Package uk.ac.bbsrc.tgac.miso.core.data

Examples of uk.ac.bbsrc.tgac.miso.core.data.Experiment


  @Deprecated
  public JSONObject previewExperiment(HttpSession session, JSONObject json) {
    String experimentId = (String) json.get("experimentId");

    try {
      Experiment e = requestManager.getExperimentById(Long.parseLong(experimentId));
      Collection<Run> runs = requestManager.listRunsByExperimentId(e.getId());

      session.setAttribute("experiment", e);

      StringBuilder rb = new StringBuilder();
      for (Run r : runs) {
        rb.append("<li><a href='/miso/run/").append(r.getId()).append("'>").append(r.getName()).append("</a></li>");
      }

      StringBuilder sb = new StringBuilder();
      if (e.getPool() != null) {
        for (Dilution dil : e.getPool().getDilutions()) {
          Sample s = dil.getLibrary().getSample();
          sb.append("<li><a href='/miso/sample/").append(s.getId()).append("'>").append(s.getName()).append("</a></li>");
        }

        /*
        if (e.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
        }
        else {
          for (Object dil : e.getPool().getDilutions()) {
            Sample s = ((emPCRDilution) dil).getEmPCR().getLibraryDilution().getLibrary().getSample();
            sb.append("<li><a href='/miso/sample/").append(s.getSampleId()).append("'>").append(s.getName()).append("</a></li>");
          }
        }
        */
      }

      StringBuilder b = new StringBuilder();
      b.append("<div onclick=\"Effect.toggle('preview"+experimentId+"','blind'); return false;\">" +
              "<img src=\"/styles/images/moreinfo.png\" class=\"previewimage\"/></div>");
      b.append("<br/><div id=\"preview"+experimentId+"\" class='exppreview'>");
      b.append("Title: <b>").append(e.getTitle()).append("</b><br/>");
      b.append("Description: <b>").append(e.getDescription()).append("</b><br/>");
      b.append("Samples: <ul class=\"bullets\">").append(sb.toString()).append("</ul>");
      b.append("Runs: <ul class=\"bullets\">").append(rb.toString()).append("</ul>");
      b.append("</div>");
      return JSONUtils.SimpleJSONResponse(b.toString());

View Full Code Here


  public JSONObject getLibraryKitDescriptors(HttpSession session, JSONObject json) {
    try {
      if (json.has("experimentId")) {
        String experimentId = json.getString("experimentId");
        String multiplexed = json.getString("multiplexed");
        Experiment e = requestManager.getExperimentById(new Long(experimentId));

        Collection<KitDescriptor> kits = requestManager.listKitDescriptorsByType(KitType.LIBRARY);
        StringBuilder lkits = new StringBuilder();
        lkits.append("[");
        int count = 0;
        for (KitDescriptor k : kits) {
          if (e.getPlatform().getPlatformType().equals(k.getPlatformType())) {
            lkits.append("{'name':'"+k.getName()+"', 'id':'"+k.getKitDescriptorId()+"', 'partNumber':'"+k.getPartNumber()+"'}");
            if (count < kits.size()) lkits.append(",");
            count++;
          }
        }
        lkits.append("]");

        StringBuilder mkits = null;
        if (multiplexed.equals("true")) {
          mkits = new StringBuilder();
          Collection<KitDescriptor> mkitds = requestManager.listKitDescriptorsByType(KitType.MULTIPLEXING);
          mkits.append("[");
          count = 0;
          for (KitDescriptor k : mkitds) {
            if (e.getPlatform().getPlatformType().equals(k.getPlatformType())) {
              mkits.append("{'name':'"+k.getName()+"', 'id':'"+k.getKitDescriptorId()+"', 'partNumber':'"+k.getPartNumber()+"'}");
              if (count < mkitds.size()) mkits.append(",");
              count++;
            }
          }
View Full Code Here

        lk.setLotNumber(lotNumber);
        if (!json.has("kitDate") || json.getString("kitDate").equals("")) {
          lk.setKitDate(new Date());
        }

        Experiment e = requestManager.getExperimentById(new Long(experimentId));
        e.addKit(lk);
        requestManager.saveExperiment(e);
        Integer newStock = kd.getStockLevel()-1;
        kd.setStockLevel(newStock);
        requestManager.saveKitDescriptor(kd);
      }
      return JSONUtils.SimpleJSONResponse("Saved kit!");
    }
    catch (IOException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError("Failed to save library kit");
    }
  }
View Full Code Here

