> resultList = entities.getListElement();
+
+ for (LiteEntity liteEntity : resultList) {
+ Entity entity = client.getCompleteEntity(liteEntity.getChebiId());
+
+ if (entity.getChebiId().trim().equalsIgnoreCase(id)) {
+ result = new Chebi(entity);
+ }
+ }
+
+ if (result != null) {
+ setCacheValue("id: " + id, chebiSerializer.objectToString(result));
+ }
+ return result;
+ } catch (ChebiWebServiceFault_Exception e) {
+ throw new ChebiSearchException("Problem with chebi", e);
+ }
+ }
+
+ /**
+ * This method returns common name for chemical identified by chebi id.
+ *
+ * @param id
+ * - chebi identifier in format (XXXXX represents numerical
+ * identifier): "CHEBI:XXXXX" or "XXXXX"
+ * @return common name of chemical
+ * @throws ChebiSearchException
+ * thrown when there is a problemw ith accessing information from
+ * external chebi database
+ */
+ protected String getChebiNameForChebiId(MiriamData id) throws ChebiSearchException {
+ if (id == null) {
+ return null;
+ }
+ Chebi chebi = getChebiElementForChebiId(id);
+ if (chebi == null) {
+ return null;
+ }
+ return chebi.getName();
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+ try {
+ MiriamData data = getChebiForChebiName("water");
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (data == null || !data.getResource().equals("CHEBI:15377")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ *
+ * @return {@link #client}
+ * @throws ChebiSearchException
+ * thrown when there is a problem with accessing information from
+ * external chebi database
+ */
+ private ChebiWebServiceClient getClient() throws ChebiSearchException {
+ if (client == null) {
+ try {
+ client = new ChebiWebServiceClient();
+ } catch (WebServiceException exception) {
+ throw new ChebiSearchException("Cannot initialize chebi connector", exception);
+ }
+ }
+ return client;
+ }
+
+ @Override
+ public void annotateElement(BioEntity element) throws AnnotatorException {
+ if (isAnnotatable(element)) {
+ try {
+ String warnPrefix = elementUtils.getElementTag(element, this);
+ if (element.getMiriamData().size() == 0) {
+
+ MiriamData chebi = getChebiForChebiName(element.getName());
+ if (chebi != null) {
+ element.addMiriamData(chebi);
+ } else {
+ logger.warn(warnPrefix + "Chemical name cannot be found in chebi: " + element.getName());
+ }
+ }
+ Chebi chebi = null;
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.CHEBI.equals(md.getDataType())) {
+ chebi = getChebiElementForChebiId(md);
+ }
+ }
+ Chemical species = (Chemical) element;
+ if (chebi != null) {
+ super.setFullName(species, chebi.getName(), warnPrefix);
+
+ setInchi(species, chebi.getInchi(), warnPrefix);
+ setInchiKey(species, chebi.getInchiKey(), warnPrefix);
+ setSmile(species, chebi.getSmiles(), warnPrefix);
+
+ if (species.getSynonyms().size() == 0) {
+ species.addSynonyms(chebi.getSynonyms());
+ } else {
+ StringSetComparator stringSetComparator = new StringSetComparator();
+ Set<String> set1 = new HashSet<String>();
+ Set<String> set2 = new HashSet<String>();
+
+ set1.addAll(species.getSynonyms());
+ set2.addAll(chebi.getSynonyms());
+
+ if (stringSetComparator.compare(set1, set2) != 0) {
+ logger.warn(warnPrefix + "Different set of synonyms: " + species.getFullName() + ", " + chebi.getName());
+ }
+ }
+ }
+ } catch (ChebiSearchException e) {
+ throw new AnnotatorException("Problem with getting information about chebi", e);
+ }
+ }
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.CHEBI.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.CHEBI.getDbHomepage();
+ }
+
+ /**
+ * @param client
+ * the client to set
+ * @see #client
+ */
+ void setClient(ChebiWebServiceClient client) {
+ this.client = client;
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
index 8ca9b43561724061b813fab1ca5c433d3673665e..a000cdc242deaf393ac42530947149713043b521 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotatorTest.java
@@ -39,808 +39,814 @@ import uk.ac.ebi.chebi.webapps.chebiWS.model.OntologyDataItem;
import uk.ac.ebi.chebi.webapps.chebiWS.model.SearchCategory;
public class ChebiAnnotatorTest extends AnnotationTestFunctions {
- static Logger logger = Logger.getLogger(ChebiAnnotatorTest.class);
-
- @Autowired
- ChebiAnnotator backend;
-
- @Autowired
- private GeneralCacheInterface cache;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetIdByName() throws Exception {
- try {
- MiriamData id = backend.getChebiForChebiName("adenine");
- assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"), id);
- id = backend.getChebiForChebiName("asdf bvclcx lcxj vxlcvkj");
