+++ /dev/null
-package jalview.ws2.slivka;
-
-import java.io.IOException;
-import java.util.Arrays;
-import java.util.EnumMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import jalview.datamodel.SequenceI;
-import jalview.ws.gui.WsJob;
-import jalview.ws.params.ArgumentI;
-import jalview.ws.params.ParamDatastoreI;
-import jalview.ws.params.WsParamSetI;
-import jalview.ws.slivkaws.SlivkaDatastore;
-import jalview.ws2.JalviewWebServiceI;
-import jalview.ws2.WSJobID;
-import jalview.ws2.WSJobTrackerI;
-import uk.ac.dundee.compbio.slivkaclient.JobState;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
-import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
-
-public abstract class SlivkaWS<R> implements JalviewWebServiceI<R>
-{
- protected final SlivkaClient client;
- protected final SlivkaService service;
- protected SlivkaDatastore store = null;
- protected final String name;
- protected final String description;
- protected final String operation;
- protected int type = 0;
-
- protected static final EnumMap<JobState, WsJob.JobState> stateMap = new EnumMap<>(JobState.class);
- {
- stateMap.put(JobState.PENDING, WsJob.JobState.QUEUED);
- stateMap.put(JobState.REJECTED, WsJob.JobState.INVALID);
- stateMap.put(JobState.ACCEPTED, WsJob.JobState.QUEUED);
- stateMap.put(JobState.QUEUED, WsJob.JobState.QUEUED);
- stateMap.put(JobState.RUNNING, WsJob.JobState.RUNNING);
- stateMap.put(JobState.COMPLETED, WsJob.JobState.FINISHED);
- stateMap.put(JobState.INTERRUPTED, WsJob.JobState.CANCELLED);
- stateMap.put(JobState.DELETED, WsJob.JobState.CANCELLED);
- stateMap.put(JobState.FAILED, WsJob.JobState.FAILED);
- stateMap.put(JobState.ERROR, WsJob.JobState.SERVERERROR);
- stateMap.put(JobState.UNKNOWN, WsJob.JobState.UNKNOWN);
- }
- protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
- WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
- WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
- ));
-
- public SlivkaWS(SlivkaClient client, SlivkaService service, String operation) {
- this.client = client;
- this.service = service;
- this.operation = operation;
- this.name = service.getName();
- this.description = "";
- }
-
- @Override
- public String getHostName()
- {
- return client.getUrl().toString();
- }
-
- @Override
- public String getName()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getDescription()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public String getOperationType()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public int getTypeFlags()
- {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public boolean canSubmitGaps()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public int getMinSequences()
- {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public int getMaxSequences()
- {
- // TODO Auto-generated method stub
- return 0;
- }
-
- @Override
- public boolean hasParameters()
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public ParamDatastoreI getParamStore()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public WSJobID submit(List<SequenceI> sequences, WsParamSetI preset,
- List<ArgumentI> parameters) throws IOException
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void updateProgress(WSJobID id, WSJobTrackerI tracker)
- throws IOException
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public R getResult(WSJobID id) throws IOException
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public void cancel(WSJobID id) throws IOException
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public boolean handleSubmissionError(WSJobID id, Throwable th,
- WSJobTrackerI tracker)
- {
- // TODO Auto-generated method stub
- return false;
- }
-
- @Override
- public boolean handleCollectionError(WSJobID id, Throwable th,
- WSJobTrackerI tracker)
- {
- // TODO Auto-generated method stub
- return false;
- }
-
-}
--- /dev/null
+package jalview.ws2.slivka;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.*;
+import java.util.concurrent.*;
+
+import jalview.bin.Cache;
+import jalview.ws2.*;
+import jalview.ws2.operations.AlignmentOperation;
+import jalview.ws2.operations.Operation;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+public class SlivkaWSDiscoverer implements WebServiceDiscoverer
+{
+ private static final String SLIVKA_HOST_URLS = "SLIVKSHOSTURLS";
+
+ private static final String DEFAULT_URL = "https://www.compbio.dundee.ac.uk/slivka/";
+
+ private static SlivkaWSDiscoverer instance = null;
+
+ private List<WebServiceI> services = List.of();
+
+ private SlivkaWSDiscoverer()
+ {
+ }
+
+ public static SlivkaWSDiscoverer getInstance()
+ {
+ if (instance == null)
+ {
+ instance = new SlivkaWSDiscoverer();
+ }
+ return instance;
+ }
+
+ @Override
+ public List<String> getUrls() {
