import jalview.bin.Cache;
import jalview.io.FileParse;
+import jalview.io.packed.DataProvider;
+import jalview.io.packed.ParsePackedSet;
+import jalview.io.packed.SimpleDataProvider;
+import jalview.io.packed.DataProvider.JvDataType;
import jalview.ws.io.mime.JalviewMimeContentHandler;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
+import java.util.ArrayList;
+import java.util.List;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
initDataSource(con);
}
- private void initDataSource(HttpResponse con) throws IOException
+ /**
+ * construct a set of dataproviders to parse a result set from this service
+ *
+ * @param resSet
+ * @return
+ */
+ public List<DataProvider> createResultDataProviders()
{
- en = con.getEntity();
- repeatable = en.isRepeatable();
+ List<DataProvider> dp = new ArrayList<DataProvider>();
+ for (JvDataType type : restJob.rsd.getResultDataTypes())
+ {
+ dp.add(new SimpleDataProvider(type, this, null));
+ }
+ return dp;
+ }
+
+ public Object[] parseResultSet() throws Exception, Error
+ {
+ List<DataProvider> dp = new ArrayList<DataProvider>();
+ Object[] results = null;
+ if (en == null)
+ {
+ throw new Error(
+ "Implementation Error: need to have an HttpResponse to process.");
+ }
+ jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
+ // Decide how we deal with content.
if (en instanceof MultipartEntity)
{
+ // Multipart messages should be properly typed, so we parse them as we go.
MultipartEntity mpe = (MultipartEntity) en;
// multipart
- jalview.io.packed.JalviewDataset ds = restJob.newJalviewDataset();
- ContentHandler handler = new JalviewMimeContentHandler(ds);
+ JalviewMimeContentHandler handler = new JalviewMimeContentHandler(ds);
MimeStreamParser parser = new MimeStreamParser();
parser.setContentHandler(handler);
try
Cache.log.warn("Failed to parse MIME multipart content", me);
en.consumeContent();
}
+ return new ParsePackedSet().getAlignment(ds,
+ handler.getJalviewDataProviders());
}
else
{
+ // Need to use hints from rest service description.
+ dp = createResultDataProviders();
+ ParsePackedSet pps = new ParsePackedSet();
+ return pps.getAlignment(ds, dp);
+ }
+ }
+
+ private void initDataSource(HttpResponse con) throws IOException
+ {
+ en = con.getEntity();
+ repeatable = en.isRepeatable();
+
+ if (!(en instanceof MultipartEntity))
+ {
// assume content is simple text stream that can be read from
- String enc = (en.getContentEncoding()==null) ? null : en.getContentEncoding().getValue();
- if (en.getContentType()!=null) {
- Cache.log.info("Result Type: " + en.getContentType().toString());
- } else {
- Cache.log.info("No Result Type Specified.");
+ String enc = (en.getContentEncoding() == null) ? null : en
+ .getContentEncoding().getValue();
+ if (en.getContentType() != null)
+ {
+ Cache.log.debug("Result Type: " + en.getContentType().toString());
+ }
+ else
+ {
+ Cache.log.debug("No Result Type Specified.");
}
if (enc == null || enc.length() < 1)
{
}
else
{
- Cache.log.debug("Result Encoded as : "+enc);
+ Cache.log.debug("Result Encoded as : " + enc);
}
// attempt to identify file and construct an appropriate DataSource
// identifier for it.
if (br != null)
{
dataIn = new BufferedReader(br);
- error=false;
+ error = false;
}
}
}
import sun.io.CharacterEncoding;
import sun.misc.CharacterEncoder;
-/** Service Input info { a sequence of [ Sequence Id vector (min,max,moltype, separator,regex,colrange(start-end)), Sequence(format-bare or alignment, moltype, min, max, separator)), Alignment(format, moltype),
- */
+/***
+ * InputType is the abstract model of each input parameter that a rest service might take.
+ * It enables the engine to validate input by providing
+ * { formatter for type, parser for type }
+ *
+ */
public abstract class InputType {
/**
* not used yet
import jalview.datamodel.SequenceGroup;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
+import jalview.gui.AlignmentPanel;
import jalview.gui.Desktop;
import jalview.gui.WebserviceInfo;
+import jalview.io.packed.DataProvider.JvDataType;
import jalview.ws.WSClient;
import jalview.ws.WSClientI;
import jalview.ws.WSMenuEntryProviderI;
{
wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n"
+ WebServiceReference);
+ wsInfo.setRenderAsHtml(true);
}
}
}
else
{
+ // TODO: try to tell the user why the job couldn't be started.
