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Commit 42d357fb authored by Piotr Gawron's avatar Piotr Gawron
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update on recon annotator after changes in API

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1 merge request!273Resolve "submenu of right click context menu doesn't work on touch table"
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annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ReconAnnotator.java
+ 284
− 223
View file @ 42d357fb
......@@ -35,244 +35,305 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/
public class ReconAnnotator extends ElementAnnotator implements IExternalService {
/**
* Address of annotation rest service for elements.
*/
private static final String ELEMENT_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/metabolites/?page_size=10000&format=json&search=";
/**
* Address of annotation rest service for elements.
*/
private static final String ELEMENT_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/metabolites/?page_size=10000&format=json&search=";
/**
* Address of annotation rest service for reactions.
*/
private static final String REACTION_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
/**
* Address of annotation rest service for reactions.
*/
private static final String REACTION_ANNOTATION_URL_PREFIX = "https://vmh.uni.lu/_api/reactions/?page_size=10000&format=json&search=";
/**
* Class used for some simple operations on {@link BioEntity} elements.
*/
private ElementUtils elementUtils = new ElementUtils();
/**
* Class used for some simple operations on {@link BioEntity} elements.
*/
private ElementUtils elementUtils = new ElementUtils();
@Override
public String refreshCacheQuery(Object query) throws SourceNotAvailable {
String name;
String result = null;
if (query instanceof String) {
name = (String) query;
if (name.startsWith("http")) {
try {
result = getWebPageContent(name);
} catch (IOException e) {
throw new SourceNotAvailable(e);
}
} else {
throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
}
} else {
throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
}
return result;
}
@Override
public String refreshCacheQuery(Object query) throws SourceNotAvailable {
String name;
String result = null;
if (query instanceof String) {
name = (String) query;
if (name.startsWith("http")) {
try {
result = getWebPageContent(name);
} catch (IOException e) {
throw new SourceNotAvailable(e);
}
} else {
throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
}
} else {
throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
}
return result;
}
/**
* Default class logger.
*/
private static Logger logger = Logger.getLogger(ReconAnnotator.class);
/**
* Default class logger.
*/
private static Logger logger = Logger.getLogger(ReconAnnotator.class);
/**
* Default constructor.
*/
public ReconAnnotator() {
super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false);
}
/**
* Default constructor.
*/
public ReconAnnotator() {
super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false);
}
@Override
public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
@Override
public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
GeneralCacheInterface cacheCopy = getCache();
this.setCache(null);
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
Logger.getRootLogger().addAppender(appender);
try {
SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id");
smallMoleculeAlias.setName("h2o");
annotateElement(smallMoleculeAlias);
status.setStatus(ExternalServiceStatusType.OK);
if (smallMoleculeAlias.getMiriamData().size() == 0) {
status.setStatus(ExternalServiceStatusType.CHANGED);
} else if (appender.getWarnings().size() > 0) {
status.setStatus(ExternalServiceStatusType.CHANGED);
}
} catch (Exception e) {
logger.error(status.getName() + " is down", e);
status.setStatus(ExternalServiceStatusType.DOWN);
}
Logger.getRootLogger().removeAppender(appender);
this.setCache(cacheCopy);
return status;
}
GeneralCacheInterface cacheCopy = getCache();
this.setCache(null);
EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
Logger.getRootLogger().addAppender(appender);
try {
SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id");
smallMoleculeAlias.setName("h2o");
annotateElement(smallMoleculeAlias);
status.setStatus(ExternalServiceStatusType.OK);
if (smallMoleculeAlias.getMiriamData().size() == 0) {
status.setStatus(ExternalServiceStatusType.CHANGED);
} else if (appender.getWarnings().size() > 0) {
status.setStatus(ExternalServiceStatusType.CHANGED);
}
} catch (Exception e) {
logger.error(status.getName() + " is down", e);
status.setStatus(ExternalServiceStatusType.DOWN);
}
Logger.getRootLogger().removeAppender(appender);
this.setCache(cacheCopy);
return status;
}
@Override
