コード例 #1
0
  @Test
  public void validFullResponse() {
    XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
    opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
    opt.setSaveNamespacesFirst();
    opt.setSaveAggressiveNamespaces();
    opt.setUseDefaultNamespace();

    XmlObject co = completeResponse();
    ArrayList errorList = new ArrayList();
    boolean validXml = Utilities.validateXml(opt, co, errorList);
    assertTrue(errorList.toString(), validXml);
  }
コード例 #2
0
  public String AsXml() {
    XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
    opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
    opt.setSaveNamespacesFirst();
    opt.setSaveAggressiveNamespaces();
    opt.setUseDefaultNamespace();

    DescribeSRSResponseDocument document = completeResponse();

    ArrayList errorList = new ArrayList();
    opt.setErrorListener(errorList);
    boolean isValid = document.validate(opt);

    // If the XML isn't valid, loop through the listener's contents,
    // printing contained messages.
    if (!isValid) {
      for (int i = 0; i < errorList.size(); i++) {
        XmlError error = (XmlError) errorList.get(i);

        System.out.println("\n");
        System.out.println("Message: " + error.getMessage() + "\n");
        System.out.println(
            "Location of invalid XML: " + error.getCursorLocation().xmlText() + "\n");
      }
    }
    return document.xmlText(opt);
  }
コード例 #3
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  public DescribeSRSResponseDocument completeResponse() {
    DescribeSRSResponseDocument document = DescribeSRSResponseDocument.Factory.newInstance();

    DescribeSRSResponseType rootDoc = document.addNewDescribeSRSResponse();

    rootDoc.newCursor().insertComment("Generated " + Calendar.getInstance().getTime());
    ListSRSResponse.QueryInfoSrs(rootDoc.addNewQueryInfo(), "URL");
    rootDoc.getQueryInfo().getQueryUrl().setName("DescribeSRS");
    Utilities.addInputStringCriteria(
        rootDoc.getQueryInfo().addNewCriteria(), "srsName", "Mouse_ABAreference_1.0");
    SRSCollection coll1 = rootDoc.addNewSRSCollection();
    coll1.setHubCode("HUBA");

    SRSList srsList = coll1.addNewSRSList();
    SRSType srs1 = srsList.addNewSRS();
    ListSRSResponse.SrsExample1(srs1);

    Orientations o = coll1.addNewOrientations();
    OrientationType orientaiton1 = o.addNewOrientation();
    // orientation(orientaiton1,code,name);
    ListSRSResponse.orientation(orientaiton1, "Left", "Left");
    orientaiton1 = o.addNewOrientation();
    ListSRSResponse.orientation(orientaiton1, "Right", "Right");
    orientaiton1 = o.addNewOrientation();
    ListSRSResponse.orientation(orientaiton1, "Ventral", "Ventral");
    orientaiton1 = o.addNewOrientation();
    ListSRSResponse.orientation(orientaiton1, "Dorsal", "Dorsal");
    orientaiton1 = o.addNewOrientation();
    ListSRSResponse.orientation(orientaiton1, "Posterior", "Posterior");
    orientaiton1 = o.addNewOrientation();
    ListSRSResponse.orientation(orientaiton1, "Anterior", "Anterior");

    Slices s = rootDoc.addNewSlices();
    exampleSlice(s.addNewSlice(), 1);
    Fiducials f = rootDoc.addNewFiducials();
    exampleFiducial(f.addNewFiducial(), 1);

    return document;
  }
コード例 #4
0
  @Override
  public void process(ProcessletInputs in, ProcessletOutputs out, ProcessletExecutionInfo info)
      throws ProcessletException {
    try {

      // validate against allowed values in process definition file
      URL processDefinitionUrl =
          this.getClass().getResource("/" + this.getClass().getSimpleName() + ".xml");

      // get validated data inputs or default values
      DataInputHandler dataInputHandler =
          new DataInputHandler(new File(processDefinitionUrl.toURI()));
      String srsName = dataInputHandler.getValidatedStringValue(in, "srsName");
      String filter = dataInputHandler.getValidatedStringValue(in, "filter");
      double x = DataInputHandler.getDoubleInputValue(in, "x");
      double y = DataInputHandler.getDoubleInputValue(in, "y");
      double z = DataInputHandler.getDoubleInputValue(in, "z");

      LOG.debug(
          String.format(
              "DataInputs: srsName: %s, poi: (%f, %f, %f), filter: %s", srsName, x, y, z, filter));

      responseValues = new ResponseValues();
      responseValues.clientSrsName = srsName;

      // transform non-AGEA coordinates to AGEA
      if (!srsName.equals("Mouse_AGEA_1.0")) {
        ABAServiceVO vo = getTransformPOI(srsName, x, y, z);
        if (vo.getTransformationXMLResponseString().startsWith("Error:")) {
          throw new OWSException(
              "Transformation Coordinates Error: ", vo.getTransformationXMLResponseString());
        }
        x = Double.parseDouble(vo.getTransformedCoordinateX());
        y = Double.parseDouble(vo.getTransformedCoordinateY());
        z = Double.parseDouble(vo.getTransformedCoordinateZ());
      }

      LOG.debug("X from Transformation Method: " + x);
      LOG.debug("Y from Transformation Method: " + y);
      LOG.debug("Z from Transformation Method: " + z);

      String srsFromClient = srsName;
      Point3d poiFromClient = new Point3d(x, y, z);

