diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorConfigParameter.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorConfigParameter.java
index 01bce8df9860d4593806612cb6abfe3d3e76e4a3..6421efe5dadc54f6949d6021cf8253b6b57026a1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorConfigParameter.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorConfigParameter.java
@@ -5,7 +5,7 @@ import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
public class AnnotatorConfigParameter extends AnnotatorParameter {
private String value;
-
+
private AnnotatorParamDefinition type;
public AnnotatorConfigParameter(AnnotatorParamDefinition type, String value) {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java
index 34ebfe92eec012dfc78373fdc4186200114c49ca..bd2ce021eddfa5dfd7e22e9cb39b543046bc884c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorException.java
@@ -8,41 +8,41 @@ package lcsb.mapviewer.annotation.services.annotators;
*/
public class AnnotatorException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Default constructor.
- *
- * @param exception
- * original exception
- */
- public AnnotatorException(Exception exception) {
- super(exception);
- }
+ /**
+ * Default constructor.
+ *
+ * @param exception
+ * original exception
+ */
+ public AnnotatorException(Exception exception) {
+ super(exception);
+ }
- /**
- * Default constructor.
- *
- * @param message
- * message associated with exception
- * @param exception
- * original exception
- */
- public AnnotatorException(String message, Exception exception) {
- super(message, exception);
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message associated with exception
+ * @param exception
+ * original exception
+ */
+ public AnnotatorException(String message, Exception exception) {
+ super(message, exception);
+ }
- /**
- * Default constructor.
- *
- * @param message
- * message associated with exception
- */
- public AnnotatorException(String message) {
- super(message);
- }
+ /**
+ * Default constructor.
+ *
+ * @param message
+ * message associated with exception
+ */
+ public AnnotatorException(String message) {
+ super(message);
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
index 9ea6a6296246dea43ae82d138a155ad13ba3243b..26c20f739fc3058b4ba9eaca2444d97033d61838 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotator.java
@@ -59,249 +59,248 @@ import lcsb.mapviewer.model.map.species.Rna;
@Service
public class BiocompendiumAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Address of the restfull API for biocompendium.
- */
- private static final String SERVICE_ADDRESS = "http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/";
-
- /**
- * Standard class logger.
- */
- private final Logger logger = Logger.getLogger(BiocompendiumAnnotator.class);
-
- /**
- * Xml parser used for processing notes into structured data.
- */
- private RestAnnotationParser rap = new RestAnnotationParser();
-
- /**
- * Default constructor.
- */
- public BiocompendiumAnnotator() {
- super(BiocompendiumAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, true);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- result = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, name));
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Returns String with annotations for species described by {@link MiriamData}
- * with {@link MiriamType#HGNC_SYMBOL} entry.
- *
- * @param md
- * description of the element by {@link MiriamData} with
- * {@link MiriamType#HGNC_SYMBOL} entry
- * @return annotation for species with given name and type from Venkata server
- * @throws IOException
- * thrown when there is a problem with connection to the server
- */
- protected String getAnnotation(MiriamData md) throws IOException {
- if (!MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
- }
-
- MiriamData miriamData = createMiriamData(md);
- miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
-
- String annotation = getCacheValue(miriamData.getResource());
- if (annotation != null) {
- return annotation;
- }
-
- CloseableHttpClient httpClient = HttpClients.createDefault();
-
- HttpPost httppost = new HttpPost(SERVICE_ADDRESS);
- MultipartEntityBuilder builder = MultipartEntityBuilder.create();
-
- // prepare a query
- String requestXml = dataToString(miriamData);
-
- // save query to a temporary file
- File tmp = File.createTempFile("annotation-plugin", "xml");
- BufferedWriter out = new BufferedWriter(new FileWriter(tmp));
- out.write(requestXml);
- out.close();
-
- builder.addBinaryBody("File", tmp, ContentType.APPLICATION_OCTET_STREAM, tmp.getName());
- HttpEntity multipart = builder.build();
- httppost.setEntity(multipart);
- CloseableHttpResponse response = httpClient.execute(httppost);
-
- HttpEntity entity2 = response.getEntity();
- if (entity2 != null) {
- InputStream instream = entity2.getContent();
- Scanner scanner = new Scanner(instream);
- try {
- Scanner s = scanner.useDelimiter("\\A");
- // get results
- String responseXml = "";
- if (s.hasNext()) {
- responseXml = s.next();
- }
- try {
- annotation = getAnnotationsFromXml(responseXml).get(miriamData.getResource());
- } catch (InvalidXmlSchemaException e) {
- throw new IOException(e);
- }
-
- } finally {
- scanner.close();
- instream.close();
- }
- }
- if (annotation != null) {
- setCacheValue(miriamData.getResource(), annotation);
- }
- return annotation;
- }
-
- /**
- * This method convert a hgnc symbol in miriam data into xml request.
- *
- * @param miriamData
- * - {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
- * @return xml string that represent a request to RESTful service
- */
- String dataToString(MiriamData miriamData) {
- if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
- }
- String requestXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
- requestXml += "<request>\n";
- requestXml += " <species name=\"" + miriamData.getResource() + "\" type=\"PROTEIN\"/>\n";
- requestXml += "</request>\n";
- return requestXml;
- }
-
- /**
- * This method parse a response xml from annotation service into a map. A key
- * in the map is a name of species and value is a annotation received from the
- * service.
- *
- * @param xml
- * - xml string to be parsed
- * @return a map with information about annotations. A key in the map is a
- * name of species and value is a annotation received from the
- * service.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
- Map<String, String> result = new HashMap<String, String>();
- // if xml is null or empty string then return empty map
- if (xml == null) {
- return result;
- }
- if (xml.isEmpty()) {
- return result;
- }
- // there is a bug in annotation service that create incorrect xml, therefore
- // we need to alter the xml
- xml = correctInvalidXml(xml);
-
- Document doc = getXmlDocumentFromString(xml);
- result = getAnnotationsFromXmlNode(doc);
- return result;
-
- }
-
- /**
- * Transforms xml retrieved from Venkata server into map of annotations. A key
- * in the map is a name of species and value is a annotation received from the
- * service.
- *
- * @param doc
- * - xml node
- * @return a map with information about annotations. A key in the map is a
- * name of species and value is a annotation received from the
- * service.
- */
- private Map<String, String> getAnnotationsFromXmlNode(Node doc) {
- Map<String, String> result = new HashMap<String, String>();
- NodeList root = doc.getChildNodes();
- Node responseNode = getNode("response", root);
- // root node is called "response"
- if (responseNode == null) {
- throw new InvalidArgumentException("Invalid xml returned by annotation service. No response root node");
- }
- NodeList list = responseNode.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- // all nodes in response are species
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equalsIgnoreCase("species")) {
- String name = getNodeAttr("name", node).replaceAll("%0A", "\n");
- String annotation = getNodeValue(node);
- if (annotation.contains("Symbol: " + name.split(" ")[0].toUpperCase())) {
- result.put(name, annotation);
- } else {
- logger.warn("Problem with annotation for: " + name);
- result.put(name, "");
- }
- } else {
- throw new InvalidArgumentException("Unknown node in xml response: " + node.getNodeName());
- }
- }
- }
- return result;
- }
-
- /**
- * Corrects invalid xml retrieved from Venkata server.
- *
- * @param xml
- * xml to correct
- * @return corrected xml
- */
- private String correctInvalidXml(String xml) {
- int size = 0;
- int size2 = 0;
- do {
- size = xml.length();
- xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*<species", "<species");
- xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*</response", "</response");
- size2 = xml.length();
- } while (size != size2);
- return xml;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- String annotations = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (annotations == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (!annotations.contains("ymbol")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
+ /**
+ * Address of the restfull API for biocompendium.
+ */
+ private static final String SERVICE_ADDRESS = "http://biocompendium.embl.de/map_annotator/REST/GetAnnotation/";
+
+ /**
+ * Standard class logger.
+ */
+ private final Logger logger = Logger.getLogger(BiocompendiumAnnotator.class);
+
+ /**
+ * Xml parser used for processing notes into structured data.
+ */
+ private RestAnnotationParser rap = new RestAnnotationParser();
+
+ /**
+ * Default constructor.
+ */
+ public BiocompendiumAnnotator() {
+ super(BiocompendiumAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, true);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ result = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, name));
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Returns String with annotations for species described by {@link MiriamData}
+ * with {@link MiriamType#HGNC_SYMBOL} entry.
+ *
+ * @param md
+ * description of the element by {@link MiriamData} with
+ * {@link MiriamType#HGNC_SYMBOL} entry
+ * @return annotation for species with given name and type from Venkata server
+ * @throws IOException
+ * thrown when there is a problem with connection to the server
+ */
+ protected String getAnnotation(MiriamData md) throws IOException {
+ if (!MiriamType.HGNC_SYMBOL.equals(md.getDataType())) {
+ throw new InvalidArgumentException(
+ "Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
+ }
+
+ MiriamData miriamData = createMiriamData(md);
+ miriamData.setResource(miriamData.getResource().replaceAll("[\n\r]+", " "));
+
+ String annotation = getCacheValue(miriamData.getResource());
+ if (annotation != null) {
+ return annotation;
+ }
+ CloseableHttpClient httpClient = HttpClients.createDefault();
+
+ HttpPost httppost = new HttpPost(SERVICE_ADDRESS);
+ MultipartEntityBuilder builder = MultipartEntityBuilder.create();
+
+ // prepare a query
+ String requestXml = dataToString(miriamData);
+
+ // save query to a temporary file
+ File tmp = File.createTempFile("annotation-plugin", "xml");
+ BufferedWriter out = new BufferedWriter(new FileWriter(tmp));
+ out.write(requestXml);
+ out.close();
+
+ builder.addBinaryBody("File", tmp, ContentType.APPLICATION_OCTET_STREAM, tmp.getName());
+ HttpEntity multipart = builder.build();
+ httppost.setEntity(multipart);
+ CloseableHttpResponse response = httpClient.execute(httppost);
+
+ HttpEntity entity2 = response.getEntity();
+ if (entity2 != null) {
+ InputStream instream = entity2.getContent();
+ Scanner scanner = new Scanner(instream);
+ try {
+ Scanner s = scanner.useDelimiter("\\A");
+ // get results
+ String responseXml = "";
+ if (s.hasNext()) {
+ responseXml = s.next();
+ }
+ try {
+ annotation = getAnnotationsFromXml(responseXml).get(miriamData.getResource());
+ } catch (InvalidXmlSchemaException e) {
+ throw new IOException(e);
+ }
+
+ } finally {
+ scanner.close();
+ instream.close();
+ }
+ }
+ if (annotation != null) {
+ setCacheValue(miriamData.getResource(), annotation);
+ }
+ return annotation;
+ }
+
+ /**
+ * This method convert a hgnc symbol in miriam data into xml request.
+ *
+ * @param miriamData
+ * - {@link MiriamData} with {@link MiriamType#HGNC_SYMBOL}
+ * @return xml string that represent a request to RESTful service
+ */
+ String dataToString(MiriamData miriamData) {
+ if (!MiriamType.HGNC_SYMBOL.equals(miriamData.getDataType())) {
+ throw new InvalidArgumentException(
+ "Only " + MiriamType.HGNC_SYMBOL.getCommonName() + " miriam registry is supported.");
+ }
+ String requestXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
+ requestXml += "<request>\n";
+ requestXml += " <species name=\"" + miriamData.getResource() + "\" type=\"PROTEIN\"/>\n";
+ requestXml += "</request>\n";
+ return requestXml;
+ }
+
+ /**
+ * This method parse a response xml from annotation service into a map. A key in
+ * the map is a name of species and value is a annotation received from the
+ * service.
+ *
+ * @param xml
+ * - xml string to be parsed
+ * @return a map with information about annotations. A key in the map is a name
+ * of species and value is a annotation received from the service.
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ Map<String, String> getAnnotationsFromXml(String xml) throws InvalidXmlSchemaException {
+ Map<String, String> result = new HashMap<String, String>();
+ // if xml is null or empty string then return empty map
+ if (xml == null) {
+ return result;
+ }
+ if (xml.isEmpty()) {
+ return result;
+ }
+ // there is a bug in annotation service that create incorrect xml, therefore
+ // we need to alter the xml
+ xml = correctInvalidXml(xml);
+
+ Document doc = getXmlDocumentFromString(xml);
+ result = getAnnotationsFromXmlNode(doc);
+ return result;
+
+ }
+
+ /**
+ * Transforms xml retrieved from Venkata server into map of annotations. A key
+ * in the map is a name of species and value is a annotation received from the
+ * service.
+ *
+ * @param doc
+ * - xml node
+ * @return a map with information about annotations. A key in the map is a name
+ * of species and value is a annotation received from the service.
+ */
+ private Map<String, String> getAnnotationsFromXmlNode(Node doc) {
+ Map<String, String> result = new HashMap<String, String>();
+ NodeList root = doc.getChildNodes();
+ Node responseNode = getNode("response", root);
+ // root node is called "response"
+ if (responseNode == null) {
+ throw new InvalidArgumentException("Invalid xml returned by annotation service. No response root node");
+ }
+ NodeList list = responseNode.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ // all nodes in response are species
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equalsIgnoreCase("species")) {
+ String name = getNodeAttr("name", node).replaceAll("%0A", "\n");
+ String annotation = getNodeValue(node);
+ if (annotation.contains("Symbol: " + name.split(" ")[0].toUpperCase())) {
+ result.put(name, annotation);
+ } else {
+ logger.warn("Problem with annotation for: " + name);
+ result.put(name, "");
+ }
+ } else {
+ throw new InvalidArgumentException("Unknown node in xml response: " + node.getNodeName());
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Corrects invalid xml retrieved from Venkata server.
+ *
+ * @param xml
+ * xml to correct
+ * @return corrected xml
+ */
+ private String correctInvalidXml(String xml) {
+ int size = 0;
+ int size2 = 0;
+ do {
+ size = xml.length();
+ xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*<species", "<species");
+ xml = xml.replaceAll("<species name=\"[^\"]*\" type=\"[^\"]*\">(\\s)*</response", "</response");
+ size2 = xml.length();
+ } while (size != size2);
+ return xml;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ String annotations = getAnnotation(createMiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (annotations == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else if (!annotations.contains("ymbol")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
@Override
public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
@@ -340,15 +339,15 @@ public class BiocompendiumAnnotator extends ElementAnnotator implements IExterna
}
- @Override
- public String getCommonName() {
- return "Biocompendium";
- }
+ @Override
+ public String getCommonName() {
+ return "Biocompendium";
+ }
- @Override
- public String getUrl() {
- return "http://biocompendium.embl.de/";
- }
+ @Override
+ public String getUrl() {
+ return "http://biocompendium.embl.de/";
+ }
@Override
public List<AnnotatorInputParameter> getAvailableInputParameters() {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
index 2a1bbd975343456d69a0eb511fb7507418aadce1..01156488e9a8c43a199da7af2b6980454cc70efe 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotator.java
@@ -11,6 +11,7 @@ import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -27,7 +28,6 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
-import org.springframework.stereotype.Service;
/**
* This is a class that implements a backend to CAZy.