- assertNull(id);
- assertNull(backend.getChebiForChebiName(null));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testNameById() throws Exception {
- try {
- String name = backend.getChebiNameForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
- assertEquals("adenine", name);
- name = backend.getChebiNameForChebiId(new MiriamData(MiriamType.CHEBI, "16708"));
- assertEquals("adenine", name);
- name = backend.getChebiNameForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708a"));
- assertNull(name);
- name = backend.getChebiNameForChebiId(null);
- assertNull(name);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiById() throws Exception {
- try {
- Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
- assertNotNull(chebi);
- assertEquals("adenine", chebi.getName());
- assertEquals("Nc1ncnc2[nH]cnc12", chebi.getSmiles());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiByIdWhenConnectionFails() throws Exception {
- try {
- cache = backend.getCache();
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
- item.setChebiId("CHEBI:18008");
- item.setType("is a");
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- when(chebiWebServiceClient.getLiteEntity(any(), any(), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenThrow(new ChebiWebServiceFault_Exception(null, null));
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
- fail("Exception expected");
-
- } catch (ChebiSearchException e) {
- assertTrue(e.getMessage().contains("Problem with chebi"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testChebiByInvalidId() throws Exception {
- try {
- backend.getChebiElementForChebiId(new MiriamData(MiriamType.WIKIPEDIA, "water"));
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebi() throws Exception {
- try {
-
- Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
- assertNotNull(chebi);
- assertEquals("adenine", chebi.getName());
- assertEquals("Nc1ncnc2[nH]cnc12", chebi.getSmiles());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiOntologyForWater() throws Exception {
- try {
-
- Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:15377"));
- assertNotNull(chebi);
- assertTrue(chebi.getIncomingChebi().size() > 0);
- assertTrue(chebi.getOutgoingChebi().size() > 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceById() throws Exception {
- String query = "id: CHEBI:28423";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, backend.getCacheType(), newRes);
- cache.invalidateByQuery(query, backend.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, backend.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test(timeout = 15000)
- public void testCachableInterfaceByName() throws Exception {
- String query = "name: water";
- String newRes = "hello";
- try {
- waitForRefreshCacheQueueToEmpty();
-
- cache.setCachedQuery(query, backend.getCacheType(), newRes);
- cache.invalidateByQuery(query, backend.getCacheType());
-
- waitForRefreshCacheQueueToEmpty();
-
- String res = cache.getStringByQuery(query, backend.getCacheType());
-
- assertNotNull(res);
-
- assertFalse("Value wasn't refreshed from db", newRes.equals(res));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiNameToId1() throws Exception {
- try {
- // easy tests with some molecule
- MiriamData result = backend.getChebiForChebiName("L-glutamate(2-)");
- assertNotNull(result);
- assertTrue(result.getResource().contains("CHEBI:29988"));
- // unknown molecule
- MiriamData string = backend.getChebiForChebiName("blablasblasblsabsal");
- assertNull(string);
-
- // and water
- result = backend.getChebiForChebiName("H2O");
- assertNotNull(result);
- assertTrue(result.getResource().contains("CHEBI:15377"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiNameToId4() throws Exception {
- try {
- // easy tests with some molecule
- MiriamData result = backend.getChebiForChebiName("Ca2+");
- assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:29108"), result);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiOntologyIds() throws Exception {
- try {
- // unknown molecule
- List<MiriamData> res = backend.getOntologyChebiIdsForChebiName("blablasblasblsabsal");
- assertNotNull(res);
- assertEquals(0, res.size());
-
- // and water
- res = backend.getOntologyChebiIdsForChebiName("h2o");
- assertNotNull(res);
- assertTrue(res.size() > 1);
- assertTrue(res.contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:24431")));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiNameToId2() throws Exception {
- try {
- // and now tests more complicated (how to find hydron?)
