+++ /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