public static RequestBuilder newCacheManagerRequest(Method httpMethod, String url) {
if (!authenticated) {
GWT.log("Attempts to build a request when no credentials present");
return null;
}
RequestBuilder request = new RequestBuilder(httpMethod, url);
request.setTimeoutMillis(35000);
request.setHeader("Authorization", base64);
request.setHeader("If-Modified-Since", "01 Jan 1970 00:00:00 GMT");
// request.setUser(defaultUsername);
// request.setPassword(defaultPassword);
return request;
}
@Override
public <A extends RestAction<?>> RequestBuilder build(A action, String securityToken)
throws ActionException {
Method httpMethod = HTTP_METHODS.get(action.getHttpMethod());
String url = buildUrl(action);
String xsrfToken = action.isSecured() ? securityToken : "";
RequestBuilder requestBuilder = httpRequestBuilderFactory.create(httpMethod, url);
requestBuilder.setTimeoutMillis(requestTimeoutMs);
buildHeaders(requestBuilder, xsrfToken, action);
buildBody(requestBuilder, action);
return requestBuilder;
}
/** Send the name from the nameField to the server and wait for a response. */
private void sendToServer(RequestBuilder.Method httpMethod) {
// Then, we send the input to the server.
textToServerLabel.setText("");
serverResponseLabel.setText("");
RequestBuilder request = buildRequest(httpMethod);
request.setTimeoutMillis(10000);
request.setCallback(
new RequestCallback() {
@Override
public void onError(Request request, Throwable exception) {
// Show the error message to the user
dialogBox.setText("RESTful Call - Failure");
serverResponseLabel.addStyleName("serverResponseLabelError");
serverResponseLabel.setHTML(SERVER_ERROR);
dialogBox.center();
closeButton.setFocus(true);
}
@Override
public void onResponseReceived(Request request, Response response) {
dialogBox.setText("RESTful Call");
serverResponseLabel.removeStyleName("serverResponseLabelError");
serverResponseLabel.setHTML(
response.getStatusCode()
+ " "
+ response.getStatusText()
+ "<p>"
+ response.getText());
dialogBox.center();
closeButton.setFocus(true);
if (response.getStatusCode() == HTTP_OK) {
parseXml(response.getText());
}
}
});
try {
request.send();
} catch (RequestException re) {
re.printStackTrace();
}
}
public Method timeout(int timeout) {
builder.setTimeoutMillis(timeout);
return this;
}
private void doSetTimeout() {
if (Defaults.getRequestTimeout() > -1) {
builder.setTimeoutMillis(Defaults.getRequestTimeout());
}
}
@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();
}
}
@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();
}
}
}
@Override
public void sendHttpRequest(
final HttpRequest httpRequest, final HttpResponseListener httpResultListener) {
if (httpRequest.getUrl() == null) {
httpResultListener.failed(
new GdxRuntimeException("can't process a HTTP request without URL set"));
return;
}
final String method = httpRequest.getMethod();
final String value = httpRequest.getContent();
final boolean valueInBody =
method.equalsIgnoreCase(HttpMethods.POST) || method.equals(HttpMethods.PUT);
RequestBuilder builder;
String url = httpRequest.getUrl();
if (method.equalsIgnoreCase(HttpMethods.GET)) {
if (value != null) {
url += "?" + value;
}
builder = new RequestBuilder(RequestBuilder.GET, url);
} else if (method.equalsIgnoreCase(HttpMethods.POST)) {
builder = new RequestBuilder(RequestBuilder.POST, url);
} else if (method.equalsIgnoreCase(HttpMethods.DELETE)) {
if (value != null) {
url += "?" + value;
}
builder = new RequestBuilder(RequestBuilder.DELETE, url);
} else if (method.equalsIgnoreCase(HttpMethods.PUT)) {
builder = new RequestBuilder(RequestBuilder.PUT, url);
} else {
throw new GdxRuntimeException("Unsupported HTTP Method");
}
Map<String, String> content = httpRequest.getHeaders();
Set<String> keySet = content.keySet();
for (String name : keySet) {
builder.setHeader(name, content.get(name));
}
builder.setTimeoutMillis(httpRequest.getTimeOut());
try {
Request request =
builder.sendRequest(
valueInBody ? value : null,
new RequestCallback() {
@Override
public void onResponseReceived(Request request, Response response) {
httpResultListener.handleHttpResponse(new HttpClientResponse(response));
requests.remove(httpRequest);
listeners.remove(httpRequest);
}
@Override
public void onError(Request request, Throwable exception) {
httpResultListener.failed(exception);
requests.remove(httpRequest);
listeners.remove(httpRequest);
}
});
requests.put(httpRequest, request);
listeners.put(httpRequest, httpResultListener);
} catch (Throwable e) {
httpResultListener.failed(e);
}
}
