Delete transyt.py

code/transyt.py

-import subprocess as sp
-import os
-import hashlib
-import sys
-from zipfile import ZipFile
-import shutil
-import logging
-
-
-def transyt(processingPath, resultsPath):
-    # Create a directory whose name is the submission ID, if it hasn't been created already
-    if not os.path.exists(resultsPath):
-        os.makedirs(resultsPath)
-
-    logPath = resultsPath + "/trace_errors.log"
-
-    logging.basicConfig(filename=logPath, level=logging.DEBUG, format='%(asctime)s: %(levelname)s: >>>%(message)s')
-
-    output_path = resultsPath + "/" # + "/results_biocoiso.json"
-    logging.info("The results path is " + output_path)
-
-    runTransyt(output_path, processingPath+"/" )
-
-    file_paths = get_all_file_paths(resultsPath + "/")
-
-    with ZipFile(resultsPath + '/results.zip', 'w') as zip:
-        # writing each file one by one
-        for file in file_paths:
-            new_file = file.split("/")[-1]
-            zip.write(file, arcname=new_file)
-        logging.info("The zip file was generated successfully.")
-
-    with open(resultsPath + "/processComplete", "w") as f:
-        f.write("Process complete: ")
-
-
-def runTransyt(output_path, processingPath):
-    # The following code will run BioCoISO and check whether the software has run correctly or not.
-
-    #logging.info(protein)
-    logging.info(output_path)
-
-    child = sp.Popen(["java", "-Xmx8192m", "-Dworkdir=/workdir", "-jar", "/home/runClassification.jar", "3", processingPath, output_path])
-
-    exit_code = child.wait()
-
-    if exit_code != 0:
-        removeFromProcessingAndResults(output_path, processingPath, exit_code)
-
-    else:
-        logging.info("TranSyT run well and the zip file and the md5 file is going to be created.")
-
-        if os.path.exists(processingPath):
-            shutil.rmtree(processingPath)
-            logging.info("The processing directory was removed succefully.")
-
-
-def get_all_file_paths(directory):
-    # initializing empty file paths list
-    file_paths = []
-
-    # crawling through directory and subdirectories
-    for root, directories, files in os.walk(directory):
-        for filename in files:
-            # join the two strings in order to form the full filepath.
-            filepath = os.path.join(root, filename)
-            file_paths.append(filepath)
-
-            # returning all file paths
-    return file_paths
-
-def removeFromProcessingAndResults(output_path, processingPath, exit_code):
-
-    logging.info("TranSyT didn't run well.")
-    if output_path is not None and os.path.exists(output_path):
-        os.remove(output_path)
-    with open(resultsPath + "/" + str(exit_code), "w") as f:
-        f.write("A error was found while running TranSyT. The exit code was: " + str(exit_code))
-    if os.path.exists(processingPath):
-        shutil.rmtree(processingPath)
-
-
-if __name__ == "__main__":
-    processingPath = sys.argv[1]
-    resultsPath = sys.argv[2]
-    transyt(processingPath, resultsPath)