Projects >> seqware >>14797e3f99bdb8158b4b17c45507e5cec300bc41

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Conflicting content 
        } else {
            Log.error("Unknown option");
        }
<<<<<<< HEAD
 
        if (mappedFiles != null) {
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        mappedFiles = separateFiles(vals, groupBy);
        launchWorkflows(mappedFiles);
        return ret;
    }
>>>>>>> 892ec5b35a172e1c90becc3c5ca337de11d6c5d6

    private void launchWorkflows(Map> mappedFiles) {
        if (mappedFiles != null) {
Solution content 
        } else {
            Log.error("Unknown option");
        }

        mappedFiles = separateFiles(vals, groupBy);
        ret = launchWorkflows(mappedFiles);
        return ret;
    }


    private ReturnValue launchWorkflows(Map> mappedFiles) {
        if (mappedFiles != null) {
File
BasicDecider.java
Developer's decision
Manual
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Attribute
If statement
Method invocation
Return statement
Variable
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                    boolean rerun = rerunWorkflowRun(previousWorkflowRuns, filesToRun);
                    iniFiles = new ArrayList();
                    iniFiles.add(createIniFile(fileString, parentAccessionString));
<<<<<<< HEAD

                	ReturnValue newRet = this.do_finalCheck(fileString, parentAccessionString);
                	if (newRet.getExitStatus() != ReturnValue.SUCCESS) {
                	      Log.stderr("The method do_finalCheck exited abnormally so the Runner will terminate here!");
                	      Log.stderr("Return value was: " + newRet.getExitStatus());
                	      ret = newRet;
                	      return ret;
                	} 
                	
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>>>>>>> 892ec5b35a172e1c90becc3c5ca337de11d6c5d6
                    if (test || (!rerun && !forceRunAll)) {
                        //don't run, but report it
                        Log.debug("NOT RUNNING. test=" + test + " or (!rerun=" + !rerun + " and !forceRunAll=" + !forceRunAll + ")");
Solution content 
                    boolean rerun = rerunWorkflowRun(previousWorkflowRuns, filesToRun);
                    iniFiles = new ArrayList();
                    iniFiles.add(createIniFile(fileString, parentAccessionString));


                	ReturnValue newRet = this.do_finalCheck(fileString, parentAccessionString);
                	if (newRet.getExitStatus() != ReturnValue.SUCCESS) {
                	      Log.stderr("The method do_finalCheck exited abnormally so the Runner will terminate here!");
                	      Log.stderr("Return value was: " + newRet.getExitStatus());
                	      ret = newRet;
                	      return ret;
                	} 
                	
                    if (test || (!rerun && !forceRunAll)) {
                        //don't run, but report it
                        Log.debug("NOT RUNNING. test=" + test + " or (!rerun=" + !rerun + " and !forceRunAll=" + !forceRunAll + ")");
File
BasicDecider.java
Developer's decision
Version 1
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If statement
Method invocation
Variable
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Conflicting content 
            return false;
        }
    }
<<<<<<< HEAD

    private void addFileToLists(ReturnValue file, FileMetadata fm, List workflowParentAccessionsToRun,
            List parentAccessionsToRun, List filesToRun) {

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    private void addFileToSets(ReturnValue file, FileMetadata fm, Collection workflowParentAccessionsToRun,
            Collection parentAccessionsToRun, Collection filesToRun) {
        if (test) {
            String studyName = (String) options.valueOf("study-name");
            try {
                StringWriter writer = new StringWriter();
                FindAllTheFiles.print(writer, file, studyName, true, fm);
                Log.stdout(writer.getBuffer().toString().trim());
            } catch (IOException ex) {
                Logger.getLogger(BasicDecider.class.getName()).log(Level.SEVERE, null, ex);
            }
        }
        
>>>>>>> 892ec5b35a172e1c90becc3c5ca337de11d6c5d6
        if (checkFileDetails(file, fm)) {
            if (test) {
                String studyName = (String) options.valueOf("study-name");
Solution content 
            return false;
        }
    }
    
    private void addFileToSets(ReturnValue file, FileMetadata fm, Collection workflowParentAccessionsToRun,
            Collection parentAccessionsToRun, Collection filesToRun) {
        if (checkFileDetails(file, fm)) {
            if (test) {
                String studyName = (String) options.valueOf("study-name");
File
BasicDecider.java
Developer's decision
Combination
Kind of conflict
If statement
Method signature