public void setUsersGroups(Set<IUserGroup> groups) {
_application.getInitializer().addCompletionMessage("User's groups initialization... ");
this.groups = groups;
}
@Override
public void annotate(
final IBioPortalTextminingRequestCompleted completionCallback,
String source,
String textContent,
String include,
String exclude)
throws IllegalArgumentException {
String url =
GWT.getModuleBaseURL()
+ "nif/annotate?format=json&content="
+ URL.encode(textContent)
+ "&url="
+ source
+ "&categoriesIn="
+ include
+ "&categoriesOut="
+ exclude;
if (!_application.isHostedMode())
url =
ApplicationUtils.getUrlBase(GWT.getModuleBaseURL())
+ "nif/annotate?format=json&content="
+ URL.encode(textContent)
+ "&url="
+ source
+ "&categoriesIn="
+ include
+ "&categoriesOut="
+ exclude;
RequestBuilder builder = new RequestBuilder(RequestBuilder.GET, url);
builder.setTimeoutMillis(10000);
try {
Request request =
builder.sendRequest(
null,
new RequestCallback() {
public void onError(Request request, Throwable exception) {
if (exception instanceof RequestTimeoutException) {
_application
.getLogger()
.exception(
this,
"Couldn't reach NIF annotator (timeout) " + exception.getMessage());
completionCallback.textMiningNotCompleted("Timeout");
} else {
_application
.getLogger()
.exception(this, "Couldn't retrieve NIF annotator JSON");
completionCallback.textMiningNotCompleted();
}
}
public void onResponseReceived(Request request, Response response) {
if (200 == response.getStatusCode()) {
JsAnnotationSet set = (JsAnnotationSet) parseJson(response.getText());
completionCallback.returnTextminingResults(set);
} else if (503 == response.getStatusCode()) {
_application.getLogger().exception(this, "503: " + response.getText());
completionCallback.textMiningNotCompleted("Couldn't run Nif Annotator (503)");
} else {
_application
.getLogger()
.exception(this, response.getStatusCode() + ": " + response.getText());
completionCallback.textMiningNotCompleted(
"Couldn't run Nif Annotator " + response.getStatusCode());
}
}
});
} catch (RequestException e) {
_application.getLogger().exception(this, "Couldn't retrieve NIF annotator JSON");
completionCallback.textMiningNotCompleted();
}
}
protected void setUser(IUser user) {
_application.getInitializer().addCompletionMessage("User's info initialization... ");
this.user = user;
}
@Override
public void searchData(
final INifDataRequestCompleted completionCallback,
String textQuery,
String type,
String vendor,
String resource,
int pageNumber,
int pageSize)
throws IllegalArgumentException {
if (resource.equals("nif-0000-07730-1")) {
String url =
GWT.getModuleBaseURL()
+ "nif/data?format=json&resource="
+ resource
+ "&query="
+ URL.encode(textQuery)
+ "&type="
+ URL.encode(type)
+ "&vendor="
+ URL.encode(vendor);
if (!_application.isHostedMode())
url =
ApplicationUtils.getUrlBase(GWT.getModuleBaseURL())
+ "nif/data?format=json&resource="
+ resource
+ "&query="
+ URL.encode(textQuery)
+ "&type="
+ URL.encode(type)
+ "&vendor="
+ URL.encode(vendor);
RequestBuilder builder = new RequestBuilder(RequestBuilder.GET, url);
builder.setTimeoutMillis(10000);
_application.getLogger().debug(this, "Search Data with url" + url);
try {
Request request =
builder.sendRequest(
null,
new RequestCallback() {
public void onError(Request request, Throwable exception) {
if (exception instanceof RequestTimeoutException) {
_application
.getLogger()
.exception(
this,
"Couldn't reach NIF data search (timeout) " + exception.getMessage());
completionCallback.reportException("Timeout");
} else {
_application
.getLogger()
.exception(
this, "Couldn't retrieve NIF data JSON " + exception.getMessage());
completionCallback.reportException();
}
}
public void onResponseReceived(Request request, Response response) {
if (200 == response.getStatusCode()) {
ArrayList<MGenericResource> data = new ArrayList<MGenericResource>();
JsoNifDataSearchResultsWrapper results =
(JsoNifDataSearchResultsWrapper) parseJson(response.getText());
JsArray<JsoNifDataEntry> res = results.getResults();
for (int i = 0; i < res.length(); i++) {
JsoNifDataEntry entry = res.get(i);
MGenericResource source =
ResourcesFactory.createGenericResource(
entry.getSourceUri(), entry.getSourceLabel());
