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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; ...@@ -35,244 +35,305 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
*/ */
public class ReconAnnotator extends ElementAnnotator implements IExternalService { public class ReconAnnotator extends ElementAnnotator implements IExternalService {
/** /**
* Address of annotation rest service for elements. * 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="; 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. * 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="; 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. * Class used for some simple operations on {@link BioEntity} elements.
*/ */
private ElementUtils elementUtils = new ElementUtils(); private ElementUtils elementUtils = new ElementUtils();
@Override @Override
public String refreshCacheQuery(Object query) throws SourceNotAvailable { public String refreshCacheQuery(Object query) throws SourceNotAvailable {
String name; String name;
String result = null; String result = null;
if (query instanceof String) { if (query instanceof String) {
name = (String) query; name = (String) query;
if (name.startsWith("http")) { if (name.startsWith("http")) {
try { try {
result = getWebPageContent(name); result = getWebPageContent(name);
} catch (IOException e) { } catch (IOException e) {
throw new SourceNotAvailable(e); throw new SourceNotAvailable(e);
} }
} else { } else {
throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\""); throw new InvalidArgumentException("Don't know what to do with string \"" + query + "\"");
} }
} else { } else {
throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass()); throw new InvalidArgumentException("Don't know what to do with class: " + query.getClass());
} }
return result; return result;
} }
/** /**
* Default class logger. * Default class logger.
*/ */
private static Logger logger = Logger.getLogger(ReconAnnotator.class); private static Logger logger = Logger.getLogger(ReconAnnotator.class);
/** /**
* Default constructor. * Default constructor.
*/ */
public ReconAnnotator() { public ReconAnnotator() {
super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false); super(ReconAnnotator.class, new Class[] { Chemical.class, Reaction.class }, false);
} }
@Override @Override
public ExternalServiceStatus getServiceStatus() { public ExternalServiceStatus getServiceStatus() {
ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl()); ExternalServiceStatus status = new ExternalServiceStatus(getCommonName(), getUrl());
GeneralCacheInterface cacheCopy = getCache(); GeneralCacheInterface cacheCopy = getCache();
this.setCache(null); this.setCache(null);
EventStorageLoggerAppender appender = new EventStorageLoggerAppender(); EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
Logger.getRootLogger().addAppender(appender); Logger.getRootLogger().addAppender(appender);
try { try {
SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id"); SimpleMolecule smallMoleculeAlias = new SimpleMolecule("some_id");
smallMoleculeAlias.setName("h2o"); smallMoleculeAlias.setName("h2o");
annotateElement(smallMoleculeAlias); annotateElement(smallMoleculeAlias);
status.setStatus(ExternalServiceStatusType.OK); status.setStatus(ExternalServiceStatusType.OK);
if (smallMoleculeAlias.getMiriamData().size() == 0) { if (smallMoleculeAlias.getMiriamData().size() == 0) {
status.setStatus(ExternalServiceStatusType.CHANGED); status.setStatus(ExternalServiceStatusType.CHANGED);
} else if (appender.getWarnings().size() > 0) { } else if (appender.getWarnings().size() > 0) {
status.setStatus(ExternalServiceStatusType.CHANGED); status.setStatus(ExternalServiceStatusType.CHANGED);
} }
} catch (Exception e) { } catch (Exception e) {
logger.error(status.getName() + " is down", e); logger.error(status.getName() + " is down", e);
status.setStatus(ExternalServiceStatusType.DOWN); status.setStatus(ExternalServiceStatusType.DOWN);
} }
Logger.getRootLogger().removeAppender(appender); Logger.getRootLogger().removeAppender(appender);
this.setCache(cacheCopy); this.setCache(cacheCopy);
return status; return status;
} }
@Override @Override
public void annotateElement(BioEntity annotatedObject) throws AnnotatorException { public void annotateElement(BioEntity annotatedObject) throws AnnotatorException {
if (isAnnotatable(annotatedObject)) { if (isAnnotatable(annotatedObject)) {
String id = annotatedObject.getAbbreviation(); String id = annotatedObject.getAbbreviation();
if (id == null || id.isEmpty()) { if (id == null || id.isEmpty()) {
