debug log files system created

code/FilesUtilities.py

+from zipfile import ZipFile
+import os
+
+def read_conf_file(path):
+    res = {}
+
+    with open(path) as file:
+        lines = file.readlines()
+        for line in lines:
+            if '=' in line:
+                prop = line.replace(" ", "").replace("\n", "")
+                l_str = prop.split('=')
+                res[l_str[0]] = l_str[1]
+
+    return res
+
+def read_workers_conf_file(path):
+    res = []
+
+    with open(path) as file:
+        lines = file.readlines()
+        for line in lines:
+            if "#" not in line[0]:
+                str = line.replace(" ", "").replace("\n", "")
+                res.append(str)
+
+    return res
+
+def compressFiles(path, savePath):
+    file_paths = get_all_file_paths(path)
+
+    zipLocation = savePath
+
+    with ZipFile(zipLocation, '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)
+
+    return zipLocation
+
+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

code/worker.py

@@ -3,7 +3,7 @@ import subprocess
 import os
 import shutil
 import datetime
-import logging
+import FilesUtilities
 
 app = Flask(__name__)
 
@@ -22,6 +22,12 @@ start_time = datetime.datetime.now()
 
 running = False
 
+@app.after_request
+def after_request(response):
+    response.headers["Cache-Control"] = "no-cache, no-store, must-revalidate, public, max-age=0"
+    response.headers["Expires"] = 0
+    response.headers["Pragma"] = "no-cache"
+    return response
 
 @app.route("/start", methods=["POST"])
 def start():
@@ -71,10 +77,29 @@ def display_msg():
 
     return jsonify({"result": "running"}), 202
 
+
 @app.route('/handshake')
 def handshake():
     return jsonify({"result": "alive"}), 200
 
 
+@app.route('/retrieveLogs')
+def retrieveLogs():
+
+    logsPath = '/workdir/logs'
+    logsZip = '/logs.zip'
+
+    if os.path.exists(logsZip):
+        os.remove(logsZip)
+
+    FilesUtilities.compressFiles(logsPath, logsZip)
+
+    if not os.path.exists(logsZip):
+        return jsonify({"Result": "Request unavailable!"}), 503
+
+    return send_file(logsZip, as_attachment=True, attachment_filename='logs.zip')
+
+
 if __name__ == "__main__":
-    app.run(host="0.0.0.0", port=80, threaded=False, debug=True)
+    app.run(host="0.0.0.0", port=80, threaded=False, debug=False)
+    app.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0

requirements/system/configurations.txt

@@ -31,7 +31,7 @@ coverage=0.8
 bitScore=50
 
 # 10 - Select the IDs to generate the reactions. Select 'ModelSEED', 'BiGG', 'MetaCyc', or 'KEGG'.
-IDsDatabase=KEGG
+IDsDatabase=BiGG
 
 # 11 - Allowed difference between compartments (set a value between 0% and 50%).
 difference=30