MGenericResource normalizedResource =
_application.getResourcesManager().cacheResource(source);
if (source == normalizedResource)
_application
.getLogger()
.debug(
this,
"Resource cache size (after insert): "
+ _application.getResourcesManager().getResourceCacheSize());
MAntibody antibody =
new MAntibody(entry.getUri(), entry.getLabel(), normalizedResource);
antibody.setCloneId(entry.getCloneId());
antibody.setVendor(entry.getVendor());
antibody.setOrganism(entry.getOrganism());
antibody.setType(entry.getType());
antibody.setCatalog(entry.getCatalog());
// antibody.setSource(normalizedResource);
data.add(antibody);
}
_application
.getLogger()
.debug(this, "Number NIF Data results: " + data.size());
completionCallback.returnData(data);
} else if (503 == response.getStatusCode()) {
_application.getLogger().exception(this, "503: " + response.getText());
completionCallback.reportException("Couldn't run Nif data search (503)");
} else {
_application
.getLogger()
.exception(this, response.getStatusCode() + ": " + response.getText());
completionCallback.reportException(
"Couldn't run Nif data search " + response.getStatusCode());
}
}
});
} catch (RequestException e) {
_application.getLogger().exception(this, "Couldn't retrieve NIF data JSON");
completionCallback.reportException();
}
} else if (resource.equals("nlx_144509-1") || resource.equals("nif-0000-08137-1")) {
String url =
GWT.getModuleBaseURL()
+ "nif/data?format=json&resource="
+ resource
+ "&query="
+ URL.encode(textQuery)
+ "&type="
+ URL.encode(type);
if (!_application.isHostedMode())
url =
ApplicationUtils.getUrlBase(GWT.getModuleBaseURL())
+ "nif/data?format=json&resource="
+ resource
+ "&query="
+ URL.encode(textQuery)
+ "&type="
+ URL.encode(type);
RequestBuilder builder = new RequestBuilder(RequestBuilder.GET, url);
builder.setTimeoutMillis(10000);
_application.getLogger().debug(this, "Search NIF resources with url" + url);
try {
Request request =
builder.sendRequest(
null,
new RequestCallback() {
public void onError(Request request, Throwable exception) {
if (exception instanceof RequestTimeoutException) {
_application
.getLogger()
.exception(
this,
"Couldn't reach NIF resources search (timeout) "
+ exception.getMessage());
completionCallback.reportException("Timeout");
} else {
_application
.getLogger()
.exception(
this,
"Couldn't retrieve NIF resources JSON " + exception.getMessage());
completionCallback.reportException();
}
}
public void onResponseReceived(Request request, Response response) {
if (200 == response.getStatusCode()) {
ArrayList<MGenericResource> data = new ArrayList<MGenericResource>();
JsoNifDataSearchResultsWrapper results =
(JsoNifDataSearchResultsWrapper) parseJson(response.getText());
JsArray<JsoNifDataEntry> res = results.getResults();
for (int i = 0; i < res.length(); i++) {
JsoNifDataEntry entry = res.get(i);
MGenericResource source =
ResourcesFactory.createGenericResource(
entry.getSourceUri(), entry.getSourceLabel());
_application
.getLogger()
.debug(
this,
"Resource cache size: "
+ _application.getResourcesManager().getResourceCacheSize());
MGenericResource normalizedResource =
_application.getResourcesManager().cacheResource(source);
_application
.getLogger()
.debug(
this,
"Resource cache size: "
+ _application.getResourcesManager().getResourceCacheSize());
MLinkedResource resource =
new MLinkedResource(
entry.getUri(), entry.getLabel(), entry.getDescription());
resource.setSource(normalizedResource);
data.add(resource);
}
_application
.getLogger()
.debug(this, "Number NIF resources results: " + data.size());
completionCallback.returnData(data);
} else if (503 == response.getStatusCode()) {
_application.getLogger().exception(this, "503: " + response.getText());
completionCallback.reportException("Couldn't run Nif resources search (503)");
} else {
_application
.getLogger()
.exception(this, response.getStatusCode() + ": " + response.getText());
completionCallback.reportException(
"Couldn't run Nif resources search " + response.getStatusCode());
}
}
});
} catch (RequestException e) {
_application.getLogger().exception(this, "Couldn't retrieve NIF resources JSON");
completionCallback.reportException();
}
}
}