@@ -38,49 +38,49 @@ import org.springframework.stereotype.Service;
@Service
public class CazyAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(CazyAnnotator.class);
-
- /**
- * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
- * tair}.
- */
- private TairAnnotator tairAnnotator;
-
- /**
- * Pattern used for finding UniProt symbol from TAIR info page .
- */
- private Pattern cazyIdMatcher = Pattern.compile("\\/((GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?)\\.html");
-
- @Autowired
- public CazyAnnotator(TairAnnotator tairAnnotator) {
- super(CazyAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
- this.tairAnnotator = tairAnnotator;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- MiriamData md = uniprotToCazy(createMiriamData(MiriamType.UNIPROT, "Q9SG95"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (md == null || !md.getResource().equalsIgnoreCase("GH5_7")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(CazyAnnotator.class);
+
+ /**
+ * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+ * tair}.
+ */
+ private TairAnnotator tairAnnotator;
+
+ /**
+ * Pattern used for finding UniProt symbol from TAIR info page .
+ */
+ private Pattern cazyIdMatcher = Pattern.compile("\\/((GT|GH|PL|CE|CBM)\\d+(\\_\\d+)?)\\.html");
+
+ @Autowired
+ public CazyAnnotator(TairAnnotator tairAnnotator) {
+ super(CazyAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ this.tairAnnotator = tairAnnotator;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = uniprotToCazy(createMiriamData(MiriamType.UNIPROT, "Q9SG95"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (md == null || !md.getResource().equalsIgnoreCase("GH5_7")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
@Override
public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
@@ -109,115 +109,115 @@ public class CazyAnnotator extends ElementAnnotator implements IExternalService
return cazyIds.size() > 0;
}
- /**
- * Returns URL to TAIR page about TAIR entry.
- *
- * @param uniProtId
- * UniProt identifier
- * @return URL to CAZY UniProt accession search result page
- */
- private String getCazyUrl(String uniProtId) {
- return "http://www.cazy.org/search?page=recherche&recherche=" + uniProtId + "&tag=10";
- }
-
- /**
- * Parse CAZy webpage to find information about
- * {@link MiriamType#CAZY} and returns them.
- *
- * @param pageContent
- * CAZy info page
- * @return CAZy family identifier found on the page
- */
- private Collection<MiriamData> parseCazy(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = cazyIdMatcher.matcher(pageContent);
- if (m.find()) {
- result.add(createMiriamData(MiriamType.CAZY, m.group(1)));
- }
- return result;
- }
-
- @Override
- public Object 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 query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- return result;
- }
-
- /**
- * Transform UniProt identifier to CAZy identifier.
- *
- * @param UniProt
- * {@link MiriamData} with UniProt identifier
- * @return {@link MiriamData} with CAZy identifier
- * @throws AnnotatorException
- * thrown when there is a problem with accessing external database
- */
- public MiriamData uniprotToCazy(MiriamData uniprot) throws AnnotatorException {
- if (uniprot == null) {
- return null;
- }
-
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
-
- String accessUrl = getCazyUrl(uniprot.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- Collection<MiriamData> collection = parseCazy(pageContent);
- if (collection.size() > 0) {
- return collection.iterator().next();
- } else {
- logger.warn("Cannot find CAZy data for UniProt id: " + uniprot.getResource());
- return null;
- }
- } catch (WrongResponseCodeIOException exception) {
- logger.warn("Wrong response code when retrieving CAZy data for UniProt id: " + uniprot.getResource());
- return null;
- } catch (IOException exception) {
- throw new AnnotatorException(exception);
- }
- }
-
- @Override
- public String getCommonName() {
- return MiriamType.CAZY.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.CAZY.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
- new AnnotatorInputParameter(MiriamType.UNIPROT));
- }
+ /**
+ * Returns URL to TAIR page about TAIR entry.
+ *
+ * @param uniProtId
+ * UniProt identifier
+ * @return URL to CAZY UniProt accession search result page
+ */
+ private String getCazyUrl(String uniProtId) {
+ return "http://www.cazy.org/search?page=recherche&recherche=" + uniProtId + "&tag=10";
+ }
+
+ /**
+ * Parse CAZy webpage to find information about {@link MiriamType#CAZY} and
+ * returns them.
+ *
+ * @param pageContent
+ * CAZy info page
+ * @return CAZy family identifier found on the page
+ */
+ private Collection<MiriamData> parseCazy(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = cazyIdMatcher.matcher(pageContent);
+ if (m.find()) {
+ result.add(createMiriamData(MiriamType.CAZY, m.group(1)));
+ }
+ return result;
+ }
+
+ @Override
+ public Object 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 query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Transform UniProt identifier to CAZy identifier.
+ *
+ * @param UniProt
+ * {@link MiriamData} with UniProt identifier
+ * @return {@link MiriamData} with CAZy identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing external database
+ */
+ public MiriamData uniprotToCazy(MiriamData uniprot) throws AnnotatorException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ String accessUrl = getCazyUrl(uniprot.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseCazy(pageContent);
+ if (collection.size() > 0) {
+ return collection.iterator().next();
+ } else {
+ logger.warn("Cannot find CAZy data for UniProt id: " + uniprot.getResource());
+ return null;
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Wrong response code when retrieving CAZy data for UniProt id: " + uniprot.getResource());
+ return null;
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.CAZY.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.CAZY.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
+ new AnnotatorInputParameter(MiriamType.UNIPROT));
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java
index 1ca1eb2705dcb808e6553ce4d39244b4b79bb5d7..727f0fdf20691feb785b43486cd18dc72ca0f229 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiSearchException.java
@@ -11,22 +11,22 @@ import lcsb.mapviewer.annotation.data.Chebi;
*/
public class ChebiSearchException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public ChebiSearchException(String message, Throwable cause) {
- super(message, cause);
- }
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public ChebiSearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
}
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 be106f4ed157c834c62b62f0381adbb077a0817b..38fea73fe98bc16af4fbe4b230b1e20b7fa52058 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
@@ -89,7 +89,7 @@ public abstract class ElementAnnotator extends CachableInterface {
*/
public void annotateElement(BioEntity element) throws AnnotatorException {
annotateElement(element, new AnnotationParameters());
- };
+ }
/**
* Annotate element using parameters.
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
index 96437e769ccb8364bf6d8ea3b60eef726c4b65e2..4d4d007003ac6f26c05caf222037d9db8aca59c0 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotator.java
@@ -43,257 +43,260 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
@Service
public class EnsemblAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Version of the rest API that is supported by this annotator.
- */
- static final String SUPPORTED_VERSION = "9.0";
-
- /**
- * Url address of ensembl restful service.
- */
- private static final String REST_SERVICE_URL = "https://rest.ensembl.org/xrefs/id/";
-
- /**
- * Suffix that is needed for getting proper result using
- * {@link #REST_SERVICE_URL}.
- */
- private static final String URL_SUFFIX = "?content-type=text/xml";
-
- /**
- * Url used for retrieving version of the restful API.
- */
- private static final String REST_SERVICE_VERSION_URL = "https://rest.ensembl.org/info/rest?content-type=text/xml";
-
- /**
- * Default constructor.
- */
- public EnsemblAnnotator() {
- super(EnsemblAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith("http")) {
- try {
- String result = getWebPageContent(name);
- return result;
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with input string: " + name);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- }
-
- /**
- * Standard class logger.
- */
- private final Logger logger = Logger.getLogger(EnsemblAnnotator.class);
-
- @Override
- public String getCommonName() {
- return MiriamType.ENSEMBL.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.ENSEMBL.getDbHomepage();
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
-
- GenericProtein proteinAlias = new GenericProtein("mock_id");
- proteinAlias.addMiriamData(createMiriamData(MiriamType.ENSEMBL, "ENSG00000157764"));
- annotateElement(proteinAlias);
-
- if (proteinAlias.getFullName() == null || proteinAlias.getFullName().isEmpty()) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else {
- status.setStatus(ExternalServiceStatusType.OK);
- }
-
- String version = getRestfulApiVersion();
- if (!SUPPORTED_VERSION.equals(version)) {
- logger.debug("Version of Ensembl API changed... (new version: " + version + ")");
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
-
- } catch (Exception e) {
- logger.error(getCommonName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- /**
- * Returns current version of restful API.
- *
- * @return version of Ensembl restful API
- * @throws IOException
- * thrown when there is a problem with accessing API
- * @throws InvalidXmlSchemaException
- * thrown when the result returned by API is invalid
- */
- private String getRestfulApiVersion() throws IOException, InvalidXmlSchemaException {
- String content = getWebPageContent(REST_SERVICE_VERSION_URL);
- Node xml = getXmlDocumentFromString(content);
- Node response = getNode("opt", xml.getChildNodes());
- Node data = getNode("data", response.getChildNodes());
-
- String version = super.getNodeAttr("release", data);
- return version;
- }
-
- @Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
- throws AnnotatorException {
- if (identifier.getDataType().equals(MiriamType.ENSEMBL)) {
- ElementUtils eu = new ElementUtils();
- String prefix = eu.getElementTag(element);
- return annotateElement(element, identifier, prefix);
- } else {
- throw new NotImplementedException();
- }
- }
-
- /**
- * Annotates element using identifier given in the parameter.
- *
- * @param annotatedObject
- * element that we want to annotate
- * @param entrezMiriamData
- * identifier that should be used for annotation
- * @param prefix
- * prefix used in warnings
- * @throws AnnotatorException
- * thrown when there is a problem with annotating element
- */
- private boolean annotateElement(BioEntity annotatedObject, MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
- String query = REST_SERVICE_URL + entrezMiriamData.getResource() + URL_SUFFIX;
- try {
- String content = getWebPageContent(query);
- Node xml = getXmlDocumentFromString(content);
- Node response = getNode("opt", xml.getChildNodes());
-
- NodeList list = response.getChildNodes();
- Set<String> synonyms = new HashSet<String>();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("data")) {
- String error = super.getNodeAttr("error", node);
- if (error != null && !error.isEmpty()) {
- logger.warn(prefix + error);
- }
- String dbname = super.getNodeAttr("dbname", node);
-
- if ("EntrezGene".equals(dbname)) {
- String entrezId = super.getNodeAttr("primary_id", node);
- if (entrezId != null && !entrezId.isEmpty()) {
- annotatedObject.addMiriamData(createMiriamData(MiriamType.ENTREZ, entrezId));
- }
- String symbol = super.getNodeAttr("display_id", node);
- if (symbol != null) {
- setSymbol(annotatedObject, symbol, prefix);
- }
- String fullName = super.getNodeAttr("description", node);
- if (symbol != null) {
- setFullName((Element) annotatedObject, fullName, prefix);
- }
- NodeList synonymNodeList = node.getChildNodes();
-
- for (int j = 0; j < synonymNodeList.getLength(); j++) {
- Node synonymNode = synonymNodeList.item(j);
- if (synonymNode.getNodeType() == Node.ELEMENT_NODE && "synonyms".equalsIgnoreCase(synonymNode.getNodeName())) {
- synonyms.add(synonymNode.getTextContent());
- }
- }
- } else if ("HGNC".equals(dbname)) {
- String hgncId = super.getNodeAttr("primary_id", node);
- if (hgncId != null && !hgncId.isEmpty()) {
- hgncId = hgncId.replaceAll("HGNC:", "");
- annotatedObject.addMiriamData(createMiriamData(MiriamType.HGNC, hgncId));
- }
- String hgncSymbol = super.getNodeAttr("display_id", node);
- if (hgncSymbol != null && !hgncSymbol.isEmpty()) {
- annotatedObject.addMiriamData(createMiriamData(MiriamType.HGNC_SYMBOL, hgncSymbol));
- }
- NodeList synonymNodeList = node.getChildNodes();
-
- for (int j = 0; j < synonymNodeList.getLength(); j++) {
- Node synonymNode = synonymNodeList.item(j);
- if (synonymNode.getNodeType() == Node.ELEMENT_NODE && "synonyms".equalsIgnoreCase(synonymNode.getNodeName())) {
- synonyms.add(synonymNode.getTextContent());
- }
- }
- }
- }
- }
- }
- if (synonyms.size() > 0) {
- setSynonyms(annotatedObject, synonyms, prefix);
- }
- return true;
- } catch (WrongResponseCodeIOException e) {
- logger.warn(prefix + "Cannot find information for ensembl: " + entrezMiriamData.getResource());
- return false;
- } catch (Exception e) {
- throw new AnnotatorException(e);
- }
- }
-
- /**
- * Converts {@link MiriamType#ENSEMBL} identifier into
- * {@link MiriamType#ENTREZ} identifier.
- *
- * @param miriamData
- * {@link MiriamData} with {@link MiriamType#ENSEMBL} identifier
- * @return {@link MiriamData} with {@link MiriamType#ENTREZ} or null if such
- * identifier doesn't exists
- * @throws AnnotatorException
- * thrown when there was problem with accessing external database or
- * any other unknown problem
- */
- public MiriamData ensemblIdToEntrezId(MiriamData miriamData) throws AnnotatorException {
- if (!MiriamType.ENSEMBL.equals(miriamData.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.ENSEMBL + " identifier is accepted as an input");
- }
- GenericProtein proteinAlias = new GenericProtein("id");
- annotateElement(proteinAlias, miriamData, "");
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.ENTREZ.equals(md.getDataType())) {
- return md;
- }
- }
- return null;
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.ENSEMBL));
- }
+ /**
+ * Version of the rest API that is supported by this annotator.
+ */
+ static final String SUPPORTED_VERSION = "9.0";
+
+ /**
+ * Url address of ensembl restful service.
+ */
+ private static final String REST_SERVICE_URL = "https://rest.ensembl.org/xrefs/id/";
+
+ /**
+ * Suffix that is needed for getting proper result using
+ * {@link #REST_SERVICE_URL}.
+ */
+ private static final String URL_SUFFIX = "?content-type=text/xml";
+
+ /**
+ * Url used for retrieving version of the restful API.
+ */
+ private static final String REST_SERVICE_VERSION_URL = "https://rest.ensembl.org/info/rest?content-type=text/xml";
+
+ /**
+ * Default constructor.
