@Override public void onReferencesRequired(final Long dbId) { String url = "/ReactomeRESTfulAPI/RESTfulWS/queryReferences/" + dbId; RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url); requestBuilder.setHeader("Accept", "application/json"); try { requestBuilder.sendRequest( null, new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { try { JSONArray list = JSONParser.parseStrict(response.getText()).isArray(); List<LiteratureReference> references = new ArrayList<LiteratureReference>(); for (int i = 0; i < list.size(); ++i) { JSONObject object = list.get(i).isObject(); references.add((LiteratureReference) ModelFactory.getDatabaseObject(object)); } DataRequiredListener.getDataRequiredListener() .setRequiredReferences(dbId, references); } catch (Exception ex) { // ModelFactoryException, NullPointerException, IllegalArgumentException, // JSONException MessageObject msgObj = new MessageObject( "The received References object for 'DbId=" + dbId + "' is empty or faulty and could not be parsed.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); DataRequiredListener.getDataRequiredListener() .setRequiredReferences(dbId, new ArrayList<LiteratureReference>()); } } @Override public void onError(Request request, Throwable exception) { if (!GWT.isScript()) { Console.error(getClass() + " ERROR: " + exception.getMessage()); } MessageObject msgObj = new MessageObject( "The request for 'DbId=" + dbId + "' received an error instead of a valid response.\n" + "ERROR: " + exception.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); DataRequiredListener.getDataRequiredListener() .setRequiredReferences(dbId, new ArrayList<LiteratureReference>()); } }); } catch (RequestException ex) { MessageObject msgObj = new MessageObject( "The requested references data for 'DbId=" + dbId + "' could not be received.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); DataRequiredListener.getDataRequiredListener() .setRequiredReferences(dbId, new ArrayList<LiteratureReference>()); } }
@Override public void onMoleculeDataRequired(final Molecule molecule) { String url = "/ReactomeRESTfulAPI/RESTfulWS/queryById/ReferenceEntity/" + molecule.getDbId(); RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url); requestBuilder.setHeader("Accept", "application/json"); try { requestBuilder.sendRequest( null, new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { try { JSONObject json = JSONParser.parseStrict(response.getText()).isObject(); Molecule molecule = new Molecule(ModelFactory.getDatabaseObject(json).getSchemaClass(), json); DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule); } catch (Exception ex) { // ModelFactoryException, NullPointerException, IllegalArgumentException, // JSONException MessageObject msgObj = new MessageObject( "The received object for Molecule '" + molecule.getDisplayName() + "' is empty or faulty and could not be parsed.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule); } } @Override public void onError(Request request, Throwable exception) { if (!GWT.isScript()) { Console.error(getClass() + " ERROR: " + exception.getMessage()); } MessageObject msgObj = new MessageObject( "The request for Molecule '" + molecule.getDisplayName() + "' received an error instead of a valid response.\n" + "ERROR: " + exception.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule); } }); } catch (RequestException ex) { MessageObject msgObj = new MessageObject( "The requested detailed data for Molecule \n'" + molecule.getDisplayName() + "' could not be received.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); DataRequiredListener.getDataRequiredListener().setRequiredMoleculeData(molecule); } }
@Override public void onDataRequired(final DatabaseObject databaseObject) { final long dbId = databaseObject.getDbId(); String url = "/ReactomeRESTfulAPI/RESTfulWS/detailedView/DatabaseObject/" + dbId; RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url); requestBuilder.setHeader("Accept", "application/json"); try { requestBuilder.sendRequest( null, new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { try { JSONObject json = JSONParser.parseStrict(response.getText()).isObject(); DatabaseObject databaseObject = ModelFactory.getDatabaseObject(json); DataRequiredListener.getDataRequiredListener() .setRequiredData(dbId, databaseObject); eventBus.fireELVEvent(ELVEventType.DETAILED_VIEW_LOADED, databaseObject); } catch (Exception ex) { // ModelFactoryException, NullPointerException, IllegalArgumentException, // JSONException MessageObject msgObj = new MessageObject( "The received object for 'DbId=" + databaseObject.getDbId() + "' is empty or faulty and could not be parsed.