- MiriamData md = backend.getChebiForChebiName("hydron");
- assertNotNull(md);
- assertTrue(md.getResource().contains("CHEBI:15378"));
- md = backend.getChebiForChebiName("H+");
- assertNotNull(md);
- assertTrue(md.getResource().contains("CHEBI:15378"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testChebiNameToId3() throws Exception {
- try {
- // and the tricky one - I couldn't find it via chebi online search tool...
- // But java API do the trick...
- // assertEquals("CHEBI:456214",converter.chebiNameToId("NADP+"));
- // however manual mapping done by chemist says different...:
- MiriamData md = backend.getChebiForChebiName("NADP+");
- assertNotNull(md);
- assertTrue(md.getResource().contains("CHEBI:18009"));
- md = backend.getChebiForChebiName("NADP(+)");
- assertNotNull(md);
- assertTrue(md.getResource().contains("CHEBI:18009"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateChemical() throws Exception {
- try {
- SimpleMolecule simpleMolecule = new SimpleMolecule("id");
- simpleMolecule.setName("water");
-
- backend.annotateElement(simpleMolecule);
-
- assertFalse(simpleMolecule.getFullName().equals(""));
- assertFalse(simpleMolecule.getInChI().equals(""));
- assertFalse(simpleMolecule.getInChIKey().equals(""));
- assertFalse(simpleMolecule.getSmiles().equals(""));
- assertFalse(simpleMolecule.getSynonyms().size() == 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateWhenConnectionFails() throws Exception {
- try {
- SimpleMolecule simpleMolecule = new SimpleMolecule("id");
- simpleMolecule.setName("water");
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
- item.setChebiId("CHEBI:18008");
- item.setType("is a");
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenThrow(new ChebiWebServiceFault_Exception(null, null));
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- backend.setCache(null);
- backend.annotateElement(simpleMolecule);
-
- fail("Exceptione expected");
- } catch (AnnotatorException e) {
- assertTrue(e.getMessage().contains("Problem with getting information about chebi"));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- backend.setCache(cache);
- backend.setClient(null);
- }
- }
-
- @Test
- public void testAnnotateChemicalWithInvalidName() throws Exception {
- try {
- SimpleMolecule simpleMolecule = new SimpleMolecule("id");
- simpleMolecule.setName("blasdh");
-
- backend.annotateElement(simpleMolecule);
-
- assertEquals(1, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateChemicalFromDb() throws Exception {
- try {
- SimpleMolecule simpleMolecule = new SimpleMolecule("id");
- simpleMolecule.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:15377"));
-
- backend.annotateElement(simpleMolecule);
-
- assertFalse("".equals(simpleMolecule.getFullName()));
- assertFalse(simpleMolecule.getInChI().equals(""));
- assertFalse(simpleMolecule.getInChIKey().equals(""));
- assertFalse(simpleMolecule.getSmiles().equals(""));
- assertFalse(simpleMolecule.getSynonyms().size() == 0);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testUpdateChemicalFromDbWithDifferentData() throws Exception {
- try {
- SimpleMolecule simpleMolecule = new SimpleMolecule("id");
- simpleMolecule.setName("water");
- simpleMolecule.setFullName("xxx");
- simpleMolecule.setInChI("x");
- simpleMolecule.setInChIKey("x");
- simpleMolecule.setSmiles("x");
- simpleMolecule.addSynonym("x");
- simpleMolecule.addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:15377"));
-
- backend.annotateElement(simpleMolecule);
-
- assertEquals(5, getWarnings().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetters() throws Exception {
- try {
- assertNotNull(backend.getCommonName());
- assertNotNull(backend.getUrl());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testRefreshGetOntology() throws Exception {
- cache = backend.getCache();
- try {
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
- item.setChebiId("CHEBI:18008");
- item.setType("is a");
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- String query = ChebiAnnotator.ONTOLOGY_PREFIX + "CHEBI:18009";
- String result = backend.refreshCacheQuery(query);
- assertNotNull(result);
- assertTrue(result.contains("CHEBI:18008"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testGetChebiForChebiNameInFormula() throws Exception {
- cache = backend.getCache();
- try {
- String chebiId = "CHEBI:18008";
- String name = "art_name";
- DataItem matchedElement = new DataItem();
- matchedElement.setData(name);
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- entity.setChebiAsciiName("");
- entity.getFormulae().add(matchedElement);
- entity.setChebiId(chebiId);
-
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
- LiteEntityList liteEntityList = new LiteEntityList();
-
- LiteEntity liteEntity = new LiteEntity();
- liteEntityList.getListElement().add(liteEntity);
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(liteEntityList);