      // get plane; defaults to sagittal
      ImageSeriesPlane desiredPlane =
          filter.equals("maptype:coronal") ? ImageSeriesPlane.CORONAL : ImageSeriesPlane.SAGITTAL;

      // 1. get strong gene(s) at POI
      List<ABAGene> strongGenes = ABAUtil.retrieveStrongGenesAtAGEAPOI(x, y, z, NBR_STRONG_GENES);

      // make sure we have something
      if (strongGenes.size() == 0) {
        throw new OWSException(
            "No 'strong genes' found at " + "coordinates, hence no images to return.",
            ControllerException.NO_APPLICABLE_CODE);
      }

      if (LOG.isDebugEnabled()) {
        StringBuilder buf = new StringBuilder();
        for (ABAGene gene : strongGenes) {
          buf.append(gene.getGenesymbol()).append(", ");
        }
        LOG.debug("Strong genes: {}", buf.toString());
      }

      // 2. get image series'es for strong genes and desired plane
      List<ImageSeries> imageSerieses = new ArrayList<ImageSeries>();
      for (ABAGene gene : strongGenes) {
        ImageSeries imageSeries = retrieveImagesSeriesForGene(gene.getGenesymbol(), desiredPlane);
        if (imageSeries != null) {
          imageSerieses.add(imageSeries);
        }
      }

      // make sure we have something
      if (imageSerieses.size() == 0) {
        throw new OWSException(
            "No image series found for 'strong "
                + "genes' and desired plane, hence no images to "
                + "return.",
            ControllerException.NO_APPLICABLE_CODE);
      }

      if (LOG.isDebugEnabled()) {
        StringBuilder buf = new StringBuilder();
        for (ImageSeries is : imageSerieses) {
          buf.append(is.imageSeriesId).append(':');
          buf.append(is.imageSeriesPlane).append(", ");
        }
        LOG.debug("Image Serieses id:plane: {}", buf.toString());
      }

      Point3d poiForProximity = new Point3d(poiFromClient);

      // divide POI coords by 100
      Point3d poi100 = new Point3d();
      poi100.scale(0.01, poiForProximity);

      LOG.debug("POI for closest position (srs, xyz): {}, {}", srsFromClient, poi100.toString());

      // 3. get ......... for each image series
      for (ImageSeries imageSeries : imageSerieses) {

        // begin to add values to image
        Image image = new Image(imageSeries.imageSeriesId);

        // get atlas map
        // find closest point, get other values including position
        // add more (atlas map) values to image
        getClosestPosition(imageSeries, poi100, image);

        LOG.debug("Position: {}", image.abaImagePosition);

        // get best image id in image series based on position
        // add more (image elements) values to image
        // match position to find image in series, get imageid
        //  /image-series/images/image/position
        //  /image-series/images/image/imageid
        retrieveImageForPosition(imageSeries.imageSeriesId, image.abaImagePosition, image);

        LOG.debug("Image id: {}", image.imageId);

        // zoom level not applicable
        // image.zoomLevel = zoomLevel;

        // assemble aba view image uri
        image.imageURI = assembleImageURI(image.downloadImagePath, HI_RES, MIME);
        image.thumbnailurl = assembleImageURI(image.downloadImagePath, THUMB, MIME);

        LOG.debug("Image URI: {}", image.imageURI.toString());

        responseValues.images.add(image);
      } // for

      // ImagesResponseDocument 'is a' org.apache.xmlbeans.XmlObject
      //	'is a' org.apache.xmlbeans.XmlTokenSource
      ImagesResponseDocument document = completeResponse();

      if (LOG.isDebugEnabled()) {
        XmlOptions opt = (new XmlOptions()).setSavePrettyPrint();
        opt.setSaveSuggestedPrefixes(Utilities.SuggestedNamespaces());
        opt.setSaveNamespacesFirst();
        opt.setSaveAggressiveNamespaces();
        opt.setUseDefaultNamespace();
        LOG.debug("Xml:\n{}", document.xmlText(opt));
      }

      // 4. Send it
      // get reader on document
      XMLStreamReader reader = document.newXMLStreamReader();

      // get ComplexOutput object from ProcessletOutput...
      ComplexOutput complexOutput = (ComplexOutput) out.getParameter("Get2DImagesByPOIOutput");

      LOG.debug("Setting complex output (requested=" + complexOutput.isRequested() + ")");

      // ComplexOutput objects can be huge so stream it
      XMLStreamWriter writer = complexOutput.getXMLStreamWriter();
      XMLAdapter.writeElement(writer, reader);

      // transform any exceptions into ProcessletException wrapping
      // OWSException
    } catch (MissingParameterException e) {
      LOG.error(e.getMessage(), e);
      throw new ProcessletException(new OWSException(e));
    } catch (InvalidParameterValueException e) {
      LOG.error(e.getMessage(), e);
      throw new ProcessletException(new OWSException(e));
    } catch (InvalidDataInputValueException e) {
      LOG.error(e.getMessage(), e);
      throw new ProcessletException(e); // is already OWSException
    } catch (OWSException e) {
      LOG.error(e.getMessage(), e);
      throw new ProcessletException(e); // is already OWSException
    } catch (Throwable e) {
      String message = "Unexpected exception occurred: " + e.getMessage();
      LOG.error(message, e);
      throw new ProcessletException(
          new OWSException(message, e, ControllerException.NO_APPLICABLE_CODE));
    }
  }