Projects >> miso-lims >>692c77c496ac1f1ec36dd5c75462fe1221464dde

Chunk
Conflicting content 
   SPC("SequencerPartitionContainer"),
   STU("Study"),
   IPO("Pool"),
<<<<<<< HEAD
   SUB("Submission"),
   WKF("Workflow"),
   WKP("WorkflowProcess");
=======
//   SPO("SolidPool"),
//   LPO("LS454Pool"),
   PPO("PacBioPool"),
//   TPO("TorrentPool"),
   SUB("Submission");
>>>>>>> 8fd179fbe93fc04129e9df1ba3bf57548d33181f

  /**
   * Field key
Solution content 
   SPC("SequencerPartitionContainer"),
   STU("Study"),
   IPO("Pool"),
   SUB("Submission"),
   WKF("Workflow"),
   WKP("WorkflowProcess");

  /**
   * Field key
File
DefaultMisoEntityPrefix.java
Developer's decision
Version 1
Kind of conflict
Comment
Enum value
Chunk
Conflicting content 
          rowsJSONArray.add(getCellValueAsString(sampleAliasCell));
          XSSFCell proceedKeyCell = row.getCell(22);
          rowsJSONArray.add(getCellValueAsString(wellCell).replaceAll("\\s",""));

<<<<<<< HEAD
=======

          String proceedKey = "A";

          if (getCellValueAsString(proceedKeyCell) != null) {
            String proceedKeyString = getCellValueAsString(proceedKeyCell).toUpperCase().replaceAll("\\s","");
            if ("L".equals(proceedKeyString)) {
              proceedKey = "L";
            }
            else if ("U".equals(proceedKeyString)) {
              proceedKey = "U";
            }
            else if ("P".equals(proceedKeyString)) {
              proceedKey = "P";
            }
          }

>>>>>>> 8fd179fbe93fc04129e9df1ba3bf57548d33181f
          String libAlias = "";
          Matcher mat = samplePattern.matcher(getCellValueAsString(sampleAliasCell));
          if (mat.matches()) {
Solution content 
          rowsJSONArray.add(getCellValueAsString(sampleAliasCell));
          rowsJSONArray.add(getCellValueAsString(wellCell).replaceAll("\\s",""));

          XSSFCell proceedKeyCell = row.getCell(22);

          String proceedKey = "A";

          if (getCellValueAsString(proceedKeyCell) != null) {
            String proceedKeyString = getCellValueAsString(proceedKeyCell).toUpperCase().replaceAll("\\s","");
            if ("L".equals(proceedKeyString)) {
              proceedKey = "L";
            }
            else if ("U".equals(proceedKeyString)) {
              proceedKey = "U";
            }
            else if ("P".equals(proceedKeyString)) {
              proceedKey = "P";
            }
          }

          String libAlias = "";
          Matcher mat = samplePattern.matcher(getCellValueAsString(sampleAliasCell));
          if (mat.matches()) {
File
FormUtils.java
Developer's decision
Version 2
Kind of conflict
If statement
Method invocation
Variable
Chunk
Conflicting content 
  }
  
  @RequestMapping(method = RequestMethod.GET)
<<<<<<< HEAD
  public @ResponseBody
  Collection jsonRest() throws IOException {
    return requestManager.listAllRuns();
=======
  public @ResponseBody String listAllRuns() throws IOException {
    Collection lr = requestManager.listAllRuns();
    ObjectMapper mapper = new ObjectMapper();
    mapper.getSerializationConfig().addMixInAnnotations(SequencerPartitionContainer.class, ContainerRecursionAvoidanceMixin.class);
    mapper.getSerializationConfig().addMixInAnnotations(User.class, UserInfoMixin.class);
    return mapper.writeValueAsString(lr);
>>>>>>> 8fd179fbe93fc04129e9df1ba3bf57548d33181f
  }
}
Solution content 
  }
  
  @RequestMapping(method = RequestMethod.GET)
  public @ResponseBody String listAllRuns() throws IOException {
    Collection lr = requestManager.listAllRuns();
    ObjectMapper mapper = new ObjectMapper();
    mapper.getSerializationConfig().addMixInAnnotations(SequencerPartitionContainer.class, ContainerRecursionAvoidanceMixin.class);
    mapper.getSerializationConfig().addMixInAnnotations(User.class, UserInfoMixin.class);
    return mapper.writeValueAsString(lr);
  }
}
File
RunRestController.java
Developer's decision
Version 2
Kind of conflict
Method invocation
Method signature
Return statement
Variable
Chunk
Conflicting content 
//                        else {
//                          lf.setPlatformType(PlatformType.PACBIO);
//                        }
<<<<<<< HEAD
                        r.addSequencerPartitionContainer(lf);
=======
                        JSONArray cells = run.getJSONArray("cells");
                        if (cells.size() > lf.getPartitions().size()) {
                          int numNewcells = cells.size()-lf.getPartitions().size();
                          lf.setPartitionLimit(cells.size());
                          for (int i=0; i>>>>>> 8fd179fbe93fc04129e9df1ba3bf57548d33181f
                      }
                      else {
                        //more than one flowcell hit to this barcode
Solution content 
//                        else {
//                          lf.setPlatformType(PlatformType.PACBIO);
//                        }
                        JSONArray cells = run.getJSONArray("cells");
                        if (cells.size() > lf.getPartitions().size()) {
                          int numNewcells = cells.size()-lf.getPartitions().size();
                          lf.setPartitionLimit(cells.size());
                          for (int i=0; i
File
PacBioNotificationMessageConsumerMechanism.java
Developer's decision
Combination
Kind of conflict
If statement
Method invocation
Variable
Chunk
Conflicting content 
                        log.info("\\_ Created new container with "+f.getPartitions().size()+" partitions");
                        long flowId = requestManager.saveSequencerPartitionContainer(f);
                        f.setId(flowId);
<<<<<<< HEAD
                        r.addSequencerPartitionContainer(f);
                        //TODO match up samples to libraries and pools?
=======
                        ((RunImpl)r).addSequencerPartitionContainer(f);
                        //TODO match up samples to libraries and pools? Or match up pool numbers
>>>>>>> 8fd179fbe93fc04129e9df1ba3bf57548d33181f
                        /*
                        for (JSONObject obj : (Iterable)cells) {
                          int cellindex = obj.getInt("index");
Solution content 
                        log.info("\\_ Created new container with "+f.getPartitions().size()+" partitions");
                        long flowId = requestManager.saveSequencerPartitionContainer(f);
                        f.setId(flowId);
                        r.addSequencerPartitionContainer(f);
                        //TODO match up samples to libraries and pools? Or match up pool numbers
                        /*
                        for (JSONObject obj : (Iterable)cells) {
                          int cellindex = obj.getInt("index");
File
PacBioNotificationMessageConsumerMechanism.java
Developer's decision
Combination
Kind of conflict
Comment
Method invocation
Chunk
Conflicting content 
                      break;
                    }
                  }
<<<<<<< HEAD
                  response.put("ok", "ok");
                  //info.append("");
=======
                  info.append(out);
>>>>>>> 8fd179fbe93fc04129e9df1ba3bf57548d33181f
                }
                else {
                  info.append("Barcode:");
Solution content 
                      break;
                    }
                  }
                  response.put("ok", "ok");
                  //info.append("");
                  info.append(out);
                }
                else {
                  info.append("Barcode:");
File
PoolControllerHelperService.java
Developer's decision
Concatenation
Kind of conflict
Comment
Method invocation