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- MiriamData result = backend.getChebiForChebiName(name);
- assertNotNull(result);
- assertEquals(chebiId, result.getResource());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testGetChebiForChebiNameInFormula2() throws Exception {
- cache = backend.getCache();
- try {
- String chebiId = "CHEBI:18008";
- String name = "art_name";
- DataItem matchedElement = new DataItem();
- matchedElement.setData(name);
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- entity.setChebiAsciiName("");
- entity.getFormulae().add(matchedElement);
- entity.setChebiId(chebiId);
-
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
- LiteEntityList liteEntityList = new LiteEntityList();
-
- LiteEntity liteEntity = new LiteEntity();
- liteEntityList.getListElement().add(liteEntity);
- // when searching by name return empty list
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(new LiteEntityList());
- // when searchng by all return list with elements
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.ALL), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(liteEntityList);
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- MiriamData result = backend.getChebiForChebiName(name);
- assertNotNull(result);
- assertEquals(chebiId, result.getResource());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testGetChebiForChebiNameInSynonym() throws Exception {
- cache = backend.getCache();
- try {
- String chebiId = "CHEBI:18008";
- String name = "art_name";
- DataItem matchedElement = new DataItem();
- matchedElement.setData(name);
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- entity.setChebiAsciiName("");
- entity.getSynonyms().add(matchedElement);
- entity.setChebiId(chebiId);
-
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
- LiteEntityList liteEntityList = new LiteEntityList();
-
- LiteEntity liteEntity = new LiteEntity();
- liteEntityList.getListElement().add(liteEntity);
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(liteEntityList);
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- MiriamData result = backend.getChebiForChebiName(name);
- assertNotNull(result);
- assertEquals(chebiId, result.getResource());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testGetChebiForChebiNameInSynonym2() throws Exception {
- cache = backend.getCache();
- try {
- String chebiId = "CHEBI:18008";
- String name = "art_name";
- DataItem matchedElement = new DataItem();
- matchedElement.setData(name);
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- entity.setChebiAsciiName("");
- entity.getSynonyms().add(matchedElement);
- entity.setChebiId(chebiId);
-
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
- LiteEntityList liteEntityList = new LiteEntityList();
-
- LiteEntity liteEntity = new LiteEntity();
- liteEntityList.getListElement().add(liteEntity);
- // when searching by name return empty list
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(new LiteEntityList());
- // when searchng by all return list with elements
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.ALL), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(liteEntityList);
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- MiriamData result = backend.getChebiForChebiName(name);
- assertNotNull(result);
- assertEquals(chebiId, result.getResource());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testGetChebiForChebiNameWithConnectionProblems() throws Exception {
- cache = backend.getCache();
- try {
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- // when searching by name return empty list
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenThrow(new ChebiWebServiceFault_Exception(null, null));
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- backend.getChebiForChebiName("bla");
-
- } catch (ChebiSearchException e) {
- assertTrue(e.getMessage().contains("Problem with chebi connection"));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testRefreshWhenProblemWithConnnector() throws Exception {
- cache = backend.getCache();
- try {
- // exclude first cached value
- backend.setCache(null);
-
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
-
- OntologyDataItem item = new OntologyDataItem();
- item.setChebiId("CHEBI:18008");
- item.setType("is a");
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenThrow(new ChebiWebServiceFault_Exception(null, null));
-
- // we will use mock object as a connection to chebi server
- backend.setClient(chebiWebServiceClient);
-
- String query = ChebiAnnotator.ONTOLOGY_PREFIX + "CHEBI:18009";
- backend.refreshCacheQuery(query);
- fail("Exception expected");
-
- } catch (SourceNotAvailable e) {
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- // restore cache for other tests
- backend.setCache(cache);
- // remove mock
- backend.setClient(null);
- }
- }
-
- @Test
- public void testRefreshInvalidQuery() throws Exception {