public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
if (isAnnotatable(annotatedObject)) {
String id = annotatedObject.getAbbreviation();
if (id == null || id.isEmpty()) {
id = annotatedObject.getName();
}
if (id.indexOf("[") > 0) {
id = id.substring(0, id.indexOf("["));
}
if (id.indexOf(" ") >= 0) {
String[] tmp = id.split(" ");
id = tmp[tmp.length - 1];
}
String url = null;
if (annotatedObject instanceof Element) {
url = ELEMENT_ANNOTATION_URL_PREFIX + id;
} else if (annotatedObject instanceof Reaction) {
url = REACTION_ANNOTATION_URL_PREFIX + id;
} else {
logger.warn("Unknown class type: " + annotatedObject.getClass());
return;
}
try {
String content = getWebPageContent(url);
@Override
public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
if (isAnnotatable(annotatedObject)) {
String id = annotatedObject.getAbbreviation();
if (id == null || id.isEmpty()) {
id = annotatedObject.getName();
}
if (id.indexOf("[") > 0) {
id = id.substring(0, id.indexOf("["));
}
if (id.indexOf(" ") >= 0) {
String[] tmp = id.split(" ");
id = tmp[tmp.length - 1];
}
String url = null;
if (annotatedObject instanceof Element) {
url = ELEMENT_ANNOTATION_URL_PREFIX + id;
} else if (annotatedObject instanceof Reaction) {
url = REACTION_ANNOTATION_URL_PREFIX + id;
} else {
logger.warn("Unknown class type: " + annotatedObject.getClass());
return;
}
try {
String content = getWebPageContent(url);
String prefix = elementUtils.getElementTag(annotatedObject, this);
if (!content.isEmpty()) {
String prefix = elementUtils.getElementTag(annotatedObject, this);
if (!content.isEmpty()) {
JsonElement jelement = new JsonParser().parse(content);
JsonObject jobject = jelement.getAsJsonObject();
if (jobject.get("results").getAsJsonArray().size() > 0) {
jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject();
JsonElement jelement = new JsonParser().parse(content);
JsonObject jobject = jelement.getAsJsonObject();
if (jobject.get("results").getAsJsonArray().size() > 0) {
jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject();
for (Entry<String, JsonElement> entry : jobject.entrySet()) {
String key = entry.getKey();
String value = null;
if (!entry.getValue().isJsonNull()) {
// if (entry.getValue().isJsonPrimitive()) {
value = entry.getValue().getAsString().trim();
}
if (value == null || value.isEmpty()) {
continue;
}
for (Entry<String, JsonElement> entry : jobject.entrySet()) {
String key = entry.getKey();
String value = null;
if (!entry.getValue().isJsonNull()) {
// if (entry.getValue().isJsonPrimitive()) {
value = entry.getValue().getAsString().trim();
}
if (value == null || value.isEmpty()) {
continue;
}
boolean unknown = false;
if (key.equals("url")) {
continue;
} else if (key.equals("rxn_id")) {
continue;
} else if (key.equals("abbreviation")) {
setAbbreviation(annotatedObject, value, prefix);
} else if (key.equals("description")) {
setDescription(annotatedObject, value);
} else if (key.equals("formula")) {
setFormula(annotatedObject, value, prefix);
} else if (key.equals("reversible")) {
continue;
} else if (key.equals("mcs")) {
if (annotatedObject instanceof Reaction) {
setMcs((Reaction) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("notes")) {
setDescription(annotatedObject, value);
} else if (key.equals("ecnumber")) {
addEcMiriam(annotatedObject, value);
} else if (key.equals("ref")) {
continue;
} else if (key.equals("lastModified")) {
continue;
} else if (key.equals("met_id")) {
continue;
} else if (key.equals("csecoida")) {
continue;
} else if (key.equals("chargedFormula")) {
setFormula(annotatedObject, value, prefix);
} else if (key.equals("charge")) {
if (annotatedObject instanceof Species) {
setCharge((Species) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("inchiString")) {
if (annotatedObject instanceof Chemical) {
setInchi((Chemical) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("cheBlId")) {
addChebiMiriam(annotatedObject, value);
} else if (key.equals("subsystem")) {
if (annotatedObject instanceof Reaction) {
setSubsystem((Reaction) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("keggId")) {
addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("fullName")) {
if (annotatedObject instanceof Element) {
setFullName((Element) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("keggorthology")) {
addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("pubChemId")) {
addPubchemMiriam(annotatedObject, value);
} else if (key.equals("hmdb")) {
addHmdbMiriam(annotatedObject, value);
} else if (key.equals("cog")) {
addCogMiriam(annotatedObject, value);
} else if (key.equals("synonyms")) {
List<String> synonyms = new ArrayList<>();
for (String str : value.split(",")) {
synonyms.add(str);
}
setSynonyms(annotatedObject, synonyms, prefix);
} else if (key.equals("pdmapName")) {
// for now we skip it...
