updated files for bigg tool

Dockerfile

@@ -4,9 +4,6 @@ COPY ./code /home
 
 WORKDIR /workdir
 
-ADD ./requirements/system /workdir/system
-ADD ./requirements/scraper /workdir/scraper
-
 RUN apt-get -y update
 RUN apt-get -y upgrade
 RUN apt-get -y install ncbi-blast+

code/blast.py

+import subprocess as sp
+import os
+import hashlib
+import sys
+from zipfile import ZipFile
+import shutil
+import logging
+
+
+def blast(processingPath, resultsPath):
+    logger.info('Blast process is Starting')
+	# 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)
+
+    runBlast(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 runBlast(output_path, processingPath):
+    # The following code will run Blast and check whether the software has run correctly or not.
+
+    logger.info('Run blast is starting')
+    logging.info(output_path)
+
+    child = sp.Popen(["java", "-jar", "-Djavax.xml.accessExternalDTD=all", "-Dworkdir=/workdir", "/home/Blast.jar"])
+
+    exit_code = child.wait()
+
+    if exit_code != 0:
+        removeFromProcessingAndResults(output_path, processingPath, exit_code)
+
+    else:
+        logger.info("Blast ran well and the GPRsResults.txt 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[0]
+	resultsPath = sys.argv[1]
+	logger.info('Calling blast method with these parameters: 'processingPath + ' ' + resultsPath)
+	blast(processingPath, resultsPath)

code/worker.py

@@ -25,11 +25,9 @@ logger.setLevel(logging.DEBUG)
 
 #####
 
-PROCESS_PATH = '/home/transyt.py'
+PROCESS_PATH = '/home/blast.py'
 SUBMISSIONS_PATH = '/workdir/workerSubmissions/'
 RESULTS_PATH = '/workdir/resultsWorker/'
-#RESULTS_PATH = "C:\\Users\\BioSystems\\Desktop\\testFolder\\resultsWorker\\"
-#SUBMISSIONS_PATH = "C:\\Users\\BioSystems\\Desktop\\testFolder\\workerSubmissions\\"
 
 if not os.path.exists(SUBMISSIONS_PATH):
     os.makedirs(SUBMISSIONS_PATH)
@@ -69,7 +67,7 @@ def start():
 
     logger.debug("directories reset complete")
 
-    try:
+    try:	
         for file in request.files.values():
             destination = "/".join([SUBMISSIONS_PATH, file.filename])
             logger.info("saving file " + destination)