+ */
+ public EnsemblAnnotator() {
+ super(EnsemblAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith("http")) {
+ try {
+ String result = getWebPageContent(name);
+ return result;
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with input string: " + name);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ }
+
+ /**
+ * Standard class logger.
+ */
+ private final Logger logger = Logger.getLogger(EnsemblAnnotator.class);
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.ENSEMBL.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.ENSEMBL.getDbHomepage();
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+
+ GenericProtein proteinAlias = new GenericProtein("mock_id");
+ proteinAlias.addMiriamData(createMiriamData(MiriamType.ENSEMBL, "ENSG00000157764"));
+ annotateElement(proteinAlias);
+
+ if (proteinAlias.getFullName() == null || proteinAlias.getFullName().isEmpty()) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ } else {
+ status.setStatus(ExternalServiceStatusType.OK);
+ }
+
+ String version = getRestfulApiVersion();
+ if (!SUPPORTED_VERSION.equals(version)) {
+ logger.debug("Version of Ensembl API changed... (new version: " + version + ")");
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+
+ } catch (Exception e) {
+ logger.error(getCommonName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ /**
+ * Returns current version of restful API.
+ *
+ * @return version of Ensembl restful API
+ * @throws IOException
+ * thrown when there is a problem with accessing API
+ * @throws InvalidXmlSchemaException
+ * thrown when the result returned by API is invalid
+ */
+ private String getRestfulApiVersion() throws IOException, InvalidXmlSchemaException {
+ String content = getWebPageContent(REST_SERVICE_VERSION_URL);
+ Node xml = getXmlDocumentFromString(content);
+ Node response = getNode("opt", xml.getChildNodes());
+ Node data = getNode("data", response.getChildNodes());
+
+ String version = super.getNodeAttr("release", data);
+ return version;
+ }
+
+ @Override
+ public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ throws AnnotatorException {
+ if (identifier.getDataType().equals(MiriamType.ENSEMBL)) {
+ ElementUtils eu = new ElementUtils();
+ String prefix = eu.getElementTag(element);
+ return annotateElement(element, identifier, prefix);
+ } else {
+ throw new NotImplementedException();
+ }
+ }
+
+ /**
+ * Annotates element using identifier given in the parameter.
+ *
+ * @param annotatedObject
+ * element that we want to annotate
+ * @param entrezMiriamData
+ * identifier that should be used for annotation
+ * @param prefix
+ * prefix used in warnings
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating element
+ */
+ private boolean annotateElement(BioEntity annotatedObject, MiriamData entrezMiriamData, String prefix)
+ throws AnnotatorException {
+ String query = REST_SERVICE_URL + entrezMiriamData.getResource() + URL_SUFFIX;
+ try {
+ String content = getWebPageContent(query);
+ Node xml = getXmlDocumentFromString(content);
+ Node response = getNode("opt", xml.getChildNodes());
+
+ NodeList list = response.getChildNodes();
+ Set<String> synonyms = new HashSet<String>();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("data")) {
+ String error = super.getNodeAttr("error", node);
+ if (error != null && !error.isEmpty()) {
+ logger.warn(prefix + error);
+ }
+ String dbname = super.getNodeAttr("dbname", node);
+
+ if ("EntrezGene".equals(dbname)) {
+ String entrezId = super.getNodeAttr("primary_id", node);
+ if (entrezId != null && !entrezId.isEmpty()) {
+ annotatedObject.addMiriamData(createMiriamData(MiriamType.ENTREZ, entrezId));
+ }
+ String symbol = super.getNodeAttr("display_id", node);
+ if (symbol != null) {
+ setSymbol(annotatedObject, symbol, prefix);
+ }
+ String fullName = super.getNodeAttr("description", node);
+ if (symbol != null) {
+ setFullName((Element) annotatedObject, fullName, prefix);
+ }
+ NodeList synonymNodeList = node.getChildNodes();
+
+ for (int j = 0; j < synonymNodeList.getLength(); j++) {
+ Node synonymNode = synonymNodeList.item(j);
+ if (synonymNode.getNodeType() == Node.ELEMENT_NODE
+ && "synonyms".equalsIgnoreCase(synonymNode.getNodeName())) {
+ synonyms.add(synonymNode.getTextContent());
+ }
+ }
+ } else if ("HGNC".equals(dbname)) {
+ String hgncId = super.getNodeAttr("primary_id", node);
+ if (hgncId != null && !hgncId.isEmpty()) {
+ hgncId = hgncId.replaceAll("HGNC:", "");
+ annotatedObject.addMiriamData(createMiriamData(MiriamType.HGNC, hgncId));
+ }
+ String hgncSymbol = super.getNodeAttr("display_id", node);
+ if (hgncSymbol != null && !hgncSymbol.isEmpty()) {
+ annotatedObject.addMiriamData(createMiriamData(MiriamType.HGNC_SYMBOL, hgncSymbol));
+ }
+ NodeList synonymNodeList = node.getChildNodes();
+
+ for (int j = 0; j < synonymNodeList.getLength(); j++) {
+ Node synonymNode = synonymNodeList.item(j);
+ if (synonymNode.getNodeType() == Node.ELEMENT_NODE
+ && "synonyms".equalsIgnoreCase(synonymNode.getNodeName())) {
+ synonyms.add(synonymNode.getTextContent());
+ }
+ }
+ }
+ }
+ }
+ }
+ if (synonyms.size() > 0) {
+ setSynonyms(annotatedObject, synonyms, prefix);
+ }
+ return true;
+ } catch (WrongResponseCodeIOException e) {
+ logger.warn(prefix + "Cannot find information for ensembl: " + entrezMiriamData.getResource());
+ return false;
+ } catch (Exception e) {
+ throw new AnnotatorException(e);
+ }
+ }
+
+ /**
+ * Converts {@link MiriamType#ENSEMBL} identifier into {@link MiriamType#ENTREZ}
+ * identifier.
+ *
+ * @param miriamData
+ * {@link MiriamData} with {@link MiriamType#ENSEMBL} identifier
+ * @return {@link MiriamData} with {@link MiriamType#ENTREZ} or null if such
+ * identifier doesn't exists
+ * @throws AnnotatorException
+ * thrown when there was problem with accessing external database or
+ * any other unknown problem
+ */
+ public MiriamData ensemblIdToEntrezId(MiriamData miriamData) throws AnnotatorException {
+ if (!MiriamType.ENSEMBL.equals(miriamData.getDataType())) {
+ throw new InvalidArgumentException("Only " + MiriamType.ENSEMBL + " identifier is accepted as an input");
+ }
+ GenericProtein proteinAlias = new GenericProtein("id");
+ annotateElement(proteinAlias, miriamData, "");
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.ENTREZ.equals(md.getDataType())) {
+ return md;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.ENSEMBL));
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
index 1e3df5ecb85e290c169b373ebd859c81534584a6..6fc9a2a0fa0c64cc3c134b498afb1cc1701a53b9 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/EntrezAnnotator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.io.StringReader;
import java.net.HttpURLConnection;
import java.util.ArrayList;
import java.util.Arrays;
@@ -10,15 +9,10 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
import org.apache.log4j.Logger;
import org.springframework.stereotype.Service;
-import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -55,345 +49,351 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
@Service
public class EntrezAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Prefix used in cache key to indicate that cached value contains information
- * about {@link MiriamType#ENTREZ} to {@link MiriamType#HGNC} conviersion.
- */
- public static final String CACHE_HGNC_ID_PREFIX = "HGNC_ID:";
-
- /**
- * Address of Entrez API that should be used for retrieving data.
- */
- private static final String REST_API_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&rettype=xml&id=";
-
- /**
- * Prefix used in cache key to indicate that cached value contains
- * {@link EntrezData} object for a given entrez id.
- */
- static final String ENTREZ_DATA_PREFIX = "ENTREZ_DATA:";
-
- /**
- * Object that allows to serialize {@link EntrezData} elements into xml string
- * and deserialize xml into {@link EntrezData} objects.
- */
- private XmlSerializer<EntrezData> entrezSerializer;
-
- /**
- * Default constructor.
- */
- public EntrezAnnotator() {
- super(EntrezAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
- entrezSerializer = new XmlSerializer<>(EntrezData.class);
- }
-
- @Override
- public String refreshCacheQuery(Object query) throws SourceNotAvailable {
- String result = null;
- try {
- if (query instanceof String) {
- String name = (String) query;
- if (name.startsWith("http")) {
- result = getWebPageContent(name);
- } else if (name.startsWith(ENTREZ_DATA_PREFIX)) {
- String id = name.replace(ENTREZ_DATA_PREFIX, "");
- result = entrezSerializer.objectToString(getEntrezForMiriamData(createMiriamData(MiriamType.ENTREZ, id), null));
- } else if (name.startsWith(CACHE_HGNC_ID_PREFIX)) {
- String id = name.replace(CACHE_HGNC_ID_PREFIX, "");
- MiriamData md = getHgncIdFromEntrez(createMiriamData(MiriamType.ENTREZ, id));
- if (md != null) {
- result = md.getResource();
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with input string: " + name);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- } catch (AnnotatorException e) {
- throw new SourceNotAvailable(e);
- } catch (IOException e) {
- throw new SourceNotAvailable(e);
- }
- return result;
- }
-
- /**
- * Standard class logger.
- */
- private final Logger logger = Logger.getLogger(EntrezAnnotator.class);
-
- @Override
- public String getCommonName() {
- return MiriamType.ENTREZ.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.ENTREZ.getDbHomepage();
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- GenericProtein proteinAlias = new GenericProtein("id");
- proteinAlias.addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.ENTREZ, "9999"));
- annotateElement(proteinAlias);
-
- if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- } else {
- status.setStatus(ExternalServiceStatusType.OK);
- }
- } catch (Exception e) {
- logger.error(getCommonName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
- throws AnnotatorException {
- if (identifier.getDataType().equals(MiriamType.ENTREZ)) {
- ElementUtils eu = new ElementUtils();
- String prefix = eu.getElementTag(element);
- return annotateElement(element, identifier, prefix);
+ /**
+ * Prefix used in cache key to indicate that cached value contains information
+ * about {@link MiriamType#ENTREZ} to {@link MiriamType#HGNC} conviersion.
+ */
+ public static final String CACHE_HGNC_ID_PREFIX = "HGNC_ID:";
+
+ /**
+ * Address of Entrez API that should be used for retrieving data.
+ */
+ private static final String REST_API_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&rettype=xml&id=";
+
+ /**
+ * Prefix used in cache key to indicate that cached value contains
+ * {@link EntrezData} object for a given entrez id.
+ */
+ static final String ENTREZ_DATA_PREFIX = "ENTREZ_DATA:";
+
+ /**
+ * Object that allows to serialize {@link EntrezData} elements into xml string
+ * and deserialize xml into {@link EntrezData} objects.
+ */
+ private XmlSerializer<EntrezData> entrezSerializer;
+
+ /**
+ * Default constructor.
+ */
+ public EntrezAnnotator() {
+ super(EntrezAnnotator.class, new Class[] { Protein.class, Rna.class, Gene.class }, false);
+ entrezSerializer = new XmlSerializer<>(EntrezData.class);
+ }
+
+ @Override
+ public String refreshCacheQuery(Object query) throws SourceNotAvailable {
+ String result = null;
+ try {
+ if (query instanceof String) {
+ String name = (String) query;
+ if (name.startsWith("http")) {
+ result = getWebPageContent(name);
+ } else if (name.startsWith(ENTREZ_DATA_PREFIX)) {
+ String id = name.replace(ENTREZ_DATA_PREFIX, "");
+ result = entrezSerializer
+ .objectToString(getEntrezForMiriamData(createMiriamData(MiriamType.ENTREZ, id), null));
+ } else if (name.startsWith(CACHE_HGNC_ID_PREFIX)) {
+ String id = name.replace(CACHE_HGNC_ID_PREFIX, "");
+ MiriamData md = getHgncIdFromEntrez(createMiriamData(MiriamType.ENTREZ, id));
+ if (md != null) {
+ result = md.getResource();
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with input string: " + name);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ } catch (AnnotatorException e) {
+ throw new SourceNotAvailable(e);
+ } catch (IOException e) {
+ throw new SourceNotAvailable(e);
+ }
+ return result;
+ }
+
+ /**
+ * Standard class logger.
+ */
+ private final Logger logger = Logger.getLogger(EntrezAnnotator.class);
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.ENTREZ.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.ENTREZ.getDbHomepage();
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ GenericProtein proteinAlias = new GenericProtein("id");
+ proteinAlias
+ .addMiriamData(createMiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.ENTREZ, "9999"));
+ annotateElement(proteinAlias);
+
+ if (proteinAlias.getFullName() == null || proteinAlias.getFullName().equals("")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
} else {
- throw new NotImplementedException();
+ status.setStatus(ExternalServiceStatusType.OK);
+ }
+ } catch (Exception e) {
+ logger.error(getCommonName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public boolean annotateElement(BioEntity element, MiriamData identifier, AnnotationParameters parameters)
+ throws AnnotatorException {
+ if (identifier.getDataType().equals(MiriamType.ENTREZ)) {
+ ElementUtils eu = new ElementUtils();
+ String prefix = eu.getElementTag(element);
+ return annotateElement(element, identifier, prefix);
+ } else {
+ throw new NotImplementedException();
+ }
+ }
+
+ /**
+ * Annotates element using identifier given in the parameter.
+ *
+ * @param element
+ * element that we want to annotate
+ * @param entrezMiriamData
+ * identifier that should be used for annotation
+ * @param prefix
+ * prefix used in warnings
+ * @throws AnnotatorException
+ * thrown when there is a problem with annotating element
+ */
+ private boolean annotateElement(BioEntity element, MiriamData entrezMiriamData, String prefix)
+ throws AnnotatorException {
+ EntrezData data = getEntrezForMiriamData(entrezMiriamData, prefix);
+ if (data != null) {
+ setSymbol(element, data.getSymbol(), prefix);
+
+ setFullName((Element) element, data.getFullName(), prefix);
+
+ element.addMiriamData(data.getMiriamData());
+ setSynonyms(element, data.getSynonyms(), prefix);
+ setDescription(element, data.getDescription());
+ return true;
+ }
+ return false;
+
+ }
+
+ /**
+ * Returns preprocessed data for entrez identifier.