JOptionPane.showMessageDialog(Desktop.desktop,
"Unable to start web service analysis",
"Internal Jalview Error", JOptionPane.WARNING_MESSAGE);
name,
"http://www.ibi.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1",
"?tool=jalview", iparams, true, false, '-');
+ // a priori knowledge of the data returned from the service
+ shmrService.addResultDatatype(JvDataType.ANNOTATION);
return new RestClient(shmrService);
}
+ public AlignmentPanel recoverAlignPanelForView()
+ {
+ AlignmentPanel[] aps = Desktop.getAlignmentPanels(av.getSequenceSetId());
+ for (AlignmentPanel alp:aps)
+ {
+ if (alp.av == av)
+ {
+ return alp;
+ }
+ }
+ return null;
+ }
+
+ public boolean isShowResultsInNewView()
+ {
+ // TODO make this a property of the service
+ return true;
+ }
+
}
package jalview.ws.rest;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Hashtable;
+import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.Vector;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.packed.DataProvider;
import jalview.io.packed.JalviewDataset;
+import jalview.io.packed.ParsePackedSet;
+import jalview.io.packed.SimpleDataProvider;
+import jalview.io.packed.DataProvider.JvDataType;
import jalview.ws.AWsJob;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.SeqGroupIndexVector;
public class RestJob extends AWsJob
{
-
+
// TODO: input alignmentview and other data for this job
RestServiceDescription rsd;
+
// boolean submitted;
boolean gotresponse;
+
boolean error;
+
boolean waiting;
+
boolean gotresult;
+
Hashtable squniq;
-
+
+ /**
+ * dataset associated with this input data.
+ */
+ AlignmentI dsForIO;
+
+ AlignmentOrder inputOrder;
+
+ /**
+ * context of input data with respect to an AlignmentView's visible contigs.
+ */
+ int[] origviscontig;
+
+ private AlignmentI contextAl=null;
+
/**
- * create a rest job using data bounded by the given start/end column.
+ * create a rest job using data bounded by the given start/end column.
+ *
* @param addJobPane
* @param restJobThread
* @param _input
+ * @param viscontigs
+ * visible contigs of an alignment view from which _input was derived
*/
public RestJob(int jobNum, RestJobThread restJobThread,
- AlignmentI _input)
+ AlignmentI _input, int[] viscontigs)
{
rsd = restJobThread.restClient.service;
jobnum = jobNum;
+ if (viscontigs != null)
+ {
+ origviscontig = new int[viscontigs.length];
+ System.arraycopy(viscontigs, 0, origviscontig, 0, viscontigs.length);
+ }
// get sequences for the alignmentI
// get groups trimmed to alignment columns
// get any annotation trimmed to start/end columns, too.
-
+
// prepare input
- // form alignment+groups+annotation,preprocess and then record references for formatters
+ // form alignment+groups+annotation,preprocess and then record references
+ // for formatters
ArrayList<InputType> alinp = new ArrayList<InputType>();
- int paramsWithData=0;
- // we cheat for moment - since we know a-priori what data is available and what inputs we have implemented so far
- for (Map.Entry<String,InputType>prm: rsd.inputParams.entrySet())
+ int paramsWithData = 0;
+ // we cheat for moment - since we know a-priori what data is available and
+ // what inputs we have implemented so far
+ for (Map.Entry<String, InputType> prm : rsd.inputParams.entrySet())
{
if (!prm.getValue().isConstant())
{
if (prm.getValue() instanceof Alignment)
- {
- alinp.add(prm.getValue());
- } else
- {
- if ((prm.getValue() instanceof SeqGroupIndexVector)
- &&(_input.getGroups()!=null && _input.getGroups().size()>0))
{
alinp.add(prm.getValue());
}
- }
- } else {
+ else
+ {
+ if ((prm.getValue() instanceof SeqGroupIndexVector)
+ && (_input.getGroups() != null && _input.getGroups()
+ .size() > 0))
+ {
+ alinp.add(prm.getValue());
+ }
+ }
+ }
+ else
+ {
paramsWithData++;
}
}
- if ((paramsWithData+alinp.size())==rsd.inputParams.size())
+ if ((paramsWithData + alinp.size()) == rsd.inputParams.size())
{
+ inputOrder = new AlignmentOrder(_input);
+ if ((dsForIO = _input.getDataset()) == null)
+ {
+ _input.setDataset(null);
+ }
+ dsForIO = _input.getDataset();
+ if (contextAl==null)
+ {
+ contextAl = _input;
+ }
setAlignmentForInputs(alinp, _input);
- validInput=true;
- } else {
+ validInput = true;
+ }
+ else
+ {
// not enough data, so we bail.