+ String surls = Cache.getDefault(SLIVKA_HOST_URLS, DEFAULT_URL);
+ String urls[] = surls.split(",");
+ ArrayList<String> valid = new ArrayList<>(urls.length);
+ for (String url : urls)
+ {
+ try
+ {
+ new URL(url);
+ valid.add(url);
+ }
+ catch (MalformedURLException e)
+ {
+ Cache.log.warn("Problem whilst trying to make a URL from '" +
+ Objects.toString(url, "<null>") + "'. " +
+ "This was probably due to malformed comma-separated-list " +
+ "in the " + SLIVKA_HOST_URLS + " entry of ${HOME}/.jalview_properties");
+ Cache.log.debug("Exception occurred while reading url list", e);
+ }
+ }
+ return valid;
+ }
+
+ @Override
+ public void setUrls(List<String> wsUrls) {
+ if (wsUrls != null && !wsUrls.isEmpty())
+ {
+ Cache.setProperty(SLIVKA_HOST_URLS, String.join(",", wsUrls));
+ }
+ else {
+ Cache.removeProperty(SLIVKA_HOST_URLS);
+ }
+ }
+
+ @Override
+ public boolean testUrl(URL url) {
+ return getStatusForUrl(url.toString()) == STATUS_OK;
+ }
+
+ @Override
+ public int getStatusForUrl(String url) {
+ try
+ {
+ List<?> services = new SlivkaClient(url).getServices();
+ return services.isEmpty() ? STATUS_NO_SERVICES : STATUS_OK;
+ }
+ catch (IOException e)
+ {
+ Cache.log.error("Slivka could not retrieve services list from " + url, e);
+ return STATUS_INVALID;
+ }
+ }
+
+ public List<WebServiceI> getServices() {
+ return Collections.unmodifiableList(services);
+ }
+
+ public boolean hasServices() {
+ return !isRunning() && services.size() > 0;
+ }
+
+ public boolean isRunning() {
+ for (Future<?> task : discoveryTasks) {
+ if (!task.isDone()) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ public boolean isDone() {
+ return !isRunning() && discoveryTasks.size() > 0;
+ }
+
+ private Vector<Future<?>> discoveryTasks = new Vector<>();
+
+ @Override
+ public CompletableFuture<WebServiceDiscoverer> startDiscoverer()
+ {
+ CompletableFuture<WebServiceDiscoverer> task = CompletableFuture
+ .supplyAsync(() -> {
+ reloadServices();
+ return SlivkaWSDiscoverer.this;
+ });
+ discoveryTasks.add(task);
+ return task;
+ }
+
+ private List<WebServiceI> reloadServices()
+ {
+ Cache.log.info("Reloading Slivka services");
+ fireServicesChanged(Collections.emptyList());
+ ArrayList<WebServiceI> allServices = new ArrayList<>();
+ for (String url : getUrls()) {
+ SlivkaClient client = new SlivkaClient(url);
+ List<SlivkaService> services;
+ try {
+ services = client.getServices();
+ } catch (IOException e) {
+ Cache.log.error("Unable to fetch services from " + url, e);
+ continue;
+ }
+ for (SlivkaService service : services) {
+ SlivkaWebService instance = new SlivkaWebService(client, service, service.getName());
+ for (String classifier : service.classifiers)
+ {
+ String[] path = classifier.split("\\s*::\\s*");
+ if (path.length >= 3 && path[0].toLowerCase().equals("operation")
+ && path[1].toLowerCase().equals("analysis"))
+ {
+ Operation op = null;
+ switch (path[path.length - 1].toLowerCase()) {
+ case "multiple sequence alignment":
+ op = new AlignmentOperation(instance, instance::getAlignment);
+ }
+ if (op != null)
+ instance.addOperation(op);
+ }
+ }
+ if (instance.operations.size() > 0) {
+ allServices.add(instance);
+ }
+ }
+ }
+ this.services = allServices;
+ Cache.log.info("Reloading slivka services finished");
+ fireServicesChanged(getServices());
+ return allServices;
+ }
+
+ @Override
+ public String getErrorMessages() {
+ return "";
+ }
+
+}
--- /dev/null
+package jalview.ws2.slivka;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.EnumMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FormatAdapter;
+import jalview.ws.gui.WsJob;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.ParamDatastoreI;
+import jalview.ws.params.WsParamSetI;
+import jalview.ws.slivkaws.SlivkaDatastore;
+import jalview.ws2.WebServiceI;
+import jalview.ws2.operations.Operation;
+import jalview.ws2.ResultSupplier;
+import jalview.ws2.WSJob;
+import jalview.ws2.WSJobStatus;
+import javajs.http.ClientProtocolException;
+import uk.ac.dundee.compbio.slivkaclient.Job;
+import uk.ac.dundee.compbio.slivkaclient.Parameter;
+import uk.ac.dundee.compbio.slivkaclient.RemoteFile;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaClient;
+import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
+
+public class SlivkaWebService implements WebServiceI
+{
+ protected final SlivkaClient client;
+ protected final SlivkaService service;
+ protected SlivkaDatastore store = null;
+ protected final String operation;
+ protected final ArrayList<Operation> operations = new ArrayList<>();
+ protected int typeFlags = 0;
+
+ protected static final EnumMap<Job.Status, WsJob.JobState> stateMap = new EnumMap<>(Job.Status.class);
+ {
+ stateMap.put(Job.Status.PENDING, WsJob.JobState.QUEUED);