// empcr
  public JSONObject getEmPcrKitDescriptors(HttpSession session, JSONObject json) {
    try {
      if (json.has("experimentId")) {
        String experimentId = json.getString("experimentId");
        Experiment e = requestManager.getExperimentById(new Long(experimentId));
       
        Collection<KitDescriptor> kits = requestManager.listKitDescriptorsByType(KitType.EMPCR);
        StringBuilder sb = new StringBuilder();
        sb.append("[");
        int count = 0;
        for (KitDescriptor k : kits) {
          if (e.getPlatform().getPlatformType().equals(k.getPlatformType())) {
            sb.append("{'name':'"+k.getName()+"', 'id':'"+k.getKitDescriptorId()+"', 'partNumber':'"+k.getPartNumber()+"'}");
            if (count < kits.size()) sb.append(",");
            count++;
          }
        }
View Full Code Here

        lk.setLotNumber(lotNumber);
        if (!json.has("kitDate") || json.getString("kitDate").equals("")) {
          lk.setKitDate(new Date());
        }

        Experiment e = requestManager.getExperimentById(new Long(experimentId));
        e.addKit(lk);
        requestManager.saveExperiment(e);
        Integer newStock = kd.getStockLevel()-1;
        kd.setStockLevel(newStock);
        requestManager.saveKitDescriptor(kd);
      }
      return JSONUtils.SimpleJSONResponse("Saved kit!");
    }
    catch (IOException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError("Failed to save EmPCR kit");
    }
  }
View Full Code Here

//clustering
  public JSONObject getClusteringKitDescriptors(HttpSession session, JSONObject json) {
    try {
      if (json.has("experimentId")) {
        String experimentId = json.getString("experimentId");
        Experiment e = requestManager.getExperimentById(new Long(experimentId));
       
        Collection<KitDescriptor> kits = requestManager.listKitDescriptorsByType(KitType.CLUSTERING);
        StringBuilder sb = new StringBuilder();
        sb.append("[");
        int count = 0;
        for (KitDescriptor k : kits) {
          if (e.getPlatform().getPlatformType().equals(k.getPlatformType())) {
            sb.append("{'name':'"+k.getName()+"', 'id':'"+k.getKitDescriptorId()+"', 'partNumber':'"+k.getPartNumber()+"'}");
            if (count < kits.size()) sb.append(",");
            count++;
          }
        }
View Full Code Here

        lk.setLotNumber(lotNumber);
        if (!json.has("kitDate") || json.getString("kitDate").equals("")) {
          lk.setKitDate(new Date());
        }

        Experiment e = requestManager.getExperimentById(new Long(experimentId));
        e.addKit(lk);
        requestManager.saveExperiment(e);
        Integer newStock = kd.getStockLevel()-1;
        kd.setStockLevel(newStock);
        requestManager.saveKitDescriptor(kd);
      }
      return JSONUtils.SimpleJSONResponse("Saved kit!");
    }
    catch (IOException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError("Failed to save clustering kit");
    }
  }
View Full Code Here

//sequencing
  public JSONObject getSequencingKitDescriptors(HttpSession session, JSONObject json) {
    try {
      if (json.has("experimentId")) {
        String experimentId = json.getString("experimentId");
        Experiment e = requestManager.getExperimentById(new Long(experimentId));
       
        Collection<KitDescriptor> kits = requestManager.listKitDescriptorsByType(KitType.SEQUENCING);
        StringBuilder sb = new StringBuilder();
        sb.append("[");
        int count = 0;
        for (KitDescriptor k : kits) {
          if (e.getPlatform().getPlatformType().equals(k.getPlatformType())) {
            sb.append("{'name':'"+k.getName()+"', 'id':'"+k.getKitDescriptorId()+"', 'partNumber':'"+k.getPartNumber()+"'}");
            if (count < kits.size()) sb.append(",");
            count++;
          }
        }
View Full Code Here

        lk.setLotNumber(lotNumber);
        if (!json.has("kitDate") || json.getString("kitDate").equals("")) {
          lk.setKitDate(new Date());
        }

        Experiment e = requestManager.getExperimentById(new Long(experimentId));
        e.addKit(lk);
        requestManager.saveExperiment(e);
        Integer newStock = kd.getStockLevel()-1;
        kd.setStockLevel(newStock);
        requestManager.saveKitDescriptor(kd);
      }
      return JSONUtils.SimpleJSONResponse("Saved kit!");
    }
    catch (IOException e) {
      e.printStackTrace();
      return JSONUtils.SimpleJSONError("Failed to save sequencing kit");
    }
  }
View Full Code Here

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