+ *
+ * @param entrezMiriamData
+ * {@link MiriamData} with {@link MiriamType#ENTREZ} id
+ * @param prefix
+ * prefix used for logs
+ * @return {@link EntrezData preprocessed data} for entrez identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with obtaining data from entrez
+ * database
+ */
+ EntrezData getEntrezForMiriamData(MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
+ EntrezData result = entrezSerializer
+ .xmlToObject(super.getCacheNode(ENTREZ_DATA_PREFIX + entrezMiriamData.getResource()));
+ if (result == null) {
+ String query = REST_API_URL + entrezMiriamData.getResource();
+ try {
+ String content = getWebPageContent(query);
+ result = new EntrezData();
+ Node xml = getXmlDocumentFromString(content, false);
+
+ Node response = getNode("Entrezgene-Set", xml.getChildNodes());
+ if (response != null) {
+ Node errorNode = getNode("Error", response.getChildNodes());
+ if (errorNode != null) {
+ logger.warn(
+ prefix + " Invalid " + MiriamType.ENTREZ + " identifier: \"" + entrezMiriamData.getResource() + "\"");
+ return null;
+ }
+ } else {
+ logger
+ .warn(prefix + "Problematic entrez response for identifier: \"" + entrezMiriamData.getResource() + "\"");
+ return null;
+ }
+
+ Node rootNode = getNode("Entrezgene", response.getChildNodes());
+
+ Node annotationNode = getNode("Entrezgene_gene", rootNode.getChildNodes());
+ Node annotationGenRefNode = getNode("Gene-ref", annotationNode.getChildNodes());
+
+ Node symbolNode = getNode("Gene-ref_locus", annotationGenRefNode.getChildNodes());
+ if (symbolNode != null) {
+ String symbol = symbolNode.getTextContent();
+ result.setSymbol(symbol);
+ }
+
+ Node fullNameNode = getNode("Gene-ref_desc", annotationGenRefNode.getChildNodes());
+ if (fullNameNode != null) {
+ String fullname = fullNameNode.getTextContent();
+ result.setFullName(fullname);
+ }
+
+ Node listNode = getNode("Gene-ref_db", annotationGenRefNode.getChildNodes());
+ Set<String> synonyms = new HashSet<String>();
+ if (listNode != null) {
+ NodeList list = getNode("Gene-ref_db", annotationGenRefNode.getChildNodes()).getChildNodes();
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("Dbtag")) {
+ Node dbNameNode = getNode("Dbtag_db", node.getChildNodes());
+ String dbName = dbNameNode.getTextContent();
+
+ Node dbIdNode1 = getNode("Dbtag_tag", node.getChildNodes());
+ Node dbIdNode2 = getNode("Object-id", dbIdNode1.getChildNodes());
+ Node dbIdNode3 = getNode("Object-id_str", dbIdNode2.getChildNodes());
+ if (dbIdNode3 == null) {
+ dbIdNode3 = getNode("Object-id_id", dbIdNode2.getChildNodes());
+ }
+ String dbId = null;
+ if (dbIdNode3 != null) {
+ dbId = dbIdNode3.getTextContent();
+ }
+ if ("HGNC".equals(dbName)) {
+ if (dbId != null && !dbId.isEmpty()) {
+ dbId = dbId.replaceAll("HGNC:", "");
+ result.addMiriamData(createMiriamData(MiriamType.HGNC, dbId));
+ }
+ } else if ("Ensembl".equals(dbName)) {
+ if (dbId != null && !dbId.isEmpty()) {
+ result.addMiriamData(createMiriamData(MiriamType.ENSEMBL, dbId));
+ }
+ }
+
+ }
+ }
+ }
+
+ }
+
+ Node synListNode = getNode("Gene-ref_syn", annotationGenRefNode.getChildNodes());
+ if (synListNode != null) {
+ NodeList list = getNode("Gene-ref_syn", annotationGenRefNode.getChildNodes()).getChildNodes();
+
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ if (node.getNodeName().equals("Gene-ref_syn_E")) {
+ synonyms.add(node.getTextContent());
+ }
+ }
+ }
+ }
+ if (synonyms.size() > 0) {
+ List<String> sortedSynonyms = new ArrayList<String>();
+ sortedSynonyms.addAll(synonyms);
+ Collections.sort(sortedSynonyms);
+ result.setSynonyms(sortedSynonyms);
+ }
+ Node notesNode = getNode("Entrezgene_summary", rootNode.getChildNodes());
+ if (notesNode != null) {
+ String notes = notesNode.getTextContent();
+ if (notes != null) {
+ result.setDescription(notes);
+ }
+ }
+ setCacheValue(ENTREZ_DATA_PREFIX + entrezMiriamData.getResource(), entrezSerializer.objectToString(result));
+ } catch (WrongResponseCodeIOException e) {
+ if (e.getResponseCode() == HttpURLConnection.HTTP_BAD_REQUEST) {
+ logger.warn(prefix + " Invalid " + MiriamType.ENTREZ.getCommonName() + " identifier found");
+ } else {
+ throw new AnnotatorException(e);
+ }
+ } catch (IOException e) {
+ throw new AnnotatorException(e);
+ } catch (InvalidXmlSchemaException e) {
+ throw new AnnotatorException(e);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Converts {@link MiriamType#ENTREZ} identifier into {@link MiriamType#HGNC}
+ * identifier.
+ *
+ * @param miriamData
+ * {@link MiriamData} with {@link MiriamType#ENTREZ} identifier
+ * @return {@link MiriamData} with {@link MiriamType#HGNC} or null if such
+ * identifier doesn't exists
+ * @throws AnnotatorException
+ * thrown when there was problem with accessing external database or
+ * any other unknown problem
+ */
+ public MiriamData getHgncIdFromEntrez(MiriamData miriamData) throws AnnotatorException {
+ if (!MiriamType.ENTREZ.equals(miriamData.getDataType())) {
+ throw new InvalidArgumentException("Only " + MiriamType.ENTREZ + " miriam type is accepted.");
+ }
+ String key = CACHE_HGNC_ID_PREFIX + miriamData.getResource();
+ String value = getCacheValue(key);
+ if (value == null) {
+ GenericProtein proteinAlias = new GenericProtein("some_id");
+ annotateElement(proteinAlias, miriamData, "");
+ for (MiriamData md : proteinAlias.getMiriamData()) {
+ if (MiriamType.HGNC.equals(md.getDataType())) {
+ setCacheValue(key, md.getResource());
+ return md;
+ }
}
- }
-
- /**
- * Annotates element using identifier given in the parameter.
- *
- * @param element
- * element that we want to annotate
- * @param entrezMiriamData
- * identifier that should be used for annotation
- * @param prefix
- * prefix used in warnings
- * @throws AnnotatorException
- * thrown when there is a problem with annotating element
- */
- private boolean annotateElement(BioEntity element, MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
- EntrezData data = getEntrezForMiriamData(entrezMiriamData, prefix);
- if (data != null) {
- setSymbol(element, data.getSymbol(), prefix);
-
- setFullName((Element) element, data.getFullName(), prefix);
-
- element.addMiriamData(data.getMiriamData());
- setSynonyms(element, data.getSynonyms(), prefix);
- setDescription(element, data.getDescription());
- return true;
- }
- return false;
-
- }
-
- /**
- * Returns preprocessed data for entrez identifier.
- *
- * @param entrezMiriamData
- * {@link MiriamData} with {@link MiriamType#ENTREZ} id
- * @param prefix
- * prefix used for logs
- * @return {@link EntrezData preprocessed data} for entrez identifier
- * @throws AnnotatorException
- * thrown when there is a problem with obtaining data from entrez
- * database
- */
- EntrezData getEntrezForMiriamData(MiriamData entrezMiriamData, String prefix) throws AnnotatorException {
- EntrezData result = entrezSerializer.xmlToObject(super.getCacheNode(ENTREZ_DATA_PREFIX + entrezMiriamData.getResource()));
- if (result == null) {
- String query = REST_API_URL + entrezMiriamData.getResource();
- try {
- String content = getWebPageContent(query);
- result = new EntrezData();
- Node xml = getXmlDocumentFromString(content, false);
-
- Node response = getNode("Entrezgene-Set", xml.getChildNodes());
- if (response != null) {
- Node errorNode = getNode("Error", response.getChildNodes());
- if (errorNode != null) {
- logger.warn(prefix + " Invalid " + MiriamType.ENTREZ + " identifier: \"" + entrezMiriamData.getResource() + "\"");
- return null;
- }
- } else {
- logger.warn(prefix + "Problematic entrez response for identifier: \"" + entrezMiriamData.getResource() + "\"");
- return null;
- }
-
- Node rootNode = getNode("Entrezgene", response.getChildNodes());
-
- Node annotationNode = getNode("Entrezgene_gene", rootNode.getChildNodes());
- Node annotationGenRefNode = getNode("Gene-ref", annotationNode.getChildNodes());
-
- Node symbolNode = getNode("Gene-ref_locus", annotationGenRefNode.getChildNodes());
- if (symbolNode != null) {
- String symbol = symbolNode.getTextContent();
- result.setSymbol(symbol);
- }
-
- Node fullNameNode = getNode("Gene-ref_desc", annotationGenRefNode.getChildNodes());
- if (fullNameNode != null) {
- String fullname = fullNameNode.getTextContent();
- result.setFullName(fullname);
- }
-
- Node listNode = getNode("Gene-ref_db", annotationGenRefNode.getChildNodes());
- Set<String> synonyms = new HashSet<String>();
- if (listNode != null) {
- NodeList list = getNode("Gene-ref_db", annotationGenRefNode.getChildNodes()).getChildNodes();
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("Dbtag")) {
- Node dbNameNode = getNode("Dbtag_db", node.getChildNodes());
- String dbName = dbNameNode.getTextContent();
-
- Node dbIdNode1 = getNode("Dbtag_tag", node.getChildNodes());
- Node dbIdNode2 = getNode("Object-id", dbIdNode1.getChildNodes());
- Node dbIdNode3 = getNode("Object-id_str", dbIdNode2.getChildNodes());
- if (dbIdNode3 == null) {
- dbIdNode3 = getNode("Object-id_id", dbIdNode2.getChildNodes());
- }
- String dbId = null;
- if (dbIdNode3 != null) {
- dbId = dbIdNode3.getTextContent();
- }
- if ("HGNC".equals(dbName)) {
- if (dbId != null && !dbId.isEmpty()) {
- dbId = dbId.replaceAll("HGNC:", "");
- result.addMiriamData(createMiriamData(MiriamType.HGNC, dbId));
- }
- } else if ("Ensembl".equals(dbName)) {
- if (dbId != null && !dbId.isEmpty()) {
- result.addMiriamData(createMiriamData(MiriamType.ENSEMBL, dbId));
- }
- }
-
- }
- }
- }
-
- }
-
- Node synListNode = getNode("Gene-ref_syn", annotationGenRefNode.getChildNodes());
- if (synListNode != null) {
- NodeList list = getNode("Gene-ref_syn", annotationGenRefNode.getChildNodes()).getChildNodes();
-
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- if (node.getNodeName().equals("Gene-ref_syn_E")) {
- synonyms.add(node.getTextContent());
- }
- }
- }
- }
- if (synonyms.size() > 0) {
- List<String> sortedSynonyms = new ArrayList<String>();
- sortedSynonyms.addAll(synonyms);
- Collections.sort(sortedSynonyms);
- result.setSynonyms(sortedSynonyms);
- }
- Node notesNode = getNode("Entrezgene_summary", rootNode.getChildNodes());
- if (notesNode != null) {
- String notes = notesNode.getTextContent();
- if (notes != null) {
- result.setDescription(notes);
- }
- }
- setCacheValue(ENTREZ_DATA_PREFIX + entrezMiriamData.getResource(), entrezSerializer.objectToString(result));
- } catch (WrongResponseCodeIOException e) {
- if (e.getResponseCode() == HttpURLConnection.HTTP_BAD_REQUEST) {
- logger.warn(prefix + " Invalid " + MiriamType.ENTREZ.getCommonName() + " identifier found");
- } else {
- throw new AnnotatorException(e);
- }
- } catch (IOException e) {
- throw new AnnotatorException(e);
- } catch (InvalidXmlSchemaException e) {
- throw new AnnotatorException(e);
- }
- }
- return result;
- }
-
- /**
- * Converts {@link MiriamType#ENTREZ} identifier into {@link MiriamType#HGNC}
- * identifier.
