--- /dev/null
+package jalview.ext.cipres;
+
+/**
+ * Example originally from cipres_java_client (Example.java there)
+ */
+import java.io.Console;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.ngbw.directclient.CiApplication;
+import org.ngbw.directclient.CiCipresException;
+import org.ngbw.directclient.CiClient;
+import org.ngbw.directclient.CiJob;
+import org.ngbw.directclient.CiResultFile;
+import org.ngbw.directclient.example.Example;
+import org.ngbw.restdatatypes.ErrorData;
+import org.ngbw.restdatatypes.LimitStatus;
+import org.ngbw.restdatatypes.ParamError;
+import org.ngbw.restdatatypes.StatusData;
+import org.ngbw.restdatatypes.ToolData;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Example command line application that shows how to use the CIPRES REST API
+ * Java Client library, i.e. the classes in the org.ngbw.directclient package.
+ * By default the example uses DIRECT authentication, but if invoked with the
+ * "-u" command line argument it switches to UMBRELLA authentication. Username,
+ * password, application name and application ID are read from ~/pycipres.conf
+ * and the information in pycipres.conf must correspond to an application
+ * registered for UMBRELLA auth or DIRECT auth respectively depending on whether
+ * you run the example with or with "-u".
+ * <p>
+ * This example repeatedly prompts the user to submit a job, list the user's
+ * already submitted jobs, retrieve a job's status, download a job's results,
+ * delete a job or quit. The example only submits one type of job: clustalw, run
+ * on the included sequence file. Consult the Users Guide for information about
+ * how to configure different kinds of jobs.
+ * <p>
+ * The gist of using the library is that you instantiate a CIClient object, then
+ * use its methods, and the objects that those methods return. When using direct
+ * auth a single CIClient can be used, but when using UMBRELLA auth, a CIClient
+ * must be instantiated for each end user. A CIClient object should not be used
+ * from multiple threads at the same time.
+ * <p>
+ */
+public class CipresExample
+{
+ @SuppressWarnings("unused")
+ private static final Logger log = LoggerFactory
+ .getLogger(Example.class.getName());
+
+ private static Console console = System.console();
+
+ private static String entry;
+
+ private static CiClient myClient;
+
+ private static String fastaFile;
+
+ private static boolean umbrella = false;
+
+ // For umbrella app's only
+ private static CiClient adminClient;
+
+ public static void main(String[] args) throws Exception
+ {
+ if (console == null)
+ {
+ System.out.println("No console");
+ return;
+ }
+
+ // If true, the example will use umbrella authentication
+ if (args.length > 0 && args[0].equals("-u"))
+ {
+ umbrella = true;
+ }
+
+ // Copy example fasta file from jar to temp file on disk
+ fastaFile = copyResource("ex1.fasta");
+
+ // Get username, password, app name, app id, url from pycipes.conf
+ CiApplication app = CiApplication.getInstance();
+
+ if (umbrella)
+ {
+ myClient = loginUser(app);
+ if (myClient == null)
+ {
+ return;
+ }
+ adminClient = new CiClient(app.getAppKey(), app.getUsername(),
+ app.getPassword(), app.getRestUrl());
+ }
+ else
+ {
+ myClient = new CiClient(app.getAppKey(), app.getUsername(),
+ app.getPassword(), app.getRestUrl());
+ }
+ String command = "";
+ while (!command.equals("q"))
+ {
+ if (umbrella)
+ {
+ System.out.println(
+ "\nEnter s(submit), v(validate), l(list), d(delete), j(job status), r(retrieve results), t(show tools), u(change end user) or q(quit):");
+ }
+ else
+ {
+ System.out.println(
+ "\nEnter s(submit), v(validate), l(list), d(delete), j(job status), r(retrieve results) or t(show tools) or q(quit):");
+ }
+ command = console.readLine();
+ try
+ {
+ if (command.equals("q"))
+ {
+ continue;
+ }
+ if (command.equals("v"))
+ {
+ validateJob();
+ }
+ else if (command.equals("s"))
+ {
+ submitJob();
+ }
+ else if (command.equals("l"))
+ {
+ listJobs();
+ }
+ else if (command.equals("d"))
+ {
+ deleteJob();
+ }
+ else if (command.equals("j"))
+ {
+ jobStatus();
+ }
+ else if (command.equals("r"))
+ {
+ retrieveResults();
+ }
+ else if (umbrella && command.equals("u"))
+ {
+ myClient = loginUser(app);
+ if (myClient == null)
+ {
+ break;
+ }
+ }
+ else if (command.equals("t"))
+ {
+ showTools();
+ }
+ else
+ {
+ System.out.println("invalid response: " + command);
+ }
+ } catch (CiCipresException ce)
+ {
+ ErrorData ed = ce.getErrorData();
+ System.out.println("Cipres error code=" + ed.code + ", message="
+ + ed.displayMessage);