- validInput=false;
+ validInput = false;
}
}
- boolean validInput=false;
+
+ boolean validInput = false;
+
@Override
public boolean hasResults()
{
@Override
public boolean isRunning()
{
- return running; // TODO: can we check the response body for status messages ?
+ return running; // TODO: can we check the response body for status messages
+ // ?
}
@Override
@Override
public boolean isFinished()
{
- return resSet!=null;
+ return resSet != null;
}
@Override
}
protected String statMessage = null;
+
public HttpResultSet resSet;
@Override
@Override
public boolean hasResponse()
{
- return statMessage!=null || resSet!=null;
+ return statMessage != null || resSet != null;
}
@Override
public void clearResponse()
{
- // only clear the transient server response
+ // only clear the transient server response
// statMessage=null;
}
- /* (non-Javadoc)
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.ws.AWsJob#getState()
*/
@Override
public String getState()
{
- // TODO generate state string - prolly should have a default abstract method for this
+ // TODO generate state string - prolly should have a default abstract method
+ // for this
return "Job is clueless";
}
public String getPostUrl()
{
-
+
// TODO Auto-generated method stub
return rsd.postUrl;
}
- public Set<Map.Entry<String,InputType>> getInputParams()
+ public Set<Map.Entry<String, InputType>> getInputParams()
{
return rsd.inputParams.entrySet();
}
/**
*
- * @return new context for parsing results from service
+ * @return the context for parsing results from service
*/
public JalviewDataset newJalviewDataset()
{
- /*
- * TODO: initialise dataset with correct input context
- */
- JalviewDataset njd = new JalviewDataset();
- return njd;
+ if (context == null)
+ {
+ context = new JalviewDataset(dsForIO, null, squniq, null);
+ if (contextAl!=null)
+ {
+ context.addAlignment(contextAl);
+ }
+
+ }
+ return context;
}
/**
- * Extract list of sequence IDs for input parameter 'token' with given molecule type
+ * Extract list of sequence IDs for input parameter 'token' with given
+ * molecule type
+ *
* @param token
* @param type
* @return
*/
- public SequenceI[] getSequencesForInput(String token, InputType.molType type) throws NoValidInputDataException
+ public SequenceI[] getSequencesForInput(String token,
+ InputType.molType type) throws NoValidInputDataException
{
Object sgdat = inputData.get(token);
// can we form an alignment from this data ?
- if (sgdat==null)
+ if (sgdat == null)
{
- throw new NoValidInputDataException("No Sequence vector data bound to input '"+token+"' for service at "+rsd.postUrl);
+ throw new NoValidInputDataException(
+ "No Sequence vector data bound to input '" + token
+ + "' for service at " + rsd.postUrl);
}
if (sgdat instanceof AlignmentI)
{
}
if (sgdat instanceof SequenceGroup)
{
- return ((SequenceGroup)sgdat).getSequencesAsArray(null);
+ return ((SequenceGroup) sgdat).getSequencesAsArray(null);
}
if (sgdat instanceof Vector)
{
- if (((Vector)sgdat).size()>0 && ((Vector)sgdat).get(0) instanceof SequenceI)
+ if (((Vector) sgdat).size() > 0
+ && ((Vector) sgdat).get(0) instanceof SequenceI)
{
- SequenceI[] sq = new SequenceI[((Vector)sgdat).size()];
- ((Vector)sgdat).copyInto(sq);
+ SequenceI[] sq = new SequenceI[((Vector) sgdat).size()];
+ ((Vector) sgdat).copyInto(sq);
return sq;
}
}
- throw new NoValidInputDataException("No Sequence vector data bound to input '"+token+"' for service at "+rsd.postUrl);
+ throw new NoValidInputDataException(
+ "No Sequence vector data bound to input '" + token
+ + "' for service at " + rsd.postUrl);
}
+
/**
- * binding between input data (AlignmentI, SequenceGroup, NJTree) and input param names.
+ * binding between input data (AlignmentI, SequenceGroup, NJTree) and input
+ * param names.
*/
- private Hashtable<String,Object> inputData=new Hashtable<String,Object>();
+ private Hashtable<String, Object> inputData = new Hashtable<String, Object>();
+
/**
* is the job fully submitted to server and apparently in progress ?