- *
- * @param miriamData
- * {@link MiriamData} with {@link MiriamType#ENTREZ} identifier
- * @return {@link MiriamData} with {@link MiriamType#HGNC} or null if such
- * identifier doesn't exists
- * @throws AnnotatorException
- * thrown when there was problem with accessing external database or
- * any other unknown problem
- */
- public MiriamData getHgncIdFromEntrez(MiriamData miriamData) throws AnnotatorException {
- if (!MiriamType.ENTREZ.equals(miriamData.getDataType())) {
- throw new InvalidArgumentException("Only " + MiriamType.ENTREZ + " miriam type is accepted.");
- }
- String key = CACHE_HGNC_ID_PREFIX + miriamData.getResource();
- String value = getCacheValue(key);
- if (value == null) {
- GenericProtein proteinAlias = new GenericProtein("some_id");
- annotateElement(proteinAlias, miriamData, "");
- for (MiriamData md : proteinAlias.getMiriamData()) {
- if (MiriamType.HGNC.equals(md.getDataType())) {
- setCacheValue(key, md.getResource());
- return md;
- }
- }
- setCacheValue(key, "null");
- return null;
- } else if (value.equals("null")) {
- return null;
- } else {
- return createMiriamData(MiriamType.HGNC, value);
- }
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- /**
- * @return the entrezSerializer
- * @see #entrezSerializer
- */
- protected XmlSerializer<EntrezData> getEntrezSerializer() {
- return entrezSerializer;
- }
-
- /**
- * @param entrezSerializer
- * the entrezSerializer to set
- * @see #entrezSerializer
- */
- protected void setEntrezSerializer(XmlSerializer<EntrezData> entrezSerializer) {
- this.entrezSerializer = entrezSerializer;
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.ENTREZ));
- }
+ setCacheValue(key, "null");
+ return null;
+ } else if (value.equals("null")) {
+ return null;
+ } else {
+ return createMiriamData(MiriamType.HGNC, value);
+ }
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ /**
+ * @return the entrezSerializer
+ * @see #entrezSerializer
+ */
+ protected XmlSerializer<EntrezData> getEntrezSerializer() {
+ return entrezSerializer;
+ }
+
+ /**
+ * @param entrezSerializer
+ * the entrezSerializer to set
+ * @see #entrezSerializer
+ */
+ protected void setEntrezSerializer(XmlSerializer<EntrezData> entrezSerializer) {
+ this.entrezSerializer = entrezSerializer;
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.ENTREZ));
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java
index be32c487daca186084e8bd073314feaf608dad62..47fcc8077857c93ed9441aaf2f0ef725fe272f2c 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/GoSearchException.java
@@ -9,22 +9,22 @@ package lcsb.mapviewer.annotation.services.annotators;
*/
public class GoSearchException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public GoSearchException(String message, Throwable cause) {
- super(message, cause);
- }
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public GoSearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
index 19eaaf98cb0368382e70fa4fa83fac4275902f6e..c610abc4fe920ae1ee0d46cfffc1f5c2f0a2db75 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotator.java
@@ -6,7 +6,6 @@ import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
index ac23a6631cd3a1458fed8ad58bd54907e107ca10..ec2609140b5b01ce6e05383fe4e57ac8943bbad1 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotator.java
@@ -5,12 +5,16 @@ import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
-import java.util.Set;
-import java.util.Map;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
+
+import com.google.gson.Gson;
+import com.google.gson.reflect.TypeToken;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -28,13 +32,9 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
import lcsb.mapviewer.model.map.species.field.Structure;
import lcsb.mapviewer.model.map.species.field.UniprotRecord;
-
-import com.google.gson.Gson;
-import com.google.gson.reflect.TypeToken;
-import org.springframework.stereotype.Service;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
/**
* This is a class that implements a backend to the EBI's PDB SIFTS REST API
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
index c3cf1c9b2c2568050b2a702af2ed6cd3a2db7abe..9f3b2eccdfc3b389f874261f27e468581f3000f5 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/PdbBestMappingEntry.java
@@ -8,33 +8,33 @@ import lcsb.mapviewer.model.map.species.field.Structure;
* @author David Hoksza
*
*/
-public class PdbBestMappingEntry {
- public String chain_id;
- public String experimental_method;
- public String pdb_id;
- public int start;
- public int end;
- public int unp_end;
- public double coverage;
- public int unp_start;
- public double resolution;
- public int tax_id;
-
- public Structure convertToStructure() {
-
- Structure s = new Structure();
-
- s.setPdbId(this.pdb_id);
- s.setChainId(this.chain_id);
- s.setCoverage(this.coverage);
- s.setResolution(this.resolution);
- s.setStructStart(this.start);
- s.setStructEnd(this.end);
- s.setUnpStart(this.unp_start);
- s.setUnpEnd(this.unp_end);
- s.setExperimentalMethod(this.experimental_method);
- s.setTaxId(this.tax_id);
-
- return s;
- }
+public class PdbBestMappingEntry {
+ public String chain_id;
+ public String experimental_method;
+ public String pdb_id;
+ public int start;
+ public int end;
+ public int unp_end;
+ public double coverage;
+ public int unp_start;
+ public double resolution;
+ public int tax_id;
+
+ public Structure convertToStructure() {
+
+ Structure s = new Structure();
+
+ s.setPdbId(this.pdb_id);
+ s.setChainId(this.chain_id);
+ s.setCoverage(this.coverage);
+ s.setResolution(this.resolution);
+ s.setStructStart(this.start);
+ s.setStructEnd(this.end);
+ s.setUnpStart(this.unp_start);
+ s.setUnpEnd(this.unp_end);
+ s.setExperimentalMethod(this.experimental_method);
+ s.setTaxId(this.tax_id);
+
+ return s;
+ }
}
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 594d30f155aad77a5e63ced55225c3c87b90bd58..7b377b71ce5bf6b8e8541c4db92689be69933925 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
@@ -7,6 +7,7 @@ import java.util.List;
import java.util.Map.Entry;
import org.apache.log4j.Logger;
+import org.springframework.stereotype.Service;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
@@ -31,7 +32,6 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
-import org.springframework.stereotype.Service;
/**
* This is a class that implements a backend to RECON database.
@@ -356,7 +356,7 @@ public class ReconAnnotator extends ElementAnnotator implements IExternalService
throw new AnnotatorException(e);
}
} else {
- throw new NotImplementedException();
+ throw new NotImplementedException();
}
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
index 6b87438e2661d96156e04fa56f4c2652cd4bbd4f..ab6b1ced8c336200359c465c9eb56a7e4613cce6 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotator.java
@@ -1,11 +1,10 @@
package lcsb.mapviewer.annotation.services.annotators;
-
import java.util.Arrays;
import java.util.List;
import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
@@ -17,10 +16,10 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
-import org.springframework.stereotype.Service;
/**
- * This is a class that implements STITCH annotation which is derived from existing ChEBI annotation.
+ * This is a class that implements STITCH annotation which is derived from
+ * existing ChEBI annotation.
*
* @author David Hoksza
*
@@ -28,38 +27,41 @@ import org.springframework.stereotype.Service;
@Service
public class StitchAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(StitchAnnotator.class);
-
- /**
- * Service used for annotation of entities using {@link MiriamType#STITCH STITCH}.
- */
- private ChebiAnnotator chebiAnnotator;
-
- /**
- * Default constructor.
- */
- public StitchAnnotator(ChebiAnnotator chebiAnnotator) {
- super(StitchAnnotator.class, new Class[] { SimpleMolecule.class }, false);
- this.chebiAnnotator = chebiAnnotator;
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- return chebiAnnotator.getServiceStatus();
- }
-
- /**
- * Returns main layer of the InchKey, * i.e. everything
- * before first hyphen: WBYWAXJHAXSJNI-VOTSOKGWSA-N -> WBYWAXJHAXSJNI
- * @param inchiKey Full inchiKey
- * @return Main layer of the InchiKey
- */
- private String inchiKeyExtractMainLayer(String inchiKey){
- return inchiKey.replaceFirst("-.*", "");
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(StitchAnnotator.class);
+
+ /**
+ * Service used for annotation of entities using {@link MiriamType#STITCH
+ * STITCH}.
+ */
+ private ChebiAnnotator chebiAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ public StitchAnnotator(ChebiAnnotator chebiAnnotator) {
+ super(StitchAnnotator.class, new Class[] { SimpleMolecule.class }, false);
+ this.chebiAnnotator = chebiAnnotator;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ return chebiAnnotator.getServiceStatus();
+ }
+
+ /**
+ * Returns main layer of the InchKey, * i.e. everything before first hyphen:
+ * WBYWAXJHAXSJNI-VOTSOKGWSA-N -> WBYWAXJHAXSJNI
+ *
+ * @param inchiKey
+ * Full inchiKey
+ * @return Main layer of the InchiKey
+ */
+ private String inchiKeyExtractMainLayer(String inchiKey) {
+ return inchiKey.replaceFirst("-.*", "");
+ }
@Override
public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
@@ -87,35 +89,34 @@ public class StitchAnnotator extends ElementAnnotator implements IExternalServic
}
}
- @Override
- public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
- return chebiAnnotator.refreshCacheQuery(query);
- }
-
-
- @Override
- public String getCommonName() {
- return MiriamType.STITCH.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.STITCH.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.CHEBI));
- }
+ @Override
+ public Object refreshCacheQuery(Object query) throws SourceNotAvailable {
+ return chebiAnnotator.refreshCacheQuery(query);
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.STITCH.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.STITCH.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.CHEBI));
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
index 7d97a67f213974f0bdd82ff15d5509ae14d3d35e..becf2954bc10b14f49e15edf47bb779ed63c6974 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/StringAnnotator.java
@@ -5,6 +5,7 @@ import java.util.Arrays;
import java.util.List;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.services.ExternalServiceStatus;
import lcsb.mapviewer.annotation.services.IExternalService;
@@ -16,7 +17,6 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
-import org.springframework.stereotype.Service;
/**
* This is a class that implements a mapping to STRING database.
@@ -26,26 +26,26 @@ import org.springframework.stereotype.Service;
*/
@Service
public class StringAnnotator extends ElementAnnotator implements IExternalService {
-
- /**
- * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
- * TAIR}.
- */
- private TairAnnotator tairAnnotator;
-
- /**
- * Default constructor.
- */
- @Autowired
- public StringAnnotator(TairAnnotator tairAnnotator) {
- super(StringAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
- this.tairAnnotator = tairAnnotator;
- }
- @Override
- public ExternalServiceStatus getServiceStatus() {
- return tairAnnotator.getServiceStatus();
- }
+ /**
+ * Service used for annotation of entities using {@link MiriamType#TAIR_LOCUS
+ * TAIR}.
+ */
+ private TairAnnotator tairAnnotator;
+
+ /**
+ * Default constructor.
+ */
+ @Autowired
+ public StringAnnotator(TairAnnotator tairAnnotator) {
+ super(StringAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ this.tairAnnotator = tairAnnotator;
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ return tairAnnotator.getServiceStatus();
+ }
@Override
public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
@@ -72,45 +72,43 @@ public class StringAnnotator extends ElementAnnotator implements IExternalServic
object.addMiriamData(mdString);
}
}
- return stringIds.size()>0;
+ return stringIds.size() > 0;
}
- /**
- * Transform UniProt {@link MiriamData} data to STRING {@link MiriamData}.
- *
- * @param UniProt
- * {@link MiriamData} with UniProt identifier
- * @return {@link MiriamData} with STRING identifier
- * @throws AnnotatorException
- * thrown when there is a problem with accessing external database
- */
- public MiriamData uniprotToString(MiriamData uniprot) throws AnnotatorException {
- if (uniprot == null) {
- return null;
- }
+ /**
+ * Transform UniProt {@link MiriamData} data to STRING {@link MiriamData}.
+ *
+ * @param UniProt
+ * {@link MiriamData} with UniProt identifier
+ * @return {@link MiriamData} with STRING identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing external database
+ */
+ public MiriamData uniprotToString(MiriamData uniprot) throws AnnotatorException {
+ if (uniprot == null) {
+ return null;
+ }
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
- return createMiriamData(MiriamType.STRING, uniprot.getResource());
- }
+ return createMiriamData(MiriamType.STRING, uniprot.getResource());
+ }
- @Override
- public String getCommonName() {
- return MiriamType.STRING.getCommonName();
- }
+ @Override
+ public String getCommonName() {
+ return MiriamType.STRING.getCommonName();
+ }
- @Override
- public String getUrl() {
- return MiriamType.STRING.getDbHomepage();
- }
+ @Override
+ public String getUrl() {
+ return MiriamType.STRING.getDbHomepage();
+ }
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
- new AnnotatorInputParameter(MiriamType.UNIPROT));
- }
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.TAIR_LOCUS),
+ new AnnotatorInputParameter(MiriamType.UNIPROT));
+ }
}
-
-
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
index 14198eae55db6c2515147b6e0ff295a60d99584c..eacf74d2892b8a79f1fe2a262ff56e55e6a0890f 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotator.java
@@ -1,7 +1,6 @@
package lcsb.mapviewer.annotation.services.annotators;
import java.io.IOException;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashSet;
@@ -10,6 +9,7 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -26,7 +26,6 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
-import org.springframework.stereotype.Service;
/**
* This is a class that implements a backend to TAIR.
@@ -37,200 +36,201 @@ import org.springframework.stereotype.Service;
@Service
public class TairAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(TairAnnotator.class);
-
- /**
- * Pattern used for finding UniProt symbol from TAIR info page .
- */
- private Pattern tairToUniprot = Pattern.compile("UniProtKB=([^-\"]*)");
-
- /**
- * Default constructor.
- */
- public TairAnnotator() {
- super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- MiriamData md = tairToUniprot(createMiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (md == null || !md.getResource().equalsIgnoreCase("Q9MAN1")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
- throws AnnotatorException {
- if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
- MiriamData mdUniprot = tairToUniprot(identifier);
- if (mdUniprot != null ) {
- object.addMiriamData(mdUniprot);
- return true;
- }
- return false;
- } else {
- throw new NotImplementedException();
- }
- }
-
- /**
- * Returns URL to TAIR page about TAIR entry.
- *
- * @param tairId
- * TAIR identifier
- * @return URL to TAIR page about the TAIR entry
- */
- private String getTairUrl(String tairId) {
- return "https://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
- }
-
- /**
- * Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR entry.
- *
- * @param tairId
- * TAIR identifier
- * @return URL to UniProt result page with the TAIR mapping
- */
- private String getUniProtUrl(String tairId) {
- return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+database%3A%28type%3Atair+"+tairId+"%29&format=list&columns=id";
- }
-
- /**
- * Parse TAIR webpage to find information about
- * {@link MiriamType#UNIPROT} and returns them.
- *
- * @param pageContent
- * tair info page
- * @return uniprot identifier found on the page
- */
- private Collection<MiriamData> parseUniprot(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = tairToUniprot.matcher(pageContent);
- if (m.find()) {
- result.add(createMiriamData(MiriamType.UNIPROT, m.group(1)));
- }
- return result;
- }
-
- /**
- * Parse UniProt result page which contains list of Uniprot ids
- * mapped to submitted TAIR id. The procedure obtains first
- * {@link MiriamType#UNIPROT} and returns it.
- *
- * @param pageContent
- * uniprot REST API result page
- * @return uniprot identifier found on the page
- */
- private Collection<MiriamData> parseUniprotUniprot(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- if (!pageContent.isEmpty()) {
- String[] sPageContent= pageContent.split("\\R");
- result.add(createMiriamData(MiriamType.UNIPROT, sPageContent[0]));
- }
- return result;
- }
-
- @Override
- public Object 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 query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- return result;
- }
-
- /**
- * Transform TAIR identifier into uniprot identifier.
- *
- * Used to use the TAIR record page, but that tends to change and
- * moreover TAIR limits number of accesses from an address. So now
- * the transformation queries directly UniProt from which the
- * mapping can be obtained as well.
- *
- * @param tair
- * {@link MiriamData} with TAIR identifier
- * @return {@link MiriamData} with UniProt identifier
- * @throws AnnotatorException
- * thrown when there is a problem with accessing external database
- */
- public MiriamData tairToUniprot(MiriamData tair) throws AnnotatorException {
- if (tair == null) {
- return null;
- }
-
- if (!MiriamType.TAIR_LOCUS.equals(tair.getDataType())) {
- throw new InvalidArgumentException(MiriamType.TAIR_LOCUS + " expected.");
- }
-
- //String accessUrl = getTairUrl(tair.getResource());
- String accessUrl = getUniProtUrl(tair.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- //Collection<MiriamData> collection = parseUniprot(pageContent);
- Collection<MiriamData> collection = parseUniprotUniprot(pageContent);
- if (collection.size() > 0) {
- return collection.iterator().next();
- } else {
- logger.warn("Cannot find uniprot data for id: " + tair.getResource() + " in the tair page");
- return null;
- }
- } catch (WrongResponseCodeIOException exception) {
- logger.warn("Wrong reponse code when accessing tair data with id: " + tair.getResource());
- return null;
- } catch (IOException exception) {
- throw new AnnotatorException(exception);
- }
- }
-
- @Override
- public String getCommonName() {
- return "TAIR";
- }
-
- @Override
- public String getUrl() {
- return MiriamType.TAIR_LOCUS.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(TairAnnotator.class);
+
+ /**
+ * Pattern used for finding UniProt symbol from TAIR info page .