+ if (ed.code == ErrorData.FORM_VALIDATION)
+ {
+ for (ParamError pe : ed.paramError)
+ {
+ System.out.println(pe.param + ": " + pe.error);
+ }
+ }
+ else if (ed.code == ErrorData.USAGE_LIMIT)
+ {
+ LimitStatus ls = ed.limitStatus;
+ System.out.println("Usage Limit Error, type=" + ls.type
+ + ", ceiling=" + ls.ceiling);
+ }
+ } catch (Exception e)
+ {
+ System.out.println(e.toString());
+ }
+ }
+ }
+
+ private static void showTools() throws CiCipresException
+ {
+ Collection<ToolData> tools = myClient.listTools();
+ System.out.println("");
+ for (ToolData td : tools)
+ {
+ System.out.println(td.toolId + " : " + td.toolName);
+ }
+ }
+
+ private static void validateJob() throws CiCipresException
+ {
+ System.out.println("Sending a canned clustalw job for validation ...");
+ sendCannedJob("fakeName", true);
+ }
+
+ private static void submitJob() throws CiCipresException
+ {
+ System.out.println(
+ "Will submit an example clustalw job. Enter a name for the job or enter a single 'n' to cancel");
+ entry = console.readLine();
+ if (entry.equals("n"))
+ {
+ return;
+ }
+ sendCannedJob(entry, false);
+ }
+
+ private static void sendCannedJob(String jobName, boolean validateOnly)
+ throws CiCipresException
+ {
+ Map<String, Collection<String>> vParams = new HashMap<>();
+ HashMap<String, String> inputParams = new HashMap<>();
+ HashMap<String, String> metadata = new HashMap<>();
+
+ vParams.put("runtime_", Arrays.asList(".2"));
+ vParams.put("hgapresidues_", Arrays.asList("A", "D"));
+ inputParams.put("infile_", fastaFile);
+
+ // See https://www.phylo.org/restusers/docs/guide.html#UseOptionalMetadata
+ // for list of available
+ // metadata keys.
+ metadata.put("statusEmail", "true");
+ metadata.put("clientJobName", jobName);
+
+ CiJob jobStatus;
+ if (validateOnly)
+ {
+ jobStatus = myClient.validateJob("CLUSTALW", vParams, inputParams,
+ metadata);
+ }
+ else
+ {
+ jobStatus = myClient.submitJob("CLUSTALW", vParams, inputParams,
+ metadata);
+ }
+ jobStatus.show(true);
+ }
+
+ private static void listJobs() throws CiCipresException
+ {
+
+ int count = 0;
+ Collection<CiJob> jobs = myClient.listJobs();
+ for (CiJob job : jobs)
+ {
+ count += 1;
+ System.out.print("\n" + count + ". ");
+ job.show(false);
+ }
+ }
+
+ private static void deleteJob() throws CiCipresException
+ {
+ System.out.println("Enter url of job to delete or n(no, cancel)");
+ entry = console.readLine();
+ if (!entry.startsWith("http"))
+ {
+ return;
+ }
+ CiJob job = myClient.getJob(entry);
+ job.delete();
+ }
+
+ private static void retrieveResults()
+ throws CiCipresException, IOException
+ {
+ boolean finalResults = true;
+ System.out.println("Enter url of job or n(no, cancel)");
+ entry = console.readLine();
+ if (!entry.startsWith("http"))
+ {
+ return;
+ }
+ CiJob job = myClient.getJob(entry);
+ if (job.isDone() == false)
+ {
+ System.out.println(
+ "Job is not finished. Enter y(yes, get working dir contents) or n(no, cancel)");
+ entry = console.readLine();
+ if (entry.equals("n"))
+ {
+ return;
+ }
+ else
+ {
+ finalResults = false;
+ }
+ }
+ Collection<CiResultFile> files = job.listResults(finalResults);
+ int count = 0;
+ for (CiResultFile file : files)
+ {
+ count = count + 1;
+ System.out.println(count + ". " + file.getName() + " ("
+ + file.getLength() + " bytes )");
+ }
+ System.out.println(
+ "Enter name of file to download or a(all) or n(no, cancel)");
+ entry = console.readLine();
+ boolean all = false;
+ if (entry.equals("a"))
+ {
+ all = true;
+ }
+ else if (entry.equals("n"))
+ {
+ return;
+ }
+ File directory = new File(new File("."), job.getJobHandle());
+ if (!directory.exists())
+ {
+ directory.mkdir();
+ }
+ for (CiResultFile file : files)
+ {
+ if (all == true || file.getName().equals(entry))
+ {
+ System.out.println("Downloading " + file.getName() + " to "
+ + directory.getAbsolutePath());
+ file.download(directory);
+ }
+ }
+ }
+
+ private static void jobStatus() throws CiCipresException
+ {
+ if (!umbrella)
+ {
+ System.out.println("Enter jobhandle or n(no, cancel)");
+ entry = console.readLine();
+ if (!entry.startsWith("NGBW"))
+ {
+ return;
+ }
+ CiJob job = myClient.getJobFromHandle(entry);
+ job.show(true);
+ }
+ else
+ {
+ /*
+ This shows how an umbrella app can get status of multiple jobs for multiple users in
+ a single call. This is the only thing an umbrella app can do with a CiClient (see
+ adminClient below) that is configured without endUserHeaders. Everything else must
+ be done for a specific end user with a CiClient configured for that user.
