/*.................................................................................................................*/ boolean checkUsernamePassword(boolean tellUserAboutCipres) { if (StringUtil.blank(username) || StringUtil.blank(password)) { MesquiteBoolean answer = new MesquiteBoolean(false); MesquiteString usernameString = new MesquiteString(); if (username != null) usernameString.setValue(username); MesquiteString passwordString = new MesquiteString(); if (password != null) passwordString.setValue(password); String help = "You will need an account on the CIPRes REST system to use this service. To register, go to https://www.phylo.org/restusers/register.action"; new UserNamePasswordDialog( ownerModule.containerOfModule(), "Sign in to CIPRes", help, "", "Username", "Password", answer, usernameString, passwordString); if (answer.getValue()) { username = usernameString.getValue(); password = passwordString.getValue(); } ownerModule.storePreferences(); } boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password); if (!success && tellUserAboutCipres) { MesquiteMessage.discreetNotifyUser( "Use of the CIPRes service requires an account with CIPRes's REST service. Go to https://www.phylo.org/restusers/register.action to register for an account"); } return success; }
/** The core method that initiates a job on CIPRes. */ public boolean postJob( HttpClient httpclient, MultipartEntityBuilder builder, MesquiteString jobURL) { if (builder == null) return false; String URL = baseURL + "/job/" + username; HttpPost httppost = new HttpPost(URL); httppost.addHeader("cipres-appkey", CIPRESkey); // some of this from // http://stackoverflow.com/questions/18964288/upload-a-file-through-an-http-form-via-multipartentitybuilder-with-a-progress HttpEntity cipresEntity = builder.build(); httppost.setEntity(cipresEntity); try { HttpResponse response = httpclient.execute(httppost); HttpEntity responseEntity = response.getEntity(); InputStream instream = responseEntity.getContent(); BufferedReader br = new BufferedReader(new InputStreamReader(instream)); StringBuffer sb = new StringBuffer(); String line = ""; while ((line = br.readLine()) != null) { sb.append(line + StringUtil.lineEnding()); } Document cipresResponseDoc = loadXMLFile("jobstatus", sb.toString()); // let's see how it went boolean success = false; if (cipresResponseDoc != null) { processJobSubmissionResponse(cipresResponseDoc, jobURL); if (verbose) ownerModule.logln(sb.toString()); if (jobURL != null) success = StringUtil.notEmpty(jobURL.getValue()); else success = true; } else { cipresResponseDoc = loadXMLFile(sb.toString()); reportError(cipresResponseDoc, "Error with CIPRes run", false); } EntityUtils.consume(response.getEntity()); return success; } catch (IOException e) { Debugg.printStackTrace(e); } return false; }
/*.................................................................................................................*/ private void recordSourceProject() { MesquiteString s = new MesquiteString(); s.setValue(getProject().getHomeFileName()); if (!QueryDialogs.queryString( containerOfModule(), "Name to Stamp", "Indicate source file name to stamp on matrix rows", s)) return; int numMatrices = getProject().getNumberCharMatrices(); NameReference sourceRef = NameReference.getNameReference("SourceFile"); for (int im = 0; im < numMatrices; im++) { CharacterData data = getProject().getCharacterMatrix(im); Taxa taxa = data.getTaxa(); Associable tInfo = data.getTaxaInfo(true); boolean anySelected = taxa.anySelected(); for (int it = 0; it < taxa.getNumTaxa(); it++) { if (data.hasDataForTaxon(it) && (!anySelected || taxa.getSelected(it))) tInfo.setAssociatedObject(sourceRef, it, s.getValue()); } } }