*/
- public boolean running=false;
+ public boolean running = false;
+
/**
*
* @param itypes
- * @param al - reference to object to be stored as input. Note - input data may be modifed by formatter
+ * @param al
+ * - reference to object to be stored as input. Note - input data may
+ * be modifed by formatter
*/
- public void setAlignmentForInputs(Collection<InputType> itypes, AlignmentI al)
+ public void setAlignmentForInputs(Collection<InputType> itypes,
+ AlignmentI al)
{
- for (InputType itype: itypes) {
+ for (InputType itype : itypes)
+ {
if (!rsd.inputParams.values().contains(itype))
{
- throw new IllegalArgumentException("InputType "+itype.getClass()+
- " is not valid for service at "+rsd.postUrl);
+ throw new IllegalArgumentException("InputType " + itype.getClass()
+ + " is not valid for service at " + rsd.postUrl);
}
if (itype instanceof AlignmentProcessor)
{
- ((AlignmentProcessor)itype).prepareAlignment(al);
+ ((AlignmentProcessor) itype).prepareAlignment(al);
}
// stash a reference for recall when the alignment data is formatted
inputData.put(itype.token, al);
}
-
+
}
+
/**
*
* @param token
* @return alignment object bound to the given token
* @throws NoValidInputDataException
*/
- public AlignmentI getAlignmentForInput(String token, InputType.molType type) throws NoValidInputDataException
+ public AlignmentI getAlignmentForInput(String token,
+ InputType.molType type) throws NoValidInputDataException
{
Object al = inputData.get(token);
// can we form an alignment from this data ?
- if (al==null || !(al instanceof AlignmentI))
+ if (al == null || !(al instanceof AlignmentI))
{
- throw new NoValidInputDataException("No alignment data bound to input '"+token+"' for service at "+rsd.postUrl);
+ throw new NoValidInputDataException(
+ "No alignment data bound to input '" + token
+ + "' for service at " + rsd.postUrl);
}
return (AlignmentI) al;
}
/**
* test to see if the job has data of type cl that's needed for the job to run
+ *
* @param cl
* @return true or false
*/
public boolean hasDataOfType(Class cl)
{
- if (AlignmentI.class.isAssignableFrom(cl)) {
+ if (AlignmentI.class.isAssignableFrom(cl))
+ {
return true;
}
- // TODO: add more source data types
-
+ // TODO: add more source data types
+
return false;
}
+ /**
+ * context used to parse results from service
+ */
+ JalviewDataset context = null;
+
+ Object[] jvresultobj = null;
+
+ /**
+ * process the results obtained from the server into jalview datamodel objects
+ * ready to be merged/added to the users' view.
+ */
+ public void parseResultSet() throws Exception, Error
+ {
+ jvresultobj = resSet.parseResultSet();
+ }
+
}
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.gui.AlignFrame;
import jalview.gui.WebserviceInfo;
import jalview.io.packed.DataProvider;
import jalview.io.packed.JalviewDataset;
import jalview.ws.AWSThread;
import jalview.ws.AWsJob;
+import java.awt.Desktop;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.IOException;
jobs = new RestJob[1];
jobs[0] = new RestJob(0, this,
restClient._input.getVisibleAlignment(restClient.service
- .getGapCharacter()));
+ .getGapCharacter()),
+ restClient._input.getVisibleContigs());
// need a function to get a range on a view/alignment and return both
// annotation, groups and selection subsetted to just that region.
}
else
{
+ int[] viscontig = restClient._input.getVisibleContigs();
AlignmentI[] viscontigals = restClient._input
.getVisibleContigAlignments(restClient.service
.getGapCharacter());
jobs = new RestJob[viscontigals.length];
for (int j = 0; j < jobs.length; j++)
{
+ int[] visc = new int[]
+ { viscontig[j * 2], viscontig[j * 2 + 1] };
if (j != 0)
{
- jobs[j] = new RestJob(j, this, viscontigals[j]);
+ jobs[j] = new RestJob(j, this, viscontigals[j], visc);
}
else
{
- jobs[j] = new RestJob(0, this, viscontigals[j]);
+ jobs[j] = new RestJob(0, this, viscontigals[j], visc);
}
}
}
throws Exception
{
StringBuffer respText = new StringBuffer();
- // con.setContentHandlerFactory(new jalview.ws.io.mime.HttpContentHandler());
+ // con.setContentHandlerFactory(new
+ // jalview.ws.io.mime.HttpContentHandler());
HttpRequestBase request = null;
String messages = "";
if (stg == Stage.SUBMIT)
processResultSet(rj, response, request);
break;
case 202:
- rj.statMessage = "Job submitted successfully. Results available at this URL:\n"
- + rj.getJobId() + "\n";
+ rj.statMessage = "<br>Job submitted successfully. Results available at this URL:\n"
+ + "<a href="
+ + rj.getJobId()
+ + "\">"
+ + rj.getJobId()
+ + "</a><br>";
rj.running = true;
break;
case 302:
rj.setAllowedServerExceptions(0);
rj.setSubjobComplete(true);
rj.error = true;
+ rj.running = false;
completeStatus(rj, response, "" + getStage(stg)
+ "failed. Reason below:\n");
break;
}
HttpEntity en = con.getEntity();
/*
- * Just show the content as a string.