+ */
+ private Pattern tairToUniprot = Pattern.compile("UniProtKB=([^-\"]*)");
+
+ /**
+ * Default constructor.
+ */
+ public TairAnnotator() {
+ super(TairAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = tairToUniprot(createMiriamData(MiriamType.TAIR_LOCUS, "AT1G01030"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (md == null || !md.getResource().equalsIgnoreCase("Q9MAN1")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ throws AnnotatorException {
+ if (identifier.getDataType().equals(MiriamType.TAIR_LOCUS)) {
+ MiriamData mdUniprot = tairToUniprot(identifier);
+ if (mdUniprot != null) {
+ object.addMiriamData(mdUniprot);
+ return true;
+ }
+ return false;
+ } else {
+ throw new NotImplementedException();
+ }
+ }
+
+ /**
+ * Returns URL to TAIR page about TAIR entry.
+ *
+ * @param tairId
+ * TAIR identifier
+ * @return URL to TAIR page about the TAIR entry
+ */
+ private String getTairUrl(String tairId) {
+ return "https://arabidopsis.org/servlets/TairObject?type=locus&name=" + tairId;
+ }
+
+ /**
+ * Returns URL to UniProt result containing mapped UniProtIds for submitted TAIR
+ * entry.
+ *
+ * @param tairId
+ * TAIR identifier
+ * @return URL to UniProt result page with the TAIR mapping
+ */
+ private String getUniProtUrl(String tairId) {
+ return "https://www.uniprot.org/uniprot/?query=database%3A%28type%3Atair%29+database%3A%28type%3Atair+" + tairId
+ + "%29&format=list&columns=id";
+ }
+
+ /**
+ * Parse TAIR webpage to find information about {@link MiriamType#UNIPROT} and
+ * returns them.
+ *
+ * @param pageContent
+ * tair info page
+ * @return uniprot identifier found on the page
+ */
+ private Collection<MiriamData> parseUniprot(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = tairToUniprot.matcher(pageContent);
+ if (m.find()) {
+ result.add(createMiriamData(MiriamType.UNIPROT, m.group(1)));
+ }
+ return result;
+ }
+
+ /**
+ * Parse UniProt result page which contains list of Uniprot ids mapped to
+ * submitted TAIR id. The procedure obtains first {@link MiriamType#UNIPROT} and
+ * returns it.
+ *
+ * @param pageContent
+ * uniprot REST API result page
+ * @return uniprot identifier found on the page
+ */
+ private Collection<MiriamData> parseUniprotUniprot(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ if (!pageContent.isEmpty()) {
+ String[] sPageContent = pageContent.split("\\R");
+ result.add(createMiriamData(MiriamType.UNIPROT, sPageContent[0]));
+ }
+ return result;
+ }
+
+ @Override
+ public Object 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 query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Transform TAIR identifier into uniprot identifier.
+ *
+ * Used to use the TAIR record page, but that tends to change and moreover TAIR
+ * limits number of accesses from an address. So now the transformation queries
+ * directly UniProt from which the mapping can be obtained as well.
+ *
+ * @param tair
+ * {@link MiriamData} with TAIR identifier
+ * @return {@link MiriamData} with UniProt identifier
+ * @throws AnnotatorException
+ * thrown when there is a problem with accessing external database
+ */
+ public MiriamData tairToUniprot(MiriamData tair) throws AnnotatorException {
+ if (tair == null) {
+ return null;
+ }
+
+ if (!MiriamType.TAIR_LOCUS.equals(tair.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.TAIR_LOCUS + " expected.");
+ }
+
+ // String accessUrl = getTairUrl(tair.getResource());
+ String accessUrl = getUniProtUrl(tair.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ // Collection<MiriamData> collection = parseUniprot(pageContent);
+ Collection<MiriamData> collection = parseUniprotUniprot(pageContent);
+ if (collection.size() > 0) {
+ return collection.iterator().next();
+ } else {
+ logger.warn("Cannot find uniprot data for id: " + tair.getResource() + " in the tair page");
+ return null;
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Wrong reponse code when accessing tair data with id: " + tair.getResource());
+ return null;
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+ }
+
+ @Override
+ public String getCommonName() {
+ return "TAIR";
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.TAIR_LOCUS.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
@Override
public List<AnnotatorInputParameter> getAvailableInputParameters() {
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
index 10bb726fad6d63f8ece1b622f28327ff349d9222..4c7a45896ef05d66e0eeec817c075d015320e8fd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotator.java
@@ -10,6 +10,7 @@ import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.apache.log4j.Logger;
+import org.springframework.stereotype.Service;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
@@ -27,7 +28,6 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.modelutils.map.ElementUtils;
-import org.springframework.stereotype.Service;
/**
* This is a class that implements a backend to uniprot restfull API.
@@ -38,273 +38,273 @@ import org.springframework.stereotype.Service;
@Service
public class UniprotAnnotator extends ElementAnnotator implements IExternalService {
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(UniprotAnnotator.class);
-
- /**
- * Pattern used for finding hgnc symbol from uniprot info page .
- */
- private Pattern uniprotToHgnc = Pattern.compile("GN[\\ ]+Name=([^;\\ ]+)");
-
- /**
- * Pattern used for finding entrez identifier from uniprot info page .
- */
- private Pattern uniprotToEntrez = Pattern.compile("DR[\\ ]+GeneID;\\ ([^;\\ ]+)");
-
- /**
- * Pattern used for finding EC symbol from UniProt info page .
- */
- private Pattern uniprotToEC = Pattern.compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
-
-
- /**
- * Class used for some simple operations on {@link BioEntity} elements.
- */
- private ElementUtils elementUtils = new ElementUtils();
-
- /**
- * Default constructor.
- */
- public UniprotAnnotator() {
- super(UniprotAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
- }
-
- @Override
- public ExternalServiceStatus getServiceStatus() {
- ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
-
- GeneralCacheInterface cacheCopy = getCache();
- this.setCache(null);
-
- try {
- MiriamData md = uniProtToHgnc(createMiriamData(MiriamType.UNIPROT, "P37840"));
-
- status.setStatus(ExternalServiceStatusType.OK);
- if (md == null) {
- status.setStatus(ExternalServiceStatusType.DOWN);
- } else if (!md.getResource().equalsIgnoreCase("SNCA")) {
- status.setStatus(ExternalServiceStatusType.CHANGED);
- }
- } catch (Exception e) {
- logger.error(status.getName() + " is down", e);
- status.setStatus(ExternalServiceStatusType.DOWN);
- }
- this.setCache(cacheCopy);
- return status;
- }
-
- @Override
- public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
- throws AnnotatorException {
- if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
-
- String accessUrl = getUniprotUrl(identifier.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- // check if we have data over there
- if (!pageContent.contains("<title>Error</title>")) {
- Set<MiriamData> annotations = new HashSet<MiriamData>();
- annotations.addAll(parseHgnc(pageContent));
- annotations.addAll(parseEntrez(pageContent));
- annotations.addAll(parseEC(pageContent));
- if (!object.getMiriamData().contains(identifier)) {
- annotations.add(createMiriamData(MiriamType.UNIPROT, identifier.getResource()));
- }
- object.addMiriamData(annotations);
- return true;
- } else {
- // this means that entry with a given uniprot id doesn't exist
- if (object.getMiriamData().contains(identifier)) {
- logger.warn(elementUtils.getElementTag(object) + " Invalid uniprot id: " + identifier);
- }
- return false;
- }
- } catch (WrongResponseCodeIOException exception) {
- logger.warn("Cannot find uniprot data for id: " + identifier);
- return false;
- } catch (IOException exception) {
- throw new AnnotatorException(exception);
- }
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(UniprotAnnotator.class);
+
+ /**
+ * Pattern used for finding hgnc symbol from uniprot info page .
+ */
+ private Pattern uniprotToHgnc = Pattern.compile("GN[\\ ]+Name=([^;\\ ]+)");
+
+ /**
+ * Pattern used for finding entrez identifier from uniprot info page .
+ */
+ private Pattern uniprotToEntrez = Pattern.compile("DR[\\ ]+GeneID;\\ ([^;\\ ]+)");
+
+ /**
+ * Pattern used for finding EC symbol from UniProt info page .
+ */
+ private Pattern uniprotToEC = Pattern
+ .compile("EC=((\\d+\\.-\\.-\\.-)|(\\d+\\.\\d+\\.-\\.-)|(\\d+\\.\\d+\\.\\d+\\.-)|(\\d+\\.\\d+\\.\\d+\\.\\d+))");
+
+ /**
+ * Class used for some simple operations on {@link BioEntity} elements.
+ */
+ private ElementUtils elementUtils = new ElementUtils();
+
+ /**
+ * Default constructor.
+ */
+ public UniprotAnnotator() {
+ super(UniprotAnnotator.class, new Class[] { Protein.class, Gene.class, Rna.class }, false);
+ }
+
+ @Override
+ public ExternalServiceStatus getServiceStatus() {
+ ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
+
+ GeneralCacheInterface cacheCopy = getCache();
+ this.setCache(null);
+
+ try {
+ MiriamData md = uniProtToHgnc(createMiriamData(MiriamType.UNIPROT, "P37840"));
+
+ status.setStatus(ExternalServiceStatusType.OK);
+ if (md == null) {
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ } else if (!md.getResource().equalsIgnoreCase("SNCA")) {
+ status.setStatus(ExternalServiceStatusType.CHANGED);
+ }
+ } catch (Exception e) {
+ logger.error(status.getName() + " is down", e);
+ status.setStatus(ExternalServiceStatusType.DOWN);
+ }
+ this.setCache(cacheCopy);
+ return status;
+ }
+
+ @Override
+ public boolean annotateElement(BioEntity object, MiriamData identifier, AnnotationParameters parameters)
+ throws AnnotatorException {
+ if (identifier.getDataType().equals(MiriamType.UNIPROT)) {
+
+ String accessUrl = getUniprotUrl(identifier.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ // check if we have data over there
+ if (!pageContent.contains("<title>Error</title>")) {
+ Set<MiriamData> annotations = new HashSet<MiriamData>();
+ annotations.addAll(parseHgnc(pageContent));
+ annotations.addAll(parseEntrez(pageContent));
+ annotations.addAll(parseEC(pageContent));
+ if (!object.getMiriamData().contains(identifier)) {
+ annotations.add(createMiriamData(MiriamType.UNIPROT, identifier.getResource()));
+ }
+ object.addMiriamData(annotations);
+ return true;
+ } else {
+ // this means that entry with a given uniprot id doesn't exist
+ if (object.getMiriamData().contains(identifier)) {
+ logger.warn(elementUtils.getElementTag(object) + " Invalid uniprot id: " + identifier);
+ }
+ return false;
+ }
+ } catch (WrongResponseCodeIOException exception) {
+ logger.warn("Cannot find uniprot data for id: " + identifier);
+ return false;
+ } catch (IOException exception) {
+ throw new AnnotatorException(exception);
+ }
+ } else {
+ throw new NotImplementedException();
+ }
+ }
+
+ /**
+ * Returns url to uniprot restfull API about uniprot entry.
+ *
+ * @param uniprotId
+ * uniprot identifier
+ * @return url to uniprot restfull API about uniprot entry
+ */
+ private String getUniprotUrl(String uniprotId) {
+ return "https://www.uniprot.org/uniprot/" + uniprotId + ".txt";
+ }
+
+ /**
+ * Parse uniprot webpage to find information about {@link MiriamType#ENTREZ} and
+ * returns them.
+ *
+ * @param pageContent
+ * uniprot info page
+ * @return set of entrez identifiers found on the webpage
+ */
+ private Collection<MiriamData> parseEntrez(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotToEntrez.matcher(pageContent);
+ if (m.find()) {
+ result.add(createMiriamData(MiriamType.ENTREZ, m.group(1)));
+ }
+ return result;
+ }
+
+ /**
+ * Parse uniprot webpage to find information about
+ * {@link MiriamType#HGNC_SYMBOL} and returns them.
+ *
+ * @param pageContent
+ * uniprot info page
+ * @return set of entrez identifiers found on the webpage
+ */
+ private Collection<MiriamData> parseHgnc(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotToHgnc.matcher(pageContent);
+ if (m.find()) {
+ result.add(createMiriamData(MiriamType.HGNC_SYMBOL, m.group(1)));
+ }
+ return result;
+ }
+
+ /**
+ * Parse UniProt webpage to find information about {@link MiriamType#EC}s and
+ * returns them.
+ *
+ * @param pageContent
+ * UniProt info page
+ * @return EC found on the page
+ */
+ private Collection<MiriamData> parseEC(String pageContent) {
+ Collection<MiriamData> result = new HashSet<MiriamData>();
+ Matcher m = uniprotToEC.matcher(pageContent);
+ while (m.find()) {
+ result.add(createMiriamData(MiriamType.EC, m.group(1)));
+ }
+ return result;
+ }
+
+ @Override
+ public Object 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 query: " + query);
+ }
+ } else {
+ throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
+ }
+ return result;
+ }
+
+ /**
+ * Transform uniprot identifier into hgnc name.
+ *
+ * @param uniprot
+ * {@link MiriamData} with uniprot identifier
+ * @return {@link MiriamData} with hgnc name
+ * @throws UniprotSearchException
+ * thrown when there is aproblem with accessing external database
+ */
+ public MiriamData uniProtToHgnc(MiriamData uniprot) throws UniprotSearchException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ String accessUrl = getUniprotUrl(uniprot.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseHgnc(pageContent);
+ if (collection.size() > 0) {
+ return collection.iterator().next();
+ } else {
+ return null;
+ }
+ } catch (IOException e) {
+ throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
+ }
+
+ }
+
+ /**
+ * Transform uniprot identifier into EC identifiers.
+ *
+ * @param uniprot
+ * {@link MiriamData} with uniprot identifier
+ * @return ArrayList of {@link MiriamData} with EC codes
+ * @throws UniprotSearchException
+ * thrown when there is a problem with accessing external database
+ */
+ public Collection<MiriamData> uniProtToEC(MiriamData uniprot) throws UniprotSearchException {
+ if (uniprot == null) {
+ return null;
+ }
+
+ if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
+ throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
+ }
+
+ String accessUrl = getUniprotUrl(uniprot.getResource());
+ try {
+ String pageContent = getWebPageContent(accessUrl);
+ Collection<MiriamData> collection = parseEC(pageContent);
+ if (collection.size() > 0) {
+ return collection;
} else {
- throw new NotImplementedException();
+ return null;
}
- }
-
- /**
- * Returns url to uniprot restfull API about uniprot entry.