- try {
- backend.refreshCacheQuery("invalid string");
-
- 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 testRefreshInvalidQuery2() throws Exception {
- try {
- backend.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 testStatus() throws Exception {
- try {
- assertEquals(ExternalServiceStatusType.OK, backend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- backend.setCache(null);
- try {
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
- when(chebiWebServiceClient.getLiteEntity(any(), any(), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenThrow(new ChebiWebServiceFault_Exception(null, null));
- backend.setClient(chebiWebServiceClient);
- assertEquals(ExternalServiceStatusType.DOWN, backend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- backend.setCache(cache);
- backend.setClient(null);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- backend.setCache(null);
- try {
- ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
- backend.setClient(chebiWebServiceClient);
-
- String chebiId = "CHEBI:18008";
- String name = "art";
- DataItem matchedElement = new DataItem();
- matchedElement.setData(name);
- // exclude first cached value
- backend.setCache(null);
-
- OntologyDataItem item = new OntologyDataItem();
-
- Entity entity = new Entity();
- entity.getOntologyChildren().add(item);
- entity.getOntologyParents().add(item);
- entity.setChebiAsciiName("");
- entity.getSynonyms().add(matchedElement);
- entity.setChebiId(chebiId);
-
- when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
- LiteEntityList liteEntityList = new LiteEntityList();
-
- LiteEntity liteEntity = new LiteEntity();
- liteEntityList.getListElement().add(liteEntity);
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(liteEntityList);
- when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.ALL), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
- .thenReturn(liteEntityList);
-
- assertEquals(ExternalServiceStatusType.CHANGED, backend.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- backend.setCache(cache);
- backend.setClient(null);
- }
- }
+ static Logger logger = Logger.getLogger(ChebiAnnotatorTest.class);
+
+ @Autowired
+ ChebiAnnotator backend;
+
+ @Autowired
+ private GeneralCacheInterface cache;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetIdByName() throws Exception {
+ try {
+ MiriamData id = backend.getChebiForChebiName("adenine");
+ assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"), id);
+ id = backend.getChebiForChebiName("asdf bvclcx lcxj vxlcvkj");
+ assertNull(id);
+ assertNull(backend.getChebiForChebiName(null));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testNameById() throws Exception {
+ try {
+ String name = backend.getChebiNameForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
+ assertEquals("adenine", name);
+ name = backend.getChebiNameForChebiId(new MiriamData(MiriamType.CHEBI, "16708"));
+ assertEquals("adenine", name);
+ name = backend.getChebiNameForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708a"));
+ assertNull(name);
+ name = backend.getChebiNameForChebiId(null);
+ assertNull(name);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiById() throws Exception {
+ try {
+ Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
+ assertNotNull(chebi);
+ assertEquals("adenine", chebi.getName());
+ assertEquals("Nc1ncnc2[nH]cnc12", chebi.getSmiles());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiByIdWhenConnectionFails() throws Exception {
+ try {
+ cache = backend.getCache();
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+ item.setChebiId("CHEBI:18008");
+ item.setType("is a");
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ when(chebiWebServiceClient.getLiteEntity(any(), any(), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API),
+ any())).thenThrow(new ChebiWebServiceFault_Exception(null, null));
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
+ fail("Exception expected");
+
+ } catch (ChebiSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with chebi"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testChebiByInvalidId() throws Exception {
+ try {
+ backend.getChebiElementForChebiId(new MiriamData(MiriamType.WIKIPEDIA, "water"));
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebi() throws Exception {
+ try {
+
+ Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:16708"));
+ assertNotNull(chebi);
+ assertEquals("adenine", chebi.getName());
+ assertEquals("Nc1ncnc2[nH]cnc12", chebi.getSmiles());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiOntologyForWater() throws Exception {
+ try {
+
+ Chebi chebi = backend.getChebiElementForChebiId(new MiriamData(MiriamType.CHEBI, "CHEBI:15377"));
+ assertNotNull(chebi);
+ assertTrue(chebi.getIncomingChebi().size() > 0);
+ assertTrue(chebi.getOutgoingChebi().size() > 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceById() throws Exception {