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); } } @Override public void onError(Request request, Throwable exception) { if (!GWT.isScript()) { Console.error(getClass() + " ERROR: " + exception.getMessage()); } MessageObject msgObj = new MessageObject( "The request for 'DbId=" + databaseObject.getDbId() + "' received an error instead of a valid response.\n" + "ERROR: " + exception.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); } }); } catch (RequestException ex) { MessageObject msgObj = new MessageObject( "The requested data for 'DbId=" + databaseObject.getDbId() + "' could not be received.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); } }
@Override public void onPathRequired(final Event event) { /* TODO Testing but never used because DataRequiredListener is used by DetailsPanel and there ancestorsRequired is unused */ final long dbId = event.getDbId(); String url = "/ReactomeRESTfulAPI/RESTfulWS/queryEventAncestors/" + dbId; RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url); requestBuilder.setHeader("Accept", "application/json"); try { requestBuilder.sendRequest( null, new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { try { JSONArray list = JSONParser.parseStrict(response.getText()).isArray(); Ancestors ancestors = new Ancestors(list); DataRequiredListener.getDataRequiredListener() .setRequiredAncestors(dbId, ancestors); } catch (Exception ex) { // ModelFactoryException, NullPointerException, IllegalArgumentException, // JSONException MessageObject msgObj = new MessageObject( "The received object for 'DbId=" + event.getDbId() + "' is empty or faulty and could not be parsed into a path or hierarchy.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); } } @Override public void onError(Request request, Throwable exception) { if (!GWT.isScript()) { Console.error(getClass() + " ERROR: " + exception.getMessage()); } MessageObject msgObj = new MessageObject( "The PathRequired request for 'DbId=" + event.getDbId() + "' received an error instead of a valid response.\n" + "ERROR: " + exception.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); } }); } catch (RequestException ex) { MessageObject msgObj = new MessageObject( "The requested data for 'DbId=" + event.getDbId() + "' could not be received.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); } }
@Override public void onResourceChosen(final String resource) { String url = AnalysisHelper.URL_PREFIX + "/token/" + token + "?page=1&resource=" + resource; RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.GET, url); requestBuilder.setHeader("Accept", "application/json"); try { requestBuilder.sendRequest( null, new RequestCallback() { @Override public void onResponseReceived(Request request, Response response) { try { AnalysisResult result = AnalysisModelFactory.getModelObject(AnalysisResult.class, response.getText()); // We have to do this here because there is no name coming from the RESTFul service result .getSummary() .setSpeciesName(speciesMap.get(result.getSummary().getSpecies())); view.clearSelection(); view.showResult(result, resource); view.selectPathway(selected); } catch (AnalysisModelException e) { MessageObject msgObj = new MessageObject( "The received object for '" + resource + "' is empty or faulty and could not be parsed.\n" + "ERROR: " + e.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + e.getMessage()); view.setInitialState(); } } @Override public void onError(Request request, Throwable exception) { // TODO Check before commit - not yet tested MessageObject msgObj = new MessageObject( "The request for '" + resource + "' received an error instead of a valid response.\n" + "ERROR: " + exception.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + exception.getMessage()); view.setInitialState(); } }); } catch (RequestException ex) { MessageObject msgObj = new MessageObject( "The requested detailed data for '" + resource + "'\nin the Analysis could not be received.\n" + "ERROR: " + ex.getMessage(), getClass(), MessageType.INTERNAL_ERROR); eventBus.fireELVEvent(ELVEventType.INTERNAL_MESSAGE, msgObj); Console.error(getClass() + " ERROR: " + ex.getMessage()); view.setInitialState(); } }