+
+ An Umbrella app could also use the code above (in the !umbrella case) to get status of a
+ single job, using a CiClient configured for the owner of the job.
+
+ */
+ System.out.println(
+ "Enter comma separated list of jobhandles or n(no, cancel)");
+ entry = console.readLine();
+ if (!entry.startsWith("NGBW"))
+ {
+ return;
+ }
+ String[] handles = entry.split(",");
+ ArrayList<String> handleList = new ArrayList<>(handles.length);
+ for (String handle : handles)
+ {
+ handleList.add(handle.trim());
+ }
+ // Collection<StatusData> jobList =
+ // adminClient.getMultipleJobStatus(handleList);
+ Collection<StatusData> jobList = myClient
+ .getMultipleJobStatus(handleList);
+ System.out.println("\n");
+ for (StatusData jobstatus : jobList)
+ {
+ String str = jobstatus.jobHandle + " ";
+ if (jobstatus.terminalStage == true)
+ {
+ if (jobstatus.failed == true)
+ {
+ str += " failed at stage " + jobstatus.jobStage;
+ }
+ else
+ {
+ str += " finished, results at " + jobstatus.resultsUri.url;
+ }
+ }
+ else
+ {
+ str += " is not finished, stage = " + jobstatus.jobStage;
+ }
+ System.out.println(str);
+ }
+ }
+ }
+
+ private static String copyResource(String name) throws IOException
+ {
+ InputStream is;
+
+ is = Example.class.getResourceAsStream("/" + name);
+ File dest = File.createTempFile("Example", ".txt");
+ dest.deleteOnExit();
+
+ CiResultFile.copyInputStreamToFile(is, dest);
+ return dest.getAbsolutePath();
+ }
+
+ private static CiClient loginUser(CiApplication app) throws Exception
+ {
+ Map<String, String> endUserHeaders = new HashMap<>();
+
+ System.out.println(
+ "\nEnter information about the current end user of this application.");
+ System.out.println("Enter username or q(quit)");
+ String username = console.readLine();
+ if (username.equals("q"))
+ {
+ return null;
+ }
+ System.out.println("Enter user's email address or q(quit)");
+ String email = console.readLine();
+ if (email.equals("q"))
+ {
+ return null;
+ }
+ System.out.println("Enter user's institution or q(quit)");
+ String institution = console.readLine();
+ if (institution.equals("q"))
+ {
+ return null;
+ }
+ System.out.println(
+ "Enter user's country code (must be 2 letters, both uppercase) or q(quit)");
+ String country = console.readLine();
+ if (country.equals("q"))
+ {
+ return null;
+ }
+ endUserHeaders.put("cipres-eu", username.trim());
+ endUserHeaders.put("cipres-eu-email", email.trim());
+ endUserHeaders.put("cipres-eu-institution", institution.trim());
+ endUserHeaders.put("cipres-eu-country", country.trim());
+ endUserHeaders.put("cipres-eu-email", email.trim());
+
+ log.debug(
+ "cipres-eu-email is " + endUserHeaders.get("cipres-eu-email"));
+ myClient = new CiClient(app.getAppKey(), app.getAppname(),
+ app.getUsername(), app.getPassword(), app.getRestUrl(),
+ endUserHeaders);
+ return myClient;
+ }
+
+}
+
git://source.jalview.org / jalview.git / commitdiff