continue;
} else if (key.equals("reconMap")) {
// for now we don't handle it
continue;
} else {
unknown = true;
}
if (unknown) {
logger.warn(prefix + "Unknown field in recon annotation: \"" + key + "\" (value: " + value + ")");
}
}
} else {
logger.warn(prefix + "No recon annotations \"" + id + "\"");
}
} else {
logger.warn(prefix + "No recon annotations \"" + id + "\"");
}
} catch (IOException e) {
throw new AnnotatorException(e);
}
}
}
boolean unknown = false;
if (key.equals("url")) {
continue;
} else if (key.equals("rxn_id")) {
continue;
} else if (key.equals("abbreviation")) {
setAbbreviation(annotatedObject, value, prefix);
} else if (key.equals("description")) {
setDescription(annotatedObject, value);
} else if (key.equals("formula")) {
setFormula(annotatedObject, value, prefix);
} else if (key.equals("reversible")) {
continue;
} else if (key.equals("mcs")) {
if (annotatedObject instanceof Reaction) {
setMcs((Reaction) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("notes")) {
setDescription(annotatedObject, value);
} else if (key.equals("ecnumber")) {
addEcMiriam(annotatedObject, value);
} else if (key.equals("ref")) {
continue;
} else if (key.equals("lastModified")) {
continue;
} else if (key.equals("met_id")) {
continue;
} else if (key.equals("csecoida")) {
continue;
} else if (key.equals("chargedFormula")) {
setFormula(annotatedObject, value, prefix);
} else if (key.equals("charge")) {
if (annotatedObject instanceof Species) {
setCharge((Species) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("inchiString")) {
if (annotatedObject instanceof Chemical) {
setInchi((Chemical) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("cheBlId")) {
addChebiMiriam(annotatedObject, value);
} else if (key.equals("subsystem")) {
if (annotatedObject instanceof Reaction) {
setSubsystem((Reaction) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("keggId")) {
addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("fullName")) {
if (annotatedObject instanceof Element) {
setFullName((Element) annotatedObject, value, prefix);
} else {
unknown = true;
}
} else if (key.equals("keggorthology")) {
addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("pubChemId")) {
addPubchemMiriam(annotatedObject, value);
} else if (key.equals("hmdb")) {
addHmdbMiriam(annotatedObject, value);
} else if (key.equals("cog")) {
addCogMiriam(annotatedObject, value);
} else if (key.equals("synonyms")) {
List<String> synonyms = new ArrayList<>();
for (String str : value.split(",")) {
synonyms.add(str);
}
setSynonyms(annotatedObject, synonyms, prefix);
} else if (key.equals("pdmapName")) {
// for now we skip it...
continue;
} else if (key.equals("reconMap")) {
// for now we don't handle it
continue;
} else if (key.equals("reconMap3")) {
// for now we don't handle it
continue;
} else if (key.equals("massbalance")) {
// for now we don't handle it
continue;
} else if (key.equals("isHuman")) {
// for now we don't handle it
continue;
} else if (key.equals("isMicrobe")) {
// for now we don't handle it
continue;
} else if (key.equals("iupac")) {
// for now we don't handle it
continue;
} else if (key.equals("avgmolweight")) {
// for now we don't handle it
continue;
} else if (key.equals("monoisotopicweight")) {
// for now we don't handle it
continue;
} else if (key.equals("miriam")) {
addMiriam(annotatedObject, value, prefix);
} else if (key.equals("biggId")) {
// for now we don't handle it
continue;
} else if (key.equals("lmId")) {
// for now we don't handle it
continue;
} else if (key.equals("hepatonetId")) {
// for now we don't handle it
continue;
} else if (key.equals("inchiKey")) {
if (annotatedObject instanceof Chemical) {
setInchiKey((Chemical) annotatedObject, value, prefix);
}
} else if (key.equals("smile")) {
if (annotatedObject instanceof Chemical) {
setSmile((Chemical) annotatedObject, value, prefix);
}
} else if (key.equals("metanetx")) {
// for now we don't handle it
continue;
} else if (key.equals("seed")) {
// for now we don't handle it
continue;
} else if (key.equals("food_db")) {
// for now we don't handle it
continue;
} else if (key.equals("chemspider")) {
addChemspider(annotatedObject, value);
} else if (key.equals("wikipedia")) {
addWikipedia(annotatedObject, value);
} else if (key.equals("metlin")) {
// for now we don't handle it
continue;
} else if (key.equals("casRegistry")) {
addCas(annotatedObject, value);
} else if (key.equals("epa_id")) {
// for now we don't handle it
continue;
} else {
unknown = true;
}
if (unknown) {
logger.warn(prefix + "Unknown field in recon annotation: \"" + key + "\" (value: " + value + ")");
}
}
} else {
logger.warn(prefix + "No recon annotations \"" + id + "\"");
}
} else {
logger.warn(prefix + "No recon annotations \"" + id + "\"");
}
} catch (IOException e) {
throw new AnnotatorException(e);
}
}
}
@Override
public String getCommonName() {
return "Recon annotator";
}
@Override
public String getCommonName() {
return "Recon annotator";
}
@Override
public String getUrl() {
return "http://humanmetabolism.org/";
}
@Override
public String getUrl() {
return "http://humanmetabolism.org/";
}
@Override
protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader();
}
@Override
protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader();
}
@Override
protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
super.setWebPageDownloader(webPageDownloader);
}
@Override
protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
super.setWebPageDownloader(webPageDownloader);
}
}
model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+ 1
− 1
View file @ 42d357fb
......@@ -674,7 +674,7 @@ public enum MiriamType {
*
* @param generalIdentifier
* identifier in the format NAME:IDENTIFIER. Where NAME is the name
* from {@link MiriamType#commonName} and IDENTIFIER is reasource
* from {@link MiriamType#commonName} and IDENTIFIER is resource
* identifier.
* @return {@link MiriamData} representing generalIdentifier, when identifier is
* invalid InvalidArgumentException is thrown
......
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