- *
- * @param uniprotId
- * uniprot identifier
- * @return url to uniprot restfull API about uniprot entry
- */
- private String getUniprotUrl(String uniprotId) {
- return "https://www.uniprot.org/uniprot/" + uniprotId + ".txt";
- }
-
- /**
- * Parse uniprot webpage to find information about {@link MiriamType#ENTREZ}
- * and returns them.
- *
- * @param pageContent
- * uniprot info page
- * @return set of entrez identifiers found on the webpage
- */
- private Collection<MiriamData> parseEntrez(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = uniprotToEntrez.matcher(pageContent);
- if (m.find()) {
- result.add(createMiriamData(MiriamType.ENTREZ, m.group(1)));
- }
- return result;
- }
-
- /**
- * Parse uniprot webpage to find information about
- * {@link MiriamType#HGNC_SYMBOL} and returns them.
- *
- * @param pageContent
- * uniprot info page
- * @return set of entrez identifiers found on the webpage
- */
- private Collection<MiriamData> parseHgnc(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = uniprotToHgnc.matcher(pageContent);
- if (m.find()) {
- result.add(createMiriamData(MiriamType.HGNC_SYMBOL, m.group(1)));
- }
- return result;
- }
-
- /**
- * Parse UniProt webpage to find information about
- * {@link MiriamType#EC}s and returns them.
- *
- * @param pageContent
- * UniProt info page
- * @return EC found on the page
- */
- private Collection<MiriamData> parseEC(String pageContent) {
- Collection<MiriamData> result = new HashSet<MiriamData>();
- Matcher m = uniprotToEC.matcher(pageContent);
- while (m.find()) {
- result.add(createMiriamData(MiriamType.EC, m.group(1)));
- }
- return result;
- }
-
- @Override
- public Object 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 query: " + query);
- }
- } else {
- throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
- }
- return result;
- }
-
- /**
- * Transform uniprot identifier into hgnc name.
- *
- * @param uniprot
- * {@link MiriamData} with uniprot identifier
- * @return {@link MiriamData} with hgnc name
- * @throws UniprotSearchException
- * thrown when there is aproblem with accessing external database
- */
- public MiriamData uniProtToHgnc(MiriamData uniprot) throws UniprotSearchException {
- if (uniprot == null) {
- return null;
- }
-
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
-
- String accessUrl = getUniprotUrl(uniprot.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- Collection<MiriamData> collection = parseHgnc(pageContent);
- if (collection.size() > 0) {
- return collection.iterator().next();
- } else {
- return null;
- }
- } catch (IOException e) {
- throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
- }
-
- }
-
- /**
- * Transform uniprot identifier into EC identifiers.
- *
- * @param uniprot
- * {@link MiriamData} with uniprot identifier
- * @return ArrayList of {@link MiriamData} with EC codes
- * @throws UniprotSearchException
- * thrown when there is a problem with accessing external database
- */
- public Collection<MiriamData> uniProtToEC(MiriamData uniprot) throws UniprotSearchException {
- if (uniprot == null) {
- return null;
- }
-
- if (!MiriamType.UNIPROT.equals(uniprot.getDataType())) {
- throw new InvalidArgumentException(MiriamType.UNIPROT + " expected.");
- }
-
- String accessUrl = getUniprotUrl(uniprot.getResource());
- try {
- String pageContent = getWebPageContent(accessUrl);
- Collection<MiriamData> collection = parseEC(pageContent);
- if (collection.size() > 0) {
- return collection;
- } else {
- return null;
- }
- } catch (IOException e) {
- throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
- }
-
- }
-
- @Override
- public String getCommonName() {
- return MiriamType.UNIPROT.getCommonName();
- }
-
- @Override
- public String getUrl() {
- return MiriamType.UNIPROT.getDbHomepage();
- }
-
- @Override
- protected WebPageDownloader getWebPageDownloader() {
- return super.getWebPageDownloader();
- }
-
- @Override
- protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
- super.setWebPageDownloader(webPageDownloader);
- }
-
- @Override
- public List<AnnotatorInputParameter> getAvailableInputParameters() {
- return Arrays.asList(new AnnotatorInputParameter(MiriamType.UNIPROT),
- new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.UNIPROT));
- }
+ } catch (IOException e) {
+ throw new UniprotSearchException("Problem with accessing uniprot webpage", e);
+ }
+
+ }
+
+ @Override
+ public String getCommonName() {
+ return MiriamType.UNIPROT.getCommonName();
+ }
+
+ @Override
+ public String getUrl() {
+ return MiriamType.UNIPROT.getDbHomepage();
+ }
+
+ @Override
+ protected WebPageDownloader getWebPageDownloader() {
+ return super.getWebPageDownloader();
+ }
+
+ @Override
+ protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
+ super.setWebPageDownloader(webPageDownloader);
+ }
+
+ @Override
+ public List<AnnotatorInputParameter> getAvailableInputParameters() {
+ return Arrays.asList(new AnnotatorInputParameter(MiriamType.UNIPROT),
+ new AnnotatorInputParameter(BioEntityField.NAME, MiriamType.UNIPROT));
+ }
}
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java
index 6b12f60e3c74aa5d75f6acf86bbf6912a318f7de..5167e746694df311606aa30e3fcc1a0992cafbac 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/UniprotSearchException.java
@@ -9,22 +9,22 @@ package lcsb.mapviewer.annotation.services.annotators;
*/
public class UniprotSearchException extends Exception {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (A <tt>null</tt> value is permitted, and indicates that
- * the cause is nonexistent or unknown.)
- */
- public UniprotSearchException(String message, Throwable cause) {
- super(message, cause);
- }
+ /**
+ * Constructs a new exception with the specified detail message and cause.
+ *
+ * @param message
+ * the detail message
+ * @param cause
+ * the cause (A <tt>null</tt> value is permitted, and indicates that
+ * the cause is nonexistent or unknown.)
+ */
+ public UniprotSearchException(String message, Throwable cause) {
+ super(message, cause);
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
index d30e43ae11d147a1020494813b00cdf72a0a520b..c9b84d136fddf571e55df1e05233e297465cab91 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AllAnnotatorTests.java
@@ -6,24 +6,24 @@ import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
@SuiteClasses({ AnnotatorExceptionTest.class,
- AnnotatorExceptionTest.class,
- BrendaAnnotatorTest.class,
- BiocompendiumAnnotatorTest.class,
- CazyAnnotatorTest.class,
- ChebiAnnotatorTest.class,
- ElementAnnotatorTest.class,
- EnsemblAnnotatorTest.class,
- EntrezAnnotatorTest.class,
- GoAnnotatorTest.class,
- HgncAnnotatorTest.class,
- KeggAnnotatorTest.class,
- MultipleAnnotatorsTest.class,
- PdbAnnotatorTest.class,
- ReconAnnotatorTest.class,
- StitchAnnotatorTest.class,
- StringAnnotatorTest.class,
- TairAnnotatorTest.class,
- UniprotAnnotatorTest.class,
+ AnnotatorExceptionTest.class,
+ BrendaAnnotatorTest.class,
+ BiocompendiumAnnotatorTest.class,
+ CazyAnnotatorTest.class,
+ ChebiAnnotatorTest.class,
+ ElementAnnotatorTest.class,
+ EnsemblAnnotatorTest.class,
+ EntrezAnnotatorTest.class,
+ GoAnnotatorTest.class,
+ HgncAnnotatorTest.class,
+ KeggAnnotatorTest.class,
+ MultipleAnnotatorsTest.class,
+ PdbAnnotatorTest.class,
+ ReconAnnotatorTest.class,
+ StitchAnnotatorTest.class,
+ StringAnnotatorTest.class,
+ TairAnnotatorTest.class,
+ UniprotAnnotatorTest.class,
})
public class AllAnnotatorTests {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
index 68f6a0176587ab7f5e5bdd4b25ba536c77c9b7ad..29befabb845bbfd0e8ae7c3b3c196f354caa3a26 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/AnnotatorExceptionTest.java
@@ -1,6 +1,6 @@
package lcsb.mapviewer.annotation.services.annotators;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
import org.junit.After;
import org.junit.AfterClass;
@@ -9,22 +9,22 @@ import org.junit.Test;
public class AnnotatorExceptionTest {
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
+ @AfterClass
+ public static void tearDownAfterClass() throws Exception {
+ }
- @Before
- public void setUp() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @After
- public void tearDown() throws Exception {
- }
+ @After
+ public void tearDown() throws Exception {
+ }
- @Test
- public void testConstructor() {
- AnnotatorException e = new AnnotatorException("messss");
- assertEquals("messss",e.getMessage());
- }
+ @Test
+ public void testConstructor() {
+ AnnotatorException e = new AnnotatorException("messss");
+ assertEquals("messss", e.getMessage());
+ }
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
index 5747fea0540177894351be9e9f92484c897f9a20..f4c2219a59ad132fc6afdf0c0cb34887531c6079 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BiocompendiumAnnotatorTest.java
@@ -301,7 +301,8 @@ public class BiocompendiumAnnotatorTest extends AnnotationTestFunctions {
@Test
public void testRefreshValueWhenProblemWithSource() throws Exception {
try {
- BiocompendiumAnnotator annotatorUnderTest = Mockito.mock(BiocompendiumAnnotator.class, Mockito.CALLS_REAL_METHODS);
+ BiocompendiumAnnotator annotatorUnderTest = Mockito.mock(BiocompendiumAnnotator.class,
+ Mockito.CALLS_REAL_METHODS);
when(annotatorUnderTest.getAnnotationsFromXml(anyString())).thenThrow(InvalidXmlSchemaException.class);
annotatorUnderTest.refreshCacheQuery(camk4.getResource());
fail("Exception expected");
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
index d0b6b11890d7264ed9de8b08b88962fac2981584..8e0ab1c8a1a46b4294f3a2d0de5f2941bf01e2df 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/BrendaAnnotatorTest.java
@@ -4,8 +4,8 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
-import static org.mockito.Matchers.nullable;
-import static org.mockito.Matchers.anyString;
+import static org.mockito.ArgumentMatchers.anyString;
+import static org.mockito.ArgumentMatchers.nullable;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -164,7 +164,8 @@ public class BrendaAnnotatorTest extends AnnotationTestFunctions {
protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "bla"));
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
uniprotAnnotator.setWebPageDownloader(mockDownloader);
brendaAnnotator.annotateElement(protein);
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
index 44ec236b94c4c21908a2365b5ca443e3fc1d8cc0..c7b943da75e2d4244579da82605667a7d914cd8c 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/CazyAnnotatorTest.java
@@ -6,8 +6,8 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.ArgumentMatchers.anyString;
-import static org.mockito.Mockito.when;
import static org.mockito.ArgumentMatchers.nullable;
+import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -257,7 +257,8 @@ public class CazyAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = cazyAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
cazyAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, cazyAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
index 166a23b64ceb772043d55a1c30c0c1d148349b82..e79f08c58eb2b46f0240391cfc171141d0a93985 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/EnsemblAnnotatorTest.java
@@ -20,7 +20,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
index 3fa39070775be126efaa7736b7f3ade839345ea8..3f14d80fd8a0eec6e9968fe23e18e82777f9ceac 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/HgncAnnotatorTest.java
@@ -22,7 +22,6 @@ import org.springframework.beans.factory.annotation.Autowired;
import lcsb.mapviewer.annotation.AnnotationTestFunctions;
import lcsb.mapviewer.annotation.cache.GeneralCacheInterface;
-import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCache;
import lcsb.mapviewer.annotation.cache.PermanentDatabaseLevelCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.annotation.cache.WebPageDownloader;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
index 947b3cb56e406f617e1397d82708243808eb6146..f5a5bb90750a09b99bee0b1d559a877fdf94f6ac 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/KeggAnnotatorTest.java
@@ -4,15 +4,14 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
-import java.util.List;
import java.util.Set;
import org.apache.http.HttpStatus;
@@ -33,7 +32,6 @@ import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.user.AnnotatorParamDefinition;
-import lcsb.mapviewer.model.user.UserAnnotatorsParam;
public class KeggAnnotatorTest extends AnnotationTestFunctions {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
index b3d6d580eccc91c5c6b42a5764006e6db9d8d696..2eac724fa920edee5164cc112ee98bd0a0e85b59 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/PdbAnnotatorTest.java
@@ -3,14 +3,15 @@ package lcsb.mapviewer.annotation.services.annotators;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.util.Set;
import org.junit.After;
import org.junit.Before;
+import org.junit.Ignore;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
@@ -27,216 +28,221 @@ import lcsb.mapviewer.model.map.species.field.UniprotRecord;
public class PdbAnnotatorTest extends AnnotationTestFunctions {
- @Autowired
- PdbAnnotator pdbAnnotator;
-
- @Autowired
- UniprotAnnotator uniprotAnnotator;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAnnotate1() throws Exception {
- try {
- String uniprotId = "P29373";
- Species protein = new GenericProtein("id");
- protein.setName(uniprotId);
- /* One needs to have the UniProt ID first.
- * This tests simulates situation when the Uniprot annotator
- * is called first.
- */
- uniprotAnnotator.annotateElement(protein);
- int cntAnnotations1 = protein.getMiriamData().size();
- pdbAnnotator.annotateElement(protein);
- int cntAnnotations2 = protein.getMiriamData().size();
-
- assertTrue(cntAnnotations2 > cntAnnotations1);
-
- boolean pdb = false;
-
- for (MiriamData md : protein.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PDB)) {
- pdb = true;
- break;
- }
- }
- assertTrue("No PDB annotation extracted from pdb annotator", pdb);
-
- Set<UniprotRecord> urs = protein.getUniprots();
- //Test whether there is a uniprot record
- assertTrue(urs.size() > 0);
- UniprotRecord ur = null;
- for (UniprotRecord ur1 : urs) {
- if (ur1.getUniprotId() == uniprotId) {
- ur = ur1;
- }
- }
- //Test whether there is a uniprot record with the uniprot ID which was stored
- assertNotNull(ur);
- //Test whether structures are there
- Set<Structure> ss = ur.getStructures();
- assertNotNull(ss);
- assertTrue(ss.size() > 0);
- //Test whether uniprot is accessible from structure
- assertTrue(ss.iterator().next().getUniprot() == ur);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-// @Test
-// public void testAnnotate2() throws Exception {
-// try {
-// Species protein = new GenericProtein("id");
-// protein.setName("P29373");
-// /* One needs to have the UniProt ID first, and Uniprot lookup
-// * through HGNC is included in PDB annotator.