+ stateMap.put(Job.Status.REJECTED, WsJob.JobState.INVALID);
+ stateMap.put(Job.Status.ACCEPTED, WsJob.JobState.QUEUED);
+ stateMap.put(Job.Status.QUEUED, WsJob.JobState.QUEUED);
+ stateMap.put(Job.Status.RUNNING, WsJob.JobState.RUNNING);
+ stateMap.put(Job.Status.COMPLETED, WsJob.JobState.FINISHED);
+ stateMap.put(Job.Status.INTERRUPTED, WsJob.JobState.CANCELLED);
+ stateMap.put(Job.Status.DELETED, WsJob.JobState.CANCELLED);
+ stateMap.put(Job.Status.FAILED, WsJob.JobState.FAILED);
+ stateMap.put(Job.Status.ERROR, WsJob.JobState.SERVERERROR);
+ stateMap.put(Job.Status.UNKNOWN, WsJob.JobState.UNKNOWN);
+ }
+ protected final Set<WsJob.JobState> failedStates = new HashSet<>(Arrays.asList(
+ WsJob.JobState.INVALID, WsJob.JobState.BROKEN, WsJob.JobState.FAILED,
+ WsJob.JobState.SERVERERROR, WsJob.JobState.CANCELLED
+ ));
+
+ public SlivkaWebService(SlivkaClient client, SlivkaService service, String operation) {
+ this.client = client;
+ this.service = service;
+ this.operation = operation;
+ }
+
+ @Override
+ public String getHostName() { return client.getUrl().toString(); }
+
+ @Override
+ public String getName() { return service.getName(); }
+
+ @Override
+ public String getDescription() { return service.getDescription(); }
+
+ @Override
+ public String getOperationType() { return operation; }
+
+ @Override
+ public List<Operation> getOperations() {
+ return operations;
+ }
+
+ void addOperation(Operation operation) {
+ operations.add(operation);
+ }
+
+ void removeOperation(Operation operation) {
+ operations.remove(operation);
+ }
+
+ @Override
+ public boolean hasParameters() {
+ return getParamStore().getServiceParameters().size() > 0;
+ }
+
+ @Override
+ public ParamDatastoreI getParamStore() {
+ if (store == null) {
+ store = new SlivkaDatastore(service);
+ }
+ return store;
+ }
+
+ @Override
+ public WSJob submit(List<SequenceI> sequences, List<ArgumentI> args) throws IOException
+ {
+ var request = new uk.ac.dundee.compbio.slivkaclient.JobRequest();
+ for (Parameter param : service.getParameters()) {
+ if (param instanceof Parameter.FileParameter) {
+ // if finds a file input, gives it sequences stream
+ Parameter.FileParameter fileParam = (Parameter.FileParameter) param;
+ FileFormat format;
+ switch (fileParam.getMediaType()) {
+ case "application/pfam":
+ format = FileFormat.Pfam;
+ break;
+ case "application/stockholm":
+ format = FileFormat.Stockholm;
+ break;
+ case "application/clustal":
+ format = FileFormat.Clustal;
+ break;
+ case "application/fasta":
+ default:
+ format = FileFormat.Fasta;
+ break;
+ }
+ InputStream stream = new ByteArrayInputStream(
+ format.getWriter(null)
+ .print(sequences.toArray(new SequenceI[0]), false)
+ .getBytes());
+ request.addFile(param.getId(), stream);
+ }
+ }
+ if (args != null) {
+ for (ArgumentI arg : args) {
+ // multiple choice field names are name$number to avoid duplications
+ // the number is stripped here
+ String paramId = arg.getName().split("\\$", 2)[0];
+ Parameter param = service.getParameter(paramId);
+ if (param instanceof Parameter.FlagParameter) {
+ if (arg.getValue() != null && !arg.getValue().isBlank())
+ request.addData(paramId, true);
+ else
+ request.addData(paramId, false);
+ }
+ else
+ {
+ request.addData(paramId, arg.getValue());
+ }
+ }
+ }
+ var job = service.submitJob(request);
+ return new WSJob("slivka", getName(), job.getId(), getHostName());
+ }
+
+ @Override
+ public void updateProgress(WSJob job)
+ throws IOException
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public void cancel(WSJob job) throws IOException
+ {
+ Cache.log.warn("Slivka does not support job cancellation yet.");
+ }
+
+ @Override
+ public boolean handleSubmissionError(WSJob job, Exception ex)
+ {
+ if (ex instanceof ClientProtocolException) {
+ Cache.log.error("Job submission failed due to exception.", ex);
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public boolean handleCollectionError(WSJob job, Exception ex)
+ {
+ // TODO Auto-generated method stub
+ return false;
+ }
+
+ public AlignmentI getAlignment(WSJob job) throws IOException {
+ Collection<RemoteFile> files;
+ var slivkaJob = client.getJob(job.getJobID());
+ files = slivkaJob.getResults();
+ for (RemoteFile f : files) {
+ if (f.getMediaType().equals("application/clustal")) {
+ return new FormatAdapter().readFile(
+ f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Clustal);
+ }
+ else if (f.getMediaType().equals("application/fasta")) {
+ return new FormatAdapter().readFile(
+ f.getContentUrl().toString(), DataSourceType.URL, FileFormat.Fasta);
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public String toString() {
+ return String.format("SlivkaWebService[%s]", getName());
+ }
+}
git://source.jalview.org / jalview.git / commitdiff