id = annotatedObject.getName(); id = annotatedObject.getName();
} }
if (id.indexOf("[") > 0) { if (id.indexOf("[") > 0) {
id = id.substring(0, id.indexOf("[")); id = id.substring(0, id.indexOf("["));
} }
if (id.indexOf(" ") >= 0) { if (id.indexOf(" ") >= 0) {
String[] tmp = id.split(" "); String[] tmp = id.split(" ");
id = tmp[tmp.length - 1]; id = tmp[tmp.length - 1];
} }
String url = null; String url = null;
if (annotatedObject instanceof Element) { if (annotatedObject instanceof Element) {
url = ELEMENT_ANNOTATION_URL_PREFIX + id; url = ELEMENT_ANNOTATION_URL_PREFIX + id;
} else if (annotatedObject instanceof Reaction) { } else if (annotatedObject instanceof Reaction) {
url = REACTION_ANNOTATION_URL_PREFIX + id; url = REACTION_ANNOTATION_URL_PREFIX + id;
} else { } else {
logger.warn("Unknown class type: " + annotatedObject.getClass()); logger.warn("Unknown class type: " + annotatedObject.getClass());
return; return;
} }
try { try {
String content = getWebPageContent(url); String content = getWebPageContent(url);
String prefix = elementUtils.getElementTag(annotatedObject, this); String prefix = elementUtils.getElementTag(annotatedObject, this);
if (!content.isEmpty()) { if (!content.isEmpty()) {
JsonElement jelement = new JsonParser().parse(content); JsonElement jelement = new JsonParser().parse(content);
JsonObject jobject = jelement.getAsJsonObject(); JsonObject jobject = jelement.getAsJsonObject();
if (jobject.get("results").getAsJsonArray().size() > 0) { if (jobject.get("results").getAsJsonArray().size() > 0) {
jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject(); jobject = jobject.get("results").getAsJsonArray().get(0).getAsJsonObject();
for (Entry<String, JsonElement> entry : jobject.entrySet()) { for (Entry<String, JsonElement> entry : jobject.entrySet()) {
String key = entry.getKey(); String key = entry.getKey();
String value = null; String value = null;
if (!entry.getValue().isJsonNull()) { if (!entry.getValue().isJsonNull()) {
// if (entry.getValue().isJsonPrimitive()) { // if (entry.getValue().isJsonPrimitive()) {
value = entry.getValue().getAsString().trim(); value = entry.getValue().getAsString().trim();
} }
if (value == null || value.isEmpty()) { if (value == null || value.isEmpty()) {
continue; continue;
} }
boolean unknown = false; boolean unknown = false;
if (key.equals("url")) { if (key.equals("url")) {
continue; continue;
} else if (key.equals("rxn_id")) { } else if (key.equals("rxn_id")) {
continue; continue;
} else if (key.equals("abbreviation")) { } else if (key.equals("abbreviation")) {
setAbbreviation(annotatedObject, value, prefix); setAbbreviation(annotatedObject, value, prefix);
} else if (key.equals("description")) { } else if (key.equals("description")) {
setDescription(annotatedObject, value); setDescription(annotatedObject, value);
} else if (key.equals("formula")) { } else if (key.equals("formula")) {
setFormula(annotatedObject, value, prefix); setFormula(annotatedObject, value, prefix);
} else if (key.equals("reversible")) { } else if (key.equals("reversible")) {
continue; continue;
} else if (key.equals("mcs")) { } else if (key.equals("mcs")) {
if (annotatedObject instanceof Reaction) { if (annotatedObject instanceof Reaction) {
setMcs((Reaction) annotatedObject, value, prefix); setMcs((Reaction) annotatedObject, value, prefix);
} else { } else {
unknown = true; unknown = true;
} }
} else if (key.equals("notes")) { } else if (key.equals("notes")) {
setDescription(annotatedObject, value); setDescription(annotatedObject, value);
} else if (key.equals("ecnumber")) { } else if (key.equals("ecnumber")) {
addEcMiriam(annotatedObject, value); addEcMiriam(annotatedObject, value);
} else if (key.equals("ref")) { } else if (key.equals("ref")) {
continue; continue;
} else if (key.equals("lastModified")) { } else if (key.equals("lastModified")) {
continue; continue;
} else if (key.equals("met_id")) { } else if (key.equals("met_id")) {
continue; continue;
} else if (key.equals("csecoida")) { } else if (key.equals("csecoida")) {
continue; continue;
} else if (key.equals("chargedFormula")) { } else if (key.equals("chargedFormula")) {
setFormula(annotatedObject, value, prefix); setFormula(annotatedObject, value, prefix);
} else if (key.equals("charge")) { } else if (key.equals("charge")) {
if (annotatedObject instanceof Species) { if (annotatedObject instanceof Species) {
setCharge((Species) annotatedObject, value, prefix); setCharge((Species) annotatedObject, value, prefix);
} else { } else {
unknown = true; unknown = true;
} }
} else if (key.equals("inchiString")) { } else if (key.equals("inchiString")) {