-// * This tests simulates situation when the PDB annotator is called first.
-// */
-// pdbAnnotator.annotateElement(protein);
-// int cntAnnotations = protein.getMiriamData().size();
-
-// assertTrue(cntAnnotations > 0);
-
-// boolean pdb = false;
-
-// for (MiriamData md : protein.getMiriamData()) {
-// if (md.getDataType().equals(MiriamType.PDB)) {
-// pdb = true;
-// break;
-// }
-// }
-// assertTrue("No PDB annotation extracted from pdb annotator", pdb);
-
-// } catch (Exception e) {
-// e.printStackTrace();
-// throw e;
-// }
-// }
-
-// @Test
-// public void testAnnotateNotUniprotAnnodated() throws Exception {
-// try {
-// Species protein = new GenericProtein("id");
-// protein.setName("P29373");
-// pdbAnnotator.annotateElement(protein);
-//
-// assertTrue("UniProt annotation in PDB annotator failed", protein.getMiriamData().size() > 0);
-
-// boolean pdb = false;
-
-// for (MiriamData md : protein.getMiriamData()) {
-// if (md.getDataType().equals(MiriamType.PDB)) {
-// pdb = true;
-// break;
-// }
-// }
-// assertTrue("No PDB annotation extracted from PDB annotator", pdb);
-
-// } catch (Exception e) {
-// e.printStackTrace();
-// throw e;
-// }
-// }
-
- @Test
- public void testAnnotateInvalidUniprot() throws Exception {
- try {
- Species protein = new GenericProtein("id");
- protein.setName("bla");
- pdbAnnotator.annotateElement(protein);
-
- assertEquals(0, protein.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateValidUniprotNonexistingPdb() throws Exception {
- try {
- Species protein = new GenericProtein("id");
- protein.setName("Q88VP8");
- pdbAnnotator.annotateElement(protein);
-
- boolean pdb = false;
- for (MiriamData md : protein.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.PDB)) {
- pdb = true;
- break;
- }
- }
- assertTrue("PDB mapping found for structure for which no should be available", !pdb);
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testSimulateDownStatus() throws Exception {
- WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
- pdbAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.DOWN, pdbAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pdbAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateChangedStatus() throws Exception {
- WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
- try {
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenReturn("{\"P29373\": [{\"xxx\": 140}]}");
- pdbAnnotator.setWebPageDownloader(mockDownloader);
- assertEquals(ExternalServiceStatusType.CHANGED, pdbAnnotator.getServiceStatus().getStatus());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pdbAnnotator.setWebPageDownloader(downloader);
- }
- }
-
- @Test
- public void testSimulateInvalidJson() throws Exception {
- WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
- try {
- Species protein = new GenericProtein("id");
- protein.setName("Q88VP8");
- uniprotAnnotator.annotateElement(protein);
- int cntAnnotations1 = protein.getMiriamData().size();
-
- WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("\"P29373\": [{\"xxx\": 140}]}");
- pdbAnnotator.setWebPageDownloader(mockDownloader);
-
- pdbAnnotator.annotateElement(protein);
- int cntAnnotations2 = protein.getMiriamData().size();
- assertTrue(cntAnnotations1 == cntAnnotations2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- } finally {
- pdbAnnotator.setWebPageDownloader(downloader);
- }
- }
+ @Autowired
+ PdbAnnotator pdbAnnotator;
+
+ @Autowired
+ UniprotAnnotator uniprotAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotate1() throws Exception {
+ try {
+ String uniprotId = "P29373";
+ Species protein = new GenericProtein("id");
+ protein.setName(uniprotId);
+ /*
+ * One needs to have the UniProt ID first. This tests simulates situation when
+ * the Uniprot annotator is called first.
+ */
+ uniprotAnnotator.annotateElement(protein);
+ int cntAnnotations1 = protein.getMiriamData().size();
+ pdbAnnotator.annotateElement(protein);
+ int cntAnnotations2 = protein.getMiriamData().size();
+
+ assertTrue(cntAnnotations2 > cntAnnotations1);
+
+ boolean pdb = false;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("No PDB annotation extracted from pdb annotator", pdb);
+
+ Set<UniprotRecord> urs = protein.getUniprots();
+ // Test whether there is a uniprot record
+ assertTrue(urs.size() > 0);
+ UniprotRecord ur = null;
+ for (UniprotRecord ur1 : urs) {
+ if (ur1.getUniprotId() == uniprotId) {
+ ur = ur1;
+ }
+ }
+ // Test whether there is a uniprot record with the uniprot ID which was stored
+ assertNotNull(ur);
+ // Test whether structures are there
+ Set<Structure> ss = ur.getStructures();
+ assertNotNull(ss);
+ assertTrue(ss.size() > 0);
+ // Test whether uniprot is accessible from structure
+ assertTrue(ss.iterator().next().getUniprot() == ur);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore
+ public void testAnnotate2() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("P29373");
+ /*
+ * One needs to have the UniProt ID first, and Uniprot lookup through HGNC is
+ * included in PDB annotator. This tests simulates situation when the PDB
+ * annotator is called first.
+ */
+ pdbAnnotator.annotateElement(protein);
+ int cntAnnotations = protein.getMiriamData().size();
+
+ assertTrue(cntAnnotations > 0);
+
+ boolean pdb = false;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("No PDB annotation extracted from pdb annotator", pdb);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ @Ignore
+ public void testAnnotateNotUniprotAnnodated() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("P29373");
+ pdbAnnotator.annotateElement(protein);
+
+ assertTrue("UniProt annotation in PDB annotator failed", protein.getMiriamData().size() > 0);
+
+ boolean pdb = false;
+
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("No PDB annotation extracted from PDB annotator", pdb);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidUniprot() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("bla");
+ pdbAnnotator.annotateElement(protein);
+
+ assertEquals(0, protein.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateValidUniprotNonexistingPdb() throws Exception {
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("Q88VP8");
+ pdbAnnotator.annotateElement(protein);
+
+ boolean pdb = false;
+ for (MiriamData md : protein.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.PDB)) {
+ pdb = true;
+ break;
+ }
+ }
+ assertTrue("PDB mapping found for structure for which no should be available", !pdb);
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testSimulateDownStatus() throws Exception {
+ WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString())).thenReturn("");
+ pdbAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.DOWN, pdbAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pdbAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateChangedStatus() throws Exception {
+ WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
+ try {
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenReturn("{\"P29373\": [{\"xxx\": 140}]}");
+ pdbAnnotator.setWebPageDownloader(mockDownloader);
+ assertEquals(ExternalServiceStatusType.CHANGED, pdbAnnotator.getServiceStatus().getStatus());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pdbAnnotator.setWebPageDownloader(downloader);
+ }
+ }
+
+ @Test
+ public void testSimulateInvalidJson() throws Exception {
+ WebPageDownloader downloader = pdbAnnotator.getWebPageDownloader();
+ try {
+ Species protein = new GenericProtein("id");
+ protein.setName("Q88VP8");
+ uniprotAnnotator.annotateElement(protein);
+ int cntAnnotations1 = protein.getMiriamData().size();
+
+ WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), anyString()))
+ .thenReturn("\"P29373\": [{\"xxx\": 140}]}");
+ pdbAnnotator.setWebPageDownloader(mockDownloader);
+
+ pdbAnnotator.annotateElement(protein);
+ int cntAnnotations2 = protein.getMiriamData().size();
+ assertTrue(cntAnnotations1 == cntAnnotations2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ } finally {
+ pdbAnnotator.setWebPageDownloader(downloader);
+ }
+ }
}
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 dc5a6896c06677f7fd3c6f8ff3a73b67c9c8f6dc..78e2ba5200e554e09935c4adc214bab89c9ce907 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
@@ -5,9 +5,9 @@ import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.any;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.doReturn;
import static org.mockito.Mockito.when;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
index b3d3e31e774356c1d25b8076f9aaee2414f0e680..eceab162f8fe8547547c2099fd669489ee85a476 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/StitchAnnotatorTest.java
@@ -15,86 +15,85 @@ import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
public class StitchAnnotatorTest extends AnnotationTestFunctions {
-
- @Autowired
- StitchAnnotator testedAnnotator;
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testAnnotate() throws Exception {
- try {
-
- Species bioEntity = new SimpleMolecule("id");
- bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "CHEBI:35697"));
-
- testedAnnotator.annotateElement(bioEntity);
-
- MiriamData mdStitch = null;
-
- for (MiriamData md : bioEntity.getMiriamData()) {
- if (md.getDataType().equals(MiriamType.STITCH)) {
- mdStitch = md; //there should be only one EC number for that TAIR<->UNIPROT record
- }
- }
-
- assertTrue("No STITCH annotation extracted from STITCH annotator", mdStitch != null);
- assertTrue("Wrong number of annotations extract from STITCH annotator", bioEntity.getMiriamData().size() == 2);
- assertTrue("Invalid STITCH annotation extracted from STITCH annotator based on CHEBI ID", mdStitch.getResource().equalsIgnoreCase("WBYWAXJHAXSJNI") );
-
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testExtractInchiMainLayer() throws Exception {
- try {
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateInvalidEmpty() throws Exception {
- try {
- Species bioEntity = new SimpleMolecule("id");
- testedAnnotator.annotateElement(bioEntity);
-
- assertEquals(0, bioEntity.getMiriamData().size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAnnotateInvalidChebi() throws Exception {
- try {
- Species bioEntity = new SimpleMolecule("id");
- bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "bla"));
- testedAnnotator.annotateElement(bioEntity);
-
- assertEquals(1, bioEntity.getMiriamData().size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-
- //All the service status tests are not necessary, since STTICH annotator
- //internally calls ChEBI annotator which has it own set of tests
+
+ @Autowired
+ StitchAnnotator testedAnnotator;
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testAnnotate() throws Exception {
+ try {
+
+ Species bioEntity = new SimpleMolecule("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "CHEBI:35697"));
+
+ testedAnnotator.annotateElement(bioEntity);
+
+ MiriamData mdStitch = null;
+
+ for (MiriamData md : bioEntity.getMiriamData()) {
+ if (md.getDataType().equals(MiriamType.STITCH)) {
+ mdStitch = md; // there should be only one EC number for that TAIR<->UNIPROT record
+ }
+ }
+
+ assertTrue("No STITCH annotation extracted from STITCH annotator", mdStitch != null);
+ assertTrue("Wrong number of annotations extract from STITCH annotator", bioEntity.getMiriamData().size() == 2);
+ assertTrue("Invalid STITCH annotation extracted from STITCH annotator based on CHEBI ID",
+ mdStitch.getResource().equalsIgnoreCase("WBYWAXJHAXSJNI"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testExtractInchiMainLayer() throws Exception {
+ try {
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidEmpty() throws Exception {
+ try {
+ Species bioEntity = new SimpleMolecule("id");
+ testedAnnotator.annotateElement(bioEntity);
+
+ assertEquals(0, bioEntity.getMiriamData().size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAnnotateInvalidChebi() throws Exception {
+ try {
+ Species bioEntity = new SimpleMolecule("id");
+ bioEntity.addMiriamData(new MiriamData(MiriamType.CHEBI, "bla"));
+ testedAnnotator.annotateElement(bioEntity);
+
+ assertEquals(1, bioEntity.getMiriamData().size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ // All the service status tests are not necessary, since STTICH annotator
+ // internally calls ChEBI annotator which has it own set of tests
}
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
index 2f34409036627a9fde17554ff95291f0df9510ed..f977f8145c6096d3ccd4f2bd598396b68e1dca86 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/TairAnnotatorTest.java
@@ -5,15 +5,14 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
import org.junit.After;
import org.junit.Before;
-import org.junit.Ignore;
import org.junit.Test;
import org.mockito.Mockito;
import org.springframework.beans.factory.annotation.Autowired;
@@ -41,7 +40,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- //@Ignore("TAIR DB restricts queries by IP")
+ // @Ignore("TAIR DB restricts queries by IP")
public void testAnnotate1() throws Exception {
try {
@@ -70,7 +69,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- //@Ignore("TAIR DB restricts queries by IP")
+ // @Ignore("TAIR DB restricts queries by IP")
public void testAnnotateExistingUniprot() throws Exception {
try {
@@ -155,7 +154,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- //@Ignore("TAIR DB restricts queries by IP")
+ // @Ignore("TAIR DB restricts queries by IP")
public void testTairToUniprot() throws Exception {
try {
assertEquals(new MiriamData(MiriamType.UNIPROT, "Q9MAN1", TairAnnotator.class),
@@ -167,7 +166,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- //@Ignore("TAIR DB restricts queries by IP")
+ // @Ignore("TAIR DB restricts queries by IP")
public void testRefreshInvalidCacheQuery() throws Exception {
try {
tairAnnotator.refreshCacheQuery("invalid_query");
@@ -205,7 +204,7 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
}
@Test
- //@Ignore("TAIR DB restricts queries by IP")
+ // @Ignore("TAIR DB restricts queries by IP")
public void testStatus() throws Exception {
try {
assertEquals(ExternalServiceStatusType.OK, tairAnnotator.getServiceStatus().getStatus());
@@ -220,7 +219,8 @@ public class TairAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = tairAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
tairAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, tairAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
index 6427c95760ee12aa7948247bc9e64a15510232dc..a08c898faad1118709d850e63b54ab6a7c32ab3e 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/annotators/UniprotAnnotatorTest.java
@@ -5,8 +5,8 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.anyString;
import static org.mockito.ArgumentMatchers.nullable;
-import static org.mockito.Matchers.anyString;
import static org.mockito.Mockito.when;
import java.io.IOException;
@@ -330,7 +330,8 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
WebPageDownloader downloader = uniprotAnnotator.getWebPageDownloader();
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
uniprotAnnotator.setWebPageDownloader(mockDownloader);
assertEquals(ExternalServiceStatusType.DOWN, uniprotAnnotator.getServiceStatus().getStatus());
} catch (Exception e) {
@@ -348,7 +349,8 @@ public class UniprotAnnotatorTest extends AnnotationTestFunctions {
uniprotAnnotator.setCache(null);
try {
WebPageDownloader mockDownloader = Mockito.mock(WebPageDownloader.class);
- when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class))).thenThrow(new IOException());
+ when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
+ .thenThrow(new IOException());
uniprotAnnotator.setWebPageDownloader(mockDownloader);
Species protein = new GenericProtein("id");
protein.addMiriamData(new MiriamData(MiriamType.UNIPROT, "P01308"));