+ String query = "id: CHEBI:28423";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, backend.getCacheType(), newRes);
+ cache.invalidateByQuery(query, backend.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, backend.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test(timeout = 15000)
+ public void testCachableInterfaceByName() throws Exception {
+ String query = "name: water";
+ String newRes = "hello";
+ try {
+ waitForRefreshCacheQueueToEmpty();
+
+ cache.setCachedQuery(query, backend.getCacheType(), newRes);
+ cache.invalidateByQuery(query, backend.getCacheType());
+
+ waitForRefreshCacheQueueToEmpty();
+
+ String res = cache.getStringByQuery(query, backend.getCacheType());
+
+ assertNotNull(res);
+
+ assertFalse("Value wasn't refreshed from db", newRes.equals(res));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiNameToId1() throws Exception {
+ try {
+ // easy tests with some molecule
+ MiriamData result = backend.getChebiForChebiName("L-glutamate(2-)");
+ assertNotNull(result);
+ assertTrue(result.getResource().contains("CHEBI:29988"));
+ // unknown molecule
+ MiriamData string = backend.getChebiForChebiName("blablasblasblsabsal");
+ assertNull(string);
+
+ // and water
+ result = backend.getChebiForChebiName("H2O");
+ assertNotNull(result);
+ assertTrue(result.getResource().contains("CHEBI:15377"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiNameToId4() throws Exception {
+ try {
+ // easy tests with some molecule
+ MiriamData result = backend.getChebiForChebiName("Ca2+");
+ assertEquals(new MiriamData(MiriamType.CHEBI, "CHEBI:29108"), result);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiOntologyIds() throws Exception {
+ try {
+ // unknown molecule
+ List<MiriamData> res = backend.getOntologyChebiIdsForChebiName("blablasblasblsabsal");
+ assertNotNull(res);
+ assertEquals(0, res.size());
+
+ // and water
+ res = backend.getOntologyChebiIdsForChebiName("h2o");
+ assertNotNull(res);
+ assertTrue(res.size() > 1);
+ assertTrue(
+ res.contains(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:24431")));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiNameToId2() throws Exception {
+ try {
+ // and now tests more complicated (how to find hydron?)
+ MiriamData md = backend.getChebiForChebiName("hydron");
+ assertNotNull(md);
+ assertTrue(md.getResource().contains("CHEBI:15378"));
+ md = backend.getChebiForChebiName("H+");
+ assertNotNull(md);
+ assertTrue(md.getResource().contains("CHEBI:15378"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testChebiNameToId3() throws Exception {
+ try {
+ // and the tricky one - I couldn't find it via chebi online search tool...
+ // But java API do the trick...
+ // assertEquals("CHEBI:456214",converter.chebiNameToId("NADP+"));
+ // however manual mapping done by chemist says different...:
+ MiriamData md = backend.getChebiForChebiName("NADP+");
+ assertNotNull(md);
+ assertTrue(md.getResource().contains("CHEBI:18009"));
+ md = backend.getChebiForChebiName("NADP(+)");
+ assertNotNull(md);
+ assertTrue(md.getResource().contains("CHEBI:18009"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateChemical() throws Exception {
+ try {
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
+ simpleMolecule.setName("water");
+
+ backend.annotateElement(simpleMolecule);
+
+ assertFalse(simpleMolecule.getFullName().equals(""));
+ assertFalse(simpleMolecule.getInChI().equals(""));
+ assertFalse(simpleMolecule.getInChIKey().equals(""));
+ assertFalse(simpleMolecule.getSmiles().equals(""));
+ assertFalse(simpleMolecule.getSynonyms().size() == 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateWhenConnectionFails() throws Exception {
+ try {
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
+ simpleMolecule.setName("water");
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+ item.setChebiId("CHEBI:18008");
+ item.setType("is a");
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
+ .thenThrow(new ChebiWebServiceFault_Exception(null, null));
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ backend.setCache(null);
+ backend.annotateElement(simpleMolecule);
+
+ fail("Exceptione expected");
+ } catch (AnnotatorException e) {
+ assertTrue(e.getMessage().contains("Problem with getting information about chebi"));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ backend.setCache(cache);
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testAnnotateChemicalWithInvalidName() throws Exception {
+ try {
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
+ simpleMolecule.setName("blasdh");
+
+ backend.annotateElement(simpleMolecule);
+
+ assertEquals(1, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateChemicalFromDb() throws Exception {
+ try {
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
+ simpleMolecule
+ .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:15377"));
+