+ * Just append the content as a string.
*/
- rj.statMessage = EntityUtils.toString(en);
+ String f;
+ StringBuffer content = new StringBuffer(f = EntityUtils.toString(en));
+ f = f.toLowerCase();
+ int body = f.indexOf("<body");
+ if (body > -1)
+ {
+ content.delete(0, f.indexOf(">", body));
+ }
+ if (body > -1 && sb.length() > 0)
+ {
+ sb.append("\n");
+ content.insert(0, sb);
+ sb = null;
+ }
+ f = null;
+ rj.statMessage = content.toString();
}
@Override
public void parseResult()
{
// crazy users will see this message
- System.err.println("WARNING: Rest job result parser is INCOMPLETE!");
+ // TODO: finish this! and remove the message below!
+ Cache.log.warn("Rest job result parser is currently INCOMPLETE!");
+ int validres = 0;
for (RestJob rj : (RestJob[]) jobs)
{
- // TODO: call each jobs processResults() method and collect valid
- // contexts.
if (rj.hasResponse() && rj.resSet != null && rj.resSet.isValid())
{
String ln = null;
- System.out.println("Parsing data for job " + rj.getJobId());
- if (!restClient.isAlignmentModified())
+ try
{
- try
- {
- /*
- * while ((ln=rj.resSet.nextLine())!=null) { System.out.println(ln);
- * } }
- */
- List<DataProvider> dp = new ArrayList<DataProvider>();
- restClient.af.newView_actionPerformed(null);
- dp.add(new SimpleDataProvider(JvDataType.ANNOTATION, rj.resSet, null));
- JalviewDataset context = new JalviewDataset(restClient.av.getAlignment().getDataset(), null, null,restClient.av.getAlignment());
- ParsePackedSet pps = new ParsePackedSet();
- pps.getAlignment(context, dp);
-
- // do an ap.refresh restClient.av.alignmentChanged(Desktop.getAlignmentPanels(restClient.av.getViewId())[0]);
- System.out.println("Finished parsing data for job "
- + rj.getJobId());
-
- } catch (Exception ex)
+ Cache.log.debug("Parsing data for job " + rj.getJobId());
+ rj.parseResultSet();
+ if (rj.hasResults())
{
- System.out.println("Failed to finish parsing data for job "
- + rj.getJobId());
- ex.printStackTrace();
+ validres++;
}
+ Cache.log.debug("Finished parsing data for job " + rj.getJobId());
+
+ } catch (Error ex)
+ {
+ Cache.log.warn("Failed to finish parsing data for job "
+ + rj.getJobId());
+ ex.printStackTrace();
+ } catch (Exception ex)
+ {
+ Cache.log.warn("Failed to finish parsing data for job "
+ + rj.getJobId());
+ ex.printStackTrace();
}
}
}
- /**
- * decisions based on job result content + state of alignFrame that
- * originated the job:
- */
- /*
- * 1. Can/Should this job automatically open a new window for results
- */
- wsInfo.setViewResultsImmediatly(false);
+ if (validres > 0)
+ {
+ // add listeners and activate result display gui elements
+ /**
+ * decisions based on job result content + state of alignFrame that
+ * originated the job:
+ */
+ /*
+ * 1. Can/Should this job automatically open a new window for results
+ */
+ if (true)
+ {
+ wsInfo.setViewResultsImmediatly(false);
+ }
+ else
+ {
+ // realiseResults(true, true);
+ }
+ // otherwise, should automatically view results
+
+ // TODO: check if at least one or more contexts are valid - if so, enable
+ // gui
+ wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ realiseResults(false);
+ }
+
+ });
+ wsInfo.mergeResults.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ realiseResults(true);
+ }
+
+ });
+
+ wsInfo.setResultsReady();
+ }
+ else
+ {
+ // tell the user nothing was returned.