if (annotatedObject instanceof Chemical) { if (annotatedObject instanceof Chemical) {
setInchi((Chemical) annotatedObject, value, prefix); setInchi((Chemical) annotatedObject, value, prefix);
} else { } else {
unknown = true; unknown = true;
} }
} else if (key.equals("cheBlId")) { } else if (key.equals("cheBlId")) {
addChebiMiriam(annotatedObject, value); addChebiMiriam(annotatedObject, value);
} else if (key.equals("subsystem")) { } else if (key.equals("subsystem")) {
if (annotatedObject instanceof Reaction) { if (annotatedObject instanceof Reaction) {
setSubsystem((Reaction) annotatedObject, value, prefix); setSubsystem((Reaction) annotatedObject, value, prefix);
} else { } else {
unknown = true; unknown = true;
} }
} else if (key.equals("keggId")) { } else if (key.equals("keggId")) {
addKeggMiriam(annotatedObject, value, prefix); addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("fullName")) { } else if (key.equals("fullName")) {
if (annotatedObject instanceof Element) { if (annotatedObject instanceof Element) {
setFullName((Element) annotatedObject, value, prefix); setFullName((Element) annotatedObject, value, prefix);
} else { } else {
unknown = true; unknown = true;
} }
} else if (key.equals("keggorthology")) { } else if (key.equals("keggorthology")) {
addKeggMiriam(annotatedObject, value, prefix); addKeggMiriam(annotatedObject, value, prefix);
} else if (key.equals("pubChemId")) { } else if (key.equals("pubChemId")) {
addPubchemMiriam(annotatedObject, value); addPubchemMiriam(annotatedObject, value);
} else if (key.equals("hmdb")) { } else if (key.equals("hmdb")) {
addHmdbMiriam(annotatedObject, value); addHmdbMiriam(annotatedObject, value);
} else if (key.equals("cog")) { } else if (key.equals("cog")) {
addCogMiriam(annotatedObject, value); addCogMiriam(annotatedObject, value);
} else if (key.equals("synonyms")) { } else if (key.equals("synonyms")) {
List<String> synonyms = new ArrayList<>(); List<String> synonyms = new ArrayList<>();
for (String str : value.split(",")) { for (String str : value.split(",")) {
synonyms.add(str); synonyms.add(str);
} }
setSynonyms(annotatedObject, synonyms, prefix); setSynonyms(annotatedObject, synonyms, prefix);
} else if (key.equals("pdmapName")) { } else if (key.equals("pdmapName")) {
// for now we skip it... // for now we skip it...
continue; continue;
} else if (key.equals("reconMap")) { } else if (key.equals("reconMap")) {
// for now we don't handle it // for now we don't handle it
continue; continue;
} else { } else if (key.equals("reconMap3")) {
unknown = true; // for now we don't handle it
} continue;
if (unknown) { } else if (key.equals("massbalance")) {
logger.warn(prefix + "Unknown field in recon annotation: \"" + key + "\" (value: " + value + ")"); // for now we don't handle it
} continue;
} } else if (key.equals("isHuman")) {
} else { // for now we don't handle it
logger.warn(prefix + "No recon annotations \"" + id + "\""); continue;
} } else if (key.equals("isMicrobe")) {
} else { // for now we don't handle it
logger.warn(prefix + "No recon annotations \"" + id + "\""); continue;
} } else if (key.equals("iupac")) {
} catch (IOException e) { // for now we don't handle it
throw new AnnotatorException(e); 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 @Override
public String getCommonName() { public String getCommonName() {
return "Recon annotator"; return "Recon annotator";
} }
@Override @Override
public String getUrl() { public String getUrl() {
return "http://humanmetabolism.org/"; return "http://humanmetabolism.org/";
} }
@Override @Override
protected WebPageDownloader getWebPageDownloader() { protected WebPageDownloader getWebPageDownloader() {
return super.getWebPageDownloader(); return super.getWebPageDownloader();
} }
@Override @Override
protected void setWebPageDownloader(WebPageDownloader webPageDownloader) { protected void setWebPageDownloader(WebPageDownloader webPageDownloader) {
super.setWebPageDownloader(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 { ...@@ -674,7 +674,7 @@ public enum MiriamType {
* *
* @param generalIdentifier * @param generalIdentifier
* identifier in the format NAME:IDENTIFIER. Where NAME is the name * 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. * identifier.
* @return {@link MiriamData} representing generalIdentifier, when identifier is * @return {@link MiriamData} representing generalIdentifier, when identifier is
* invalid InvalidArgumentException is thrown * invalid InvalidArgumentException is thrown
......
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