+ backend.annotateElement(simpleMolecule);
+
+ assertFalse("".equals(simpleMolecule.getFullName()));
+ assertFalse(simpleMolecule.getInChI().equals(""));
+ assertFalse(simpleMolecule.getInChIKey().equals(""));
+ assertFalse(simpleMolecule.getSmiles().equals(""));
+ assertFalse(simpleMolecule.getSynonyms().size() == 0);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testUpdateChemicalFromDbWithDifferentData() throws Exception {
+ try {
+ SimpleMolecule simpleMolecule = new SimpleMolecule("id");
+ simpleMolecule.setName("water");
+ simpleMolecule.setFullName("xxx");
+ simpleMolecule.setInChI("x");
+ simpleMolecule.setInChIKey("x");
+ simpleMolecule.setSmiles("x");
+ simpleMolecule.addSynonym("x");
+ simpleMolecule
+ .addMiriamData(new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.CHEBI, "CHEBI:15377"));
+
+ backend.annotateElement(simpleMolecule);
+
+ assertEquals(5, getWarnings().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetters() throws Exception {
+ try {
+ assertNotNull(backend.getCommonName());
+ assertNotNull(backend.getUrl());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testRefreshGetOntology() throws Exception {
+ cache = backend.getCache();
+ try {
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+ item.setChebiId("CHEBI:18008");
+ item.setType("is a");
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ String query = ChebiAnnotator.ONTOLOGY_PREFIX + "CHEBI:18009";
+ String result = backend.refreshCacheQuery(query);
+ assertNotNull(result);
+ assertTrue(result.contains("CHEBI:18008"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testGetChebiForChebiNameInFormula() throws Exception {
+ cache = backend.getCache();
+ try {
+ String chebiId = "CHEBI:18008";
+ String name = "art_name";
+ DataItem matchedElement = new DataItem();
+ matchedElement.setData(name);
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ entity.setChebiAsciiName("");
+ entity.getFormulae().add(matchedElement);
+ entity.setChebiId(chebiId);
+
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
+ LiteEntityList liteEntityList = new LiteEntityList();
+
+ LiteEntity liteEntity = new LiteEntity();
+ liteEntityList.getListElement().add(liteEntity);
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(liteEntityList);
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ MiriamData result = backend.getChebiForChebiName(name);
+ assertNotNull(result);
+ assertEquals(chebiId, result.getResource());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testGetChebiForChebiNameInFormula2() throws Exception {
+ cache = backend.getCache();
+ try {
+ String chebiId = "CHEBI:18008";
+ String name = "art_name";
+ DataItem matchedElement = new DataItem();
+ matchedElement.setData(name);
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ entity.setChebiAsciiName("");
+ entity.getFormulae().add(matchedElement);
+ entity.setChebiId(chebiId);
+
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
+ LiteEntityList liteEntityList = new LiteEntityList();
+
+ LiteEntity liteEntity = new LiteEntity();
+ liteEntityList.getListElement().add(liteEntity);
+ // when searching by name return empty list
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(new LiteEntityList());
+ // when searchng by all return list with elements
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.ALL),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(liteEntityList);
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ MiriamData result = backend.getChebiForChebiName(name);
+ assertNotNull(result);
+ assertEquals(chebiId, result.getResource());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testGetChebiForChebiNameInSynonym() throws Exception {
+ cache = backend.getCache();
+ try {
+ String chebiId = "CHEBI:18008";
+ String name = "art_name";
+ DataItem matchedElement = new DataItem();
+ matchedElement.setData(name);
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ entity.setChebiAsciiName("");
+ entity.getSynonyms().add(matchedElement);
+ entity.setChebiId(chebiId);
+
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
+ LiteEntityList liteEntityList = new LiteEntityList();
+
+ LiteEntity liteEntity = new LiteEntity();
+ liteEntityList.getListElement().add(liteEntity);
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(liteEntityList);
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ MiriamData result = backend.getChebiForChebiName(name);
+ assertNotNull(result);
+ assertEquals(chebiId, result.getResource());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testGetChebiForChebiNameInSynonym2() throws Exception {
+ cache = backend.getCache();
+ try {
+ String chebiId = "CHEBI:18008";
+ String name = "art_name";
+ DataItem matchedElement = new DataItem();
+ matchedElement.setData(name);
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ entity.setChebiAsciiName("");
+ entity.getSynonyms().add(matchedElement);