+ }
+ }
+
+ public void realiseResults(boolean merge)
+ {
/*
* 2. Should the job modify the parent alignment frame/view(s) (if they
* still exist and the alignment hasn't been edited) in order to display new
* aligned to it ?
*
*/
- // TODO: check if at least one or more contexts are valid - if so, enable
- // gui
- wsInfo.showResultsNewFrame.addActionListener(new ActionListener()
+ jalview.gui.AlignmentPanel destPanel = null;
+ if (merge)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ if (!restClient.isAlignmentModified())
{
- // TODO: call method to show results in new window
+ destPanel = restClient.recoverAlignPanelForView();
+ if (restClient.isShowResultsInNewView())
+ {
+ destPanel = destPanel.alignFrame.newView(false);
+ }
}
-
- });
- wsInfo.mergeResults.addActionListener(new ActionListener()
+ }
+ if (destPanel == null)
{
-
- @Override
- public void actionPerformed(ActionEvent e)
+ Object[] idat = input.getAlignmentAndColumnSelection(restClient.av.getGapCharacter());
+ AlignFrame af = new AlignFrame((AlignmentI) idat[0],
+ (ColumnSelection) idat[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ jalview.gui.Desktop.addInternalFrame(af,
+ "Results for " + restClient.service.details.Name + " "
+ + restClient.service.details.Action + " on "
+ + restClient.af.getTitle(), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ destPanel = af.alignPanel;
+ // create totally new alignment from stashed data/results
+ }
+ else
+ {
+ for (int j = 0; j < jobs.length; j++)
{
- // TODO: call method to merge results into existing window
+ RestJob rj = (RestJob) jobs[j];
+ if (rj.jvresultobj!=null && rj.jvresultobj.length>0) {
+ // transfer results onto panel
+
+ }
}
-
- });
-
- wsInfo.setResultsReady();
+ }
+ destPanel.adjustAnnotationHeight();
+
}
import jalview.datamodel.SequenceI;
+import jalview.io.packed.DataProvider;
+import jalview.io.packed.SimpleDataProvider;
+import jalview.io.packed.DataProvider.JvDataType;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.Platform;
import jalview.ws.rest.params.Alignment;
import jalview.ws.rest.params.AnnotationFile;
import jalview.ws.rest.params.SeqGroupIndexVector;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.Hashtable;
+import java.util.List;
import java.util.Map;
*/
String urlSuffix;
- /***
- * modelling the io:
- * validation of input
- * { formatter for type, parser for type }
- *
- */
/** input info given as key/value pairs - mapped to post arguments
*/
Map<String,InputType> inputParams=new HashMap();
/**
+ * assigns the given inputType it to its corresponding input parameter token it.token
+ * @param it
+ */
+ public void setInputParam(InputType it)
+ {
+ inputParams.put(it.token, it);
+ }
+ /**
+ * remove the given input type it from the set of service input parameters.
+ * @param it
+ */
+ public void removeInputParam(InputType it)
+ {
+ inputParams.remove(it.token);
+ }
+ /**
* service requests alignment data
*/
boolean aligndata;
// TODO: correctly write ?/& appropriate to result URL format.
return jobId+urlSuffix;
}
+ private List<JvDataType> resultData;
+ public void addResultDatatype(JvDataType dt)
+ {
+ if (resultData==null)
+ {
+ resultData = new ArrayList<JvDataType>();
+ }
+ resultData.add(dt);
+ }
+ public boolean removeRsultDatatype(JvDataType dt)
+ {
+ if (resultData!=null)
+ {
+ return resultData.remove(dt);
+ }
+ return false;
+ }
+ public List<JvDataType> getResultDataTypes()
+ {
+ return resultData;
+ }
}
throw new NoValidInputDataException("Couldn't write out alignment to file.",ex);
}
} else {
- StringBody sb = new StringBody(new jalview.io.FormatAdapter().formatSequences(format, alignment, jvsuffix), "text/plain", Charset.forName("UTF-8"));
- sb.getContentTypeParameters().put("filename", "alignment.fa");
+ StringBody sb = new StringBody(new jalview.io.FormatAdapter().formatSequences(format, alignment, jvsuffix)); // , "text/plain", Charset.forName("UTF-8"));
+ // sb.getContentTypeParameters().put("filename", "alignment.fa");
return sb;
}
}
git://source.jalview.org / jalview.git / commitdiff