changes to manager and workersManager

code/manager.py

@@ -63,37 +63,11 @@ def submit():
     logger.info('New submission')
     files = request.files.getlist("file")
 
-    option = request.form["option"]
-    
-    if(option == '2' or option == '3'):
-        choices = request.form["choices"]
-    else:
-        choices = ""
-
-    eValue = request.form["eValue"]
-
-    bitScore = request.form["bitScore"]
-
-    queryCoverage = request.form["queryCoverage"]
-
-    return run(files, option, choices, eValue, bitScore, queryCoverage, False)
-
-
-@app.route("/submitMerlinPlugin/<option>/<choices>", methods=["POST"])
-def submitMerlinPlugin(taxonomyId, option, choices):
-    logger.info('Merlin plugin submission')
-    
-    files = request.files.getlist("file")
-
-    logger.info("files in submission " + str(files))
-
-    return run(files, option, choices, True)
+    return run(files, True)
 
 
-def run(files, option, choices, eValue, bitScore, queryCoverage, isRest):
+def run(files, isRest):
     logger.info('New submission in progress...')
-    logger.info("Option: " + option)
-    logger.info("Choices: " + choices)
 
     total = len(os.listdir(SUBMISSIONS_PATH))
 
@@ -114,41 +88,24 @@ def run(files, option, choices, eValue, bitScore, queryCoverage, isRest):
     os.makedirs(submission_path)
 
     logger.debug("Submission " + str(last_submission_ID) + " folder created!")
-
-    inputCheck = []
 	
     for file in files:
 
-        formats = {".faa": "queryGenome.faa", ".fasta": "queryGenome.faa"}
+#        formats = {".faa": "queryGenome.faa", ".fasta": "queryGenome.faa", ".txt": "params.txt"}
 
         fileName = file.filename
-        inFormats = False
-        for key in formats:
-            if fileName.endswith(key):
-                fileName = formats[key]
-                inFormats = True
-                inputCheck.append(formats[key])
+        
+#        inFormats = False
+#        for key in formats:
+#            if fileName.endswith(key):
+#                fileName = formats[key]
+#                inFormats = True
+
 
         destination = "/".join([submission_path, fileName])
         logger.debug('Saving file ' + fileName + ' at ' + destination)
         file.save(destination)
 
-    validInputs = [["queryGenome.faa"]]
-
-    logger.info("option -> " + option)
-    logger.info("inputCheck -> " + str(inputCheck))
-
-    if inputCheck in validInputs:
-        with open("/".join([submission_path, "params.txt"]), "w") as paramsFile:
-            paramsFile.write(option + "\n")  # write option to file
-            paramsFile.write(choices + "\n")  # write choices to file
-            paramsFile.write(eValue + "\n")  # write eValue to file
-            paramsFile.write(bitScore + "\n")  # write bitScore to file
-            paramsFile.write(queryCoverage + "\n")  # write queryCoverage to file
-
-    else:
-        return jsonify({"Genome": "Input genome must be in .faa or .fasta format"}), 415
-
     with open(submission_path + "/submissionComplete", "w") as f:
         f.write("Submission of files complete: ")
 
@@ -163,11 +120,13 @@ def run(files, option, choices, eValue, bitScore, queryCoverage, isRest):
                         "queue": total,
                         "submissionID": str(last_submission_ID)}), 201
 
+
     return display_msg(str(last_submission_ID), isRest)
 
 
 @app.route('/status/<submissionID>/<isRest>')
 def display_msg(submissionID, isRest):
+    
     if isRest == 'False':
         isRest = False
     elif isRest == 'True':
@@ -188,6 +147,7 @@ def display_msg(submissionID, isRest):
                             "message": "Waiting in queue with " + str(total + 1) + " submissions!",
                             "queue": str(inQueue)}), 201
 
+
     folders = os.listdir(PROCESSING_PATH)
 
     logger.info("processing " + str(folders))
@@ -197,6 +157,7 @@ def display_msg(submissionID, isRest):
         if isRest:
             return jsonify({"result": "processing", "message": "accepted but process still running, please wait."}), 202
 
+
     folders = os.listdir(RESULTS_PATH)
 
     logger.info("results " + str(folders))

code/workersManager.py

@@ -76,8 +76,9 @@ def run():
                 shutil.move(SUBMISSIONS_PATH + submissionID, processingPath)
 
                 files = {
-                    'queryGenome': open(processingPath + 'queryGenome.faa', 'rb'),
-                    'params': open(processingPath + 'params.txt', 'rb')}
+                    'queryGenome': open(processingPath + 'protein.faa', 'rb'),
+                    'params': open(processingPath + 'params.txt', 'rb'),
+                    'idGenes': open(processingPath + 'idGenes.txt', 'rb')}
 
                 logger.info("Sending request to start to " + str(workerID))
                 logger.info("Sending files: " + str(files))