+ entity.setChebiId(chebiId);
+
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
+ LiteEntityList liteEntityList = new LiteEntityList();
+
+ LiteEntity liteEntity = new LiteEntity();
+ liteEntityList.getListElement().add(liteEntity);
+ // when searching by name return empty list
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(new LiteEntityList());
+ // when searchng by all return list with elements
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.ALL),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(liteEntityList);
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ MiriamData result = backend.getChebiForChebiName(name);
+ assertNotNull(result);
+ assertEquals(chebiId, result.getResource());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testGetChebiForChebiNameWithConnectionProblems() throws Exception {
+ cache = backend.getCache();
+ try {
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ // when searching by name return empty list
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any()))
+ .thenThrow(new ChebiWebServiceFault_Exception(null, null));
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ backend.getChebiForChebiName("bla");
+
+ } catch (ChebiSearchException e) {
+ assertTrue(e.getMessage().contains("Problem with chebi connection"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testRefreshWhenProblemWithConnnector() throws Exception {
+ cache = backend.getCache();
+ try {
+ // exclude first cached value
+ backend.setCache(null);
+
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+
+ OntologyDataItem item = new OntologyDataItem();
+ item.setChebiId("CHEBI:18008");
+ item.setType("is a");
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class)))
+ .thenThrow(new ChebiWebServiceFault_Exception(null, null));
+
+ // we will use mock object as a connection to chebi server
+ backend.setClient(chebiWebServiceClient);
+
+ String query = ChebiAnnotator.ONTOLOGY_PREFIX + "CHEBI:18009";
+ backend.refreshCacheQuery(query);
+ fail("Exception expected");
+
+ } catch (SourceNotAvailable e) {
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ // restore cache for other tests
+ backend.setCache(cache);
+ // remove mock
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testRefreshInvalidQuery() throws Exception {
+ try {
+ backend.refreshCacheQuery("invalid string");
+
+ 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 testRefreshInvalidQuery2() throws Exception {
+ try {
+ backend.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 testStatus() throws Exception {
+ try {
+ assertEquals(ExternalServiceStatusType.OK, backend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ backend.setCache(null);
+ try {
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+ when(chebiWebServiceClient.getLiteEntity(any(), any(), eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API),
+ any())).thenThrow(new ChebiWebServiceFault_Exception(null, null));
+ backend.setClient(chebiWebServiceClient);
+ assertEquals(ExternalServiceStatusType.DOWN, backend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ backend.setCache(cache);
+ backend.setClient(null);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ backend.setCache(null);
+ try {
+ ChebiWebServiceClient chebiWebServiceClient = Mockito.mock(ChebiWebServiceClient.class);
+ backend.setClient(chebiWebServiceClient);
+
+ String chebiId = "CHEBI:18008";
+ String name = "art";
+ DataItem matchedElement = new DataItem();
+ matchedElement.setData(name);
+ // exclude first cached value
+ backend.setCache(null);
+
+ OntologyDataItem item = new OntologyDataItem();
+
+ Entity entity = new Entity();
+ entity.getOntologyChildren().add(item);
+ entity.getOntologyParents().add(item);
+ entity.setChebiAsciiName("");
+ entity.getSynonyms().add(matchedElement);
+ entity.setChebiId(chebiId);
+
+ when(chebiWebServiceClient.getCompleteEntity(any(String.class))).thenReturn(entity);
+ LiteEntityList liteEntityList = new LiteEntityList();
+
+ LiteEntity liteEntity = new LiteEntity();
+ liteEntityList.getListElement().add(liteEntity);
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.CHEBI_NAME),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(liteEntityList);
+ when(chebiWebServiceClient.getLiteEntity(any(), eq(SearchCategory.ALL),
+ eq(ChebiAnnotator.MAX_SEARCH_RESULTS_FROM_CHEBI_API), any())).thenReturn(liteEntityList);
+
+ assertEquals(ExternalServiceStatusType.CHANGED, backend.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ backend.setCache(cache);
+ backend.setClient(null);
+ }
+ }
}
diff --git a/pom.xml b/pom.xml
index c4ae7d49e1981914751eb1164fe8e0733c5f00b6..6da6fa5d7c9371f53a610c110362519bd0d1d82c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -58,7 +58,7 @@
<gson.version>2.2.2</gson.version>
- <chebi-ws.version>2.2.2</chebi-ws.version>
+ <chebi-ws.version>2.3.2</chebi-ws.version>
<miriam-lib.version>1.1.5</miriam-lib.version>