bug fix

app.py

@@ -6,7 +6,7 @@
 from rq import Queue
 from werkzeug.utils import redirect
 
-from forms import SubmitJob
+from forms import SubmitJob, Testjob
 from job import *
 
 app = Flask(__name__)
@@ -37,7 +37,7 @@ def submit():
         else:
             # User Submits Job #
             # (1) Create unique ID for each submission
-            timestamp = datetime.datetime.now().strftime('%Y%m%d%H%M%S%f')
+            timestamp = datetime.now().strftime('%Y%m%d%H%M%S%f')
             target_dir = os.path.join(UPLOAD_FOLDER, timestamp)
             # (2) Log to Database
             if not os.path.isfile('database.db'):
@@ -116,7 +116,7 @@ def submit_test():
         else:
             # User Submits Job #
             # (1) Create unique ID for each submission
-            timestamp = datetime.datetime.now().strftime('%Y%m%d%H%M%S%f')
+            timestamp = datetime.now().strftime('%Y%m%d%H%M%S%f')
             target_dir = os.path.join(UPLOAD_FOLDER, timestamp)
             # (2) Log to Database
             if not os.path.isfile('database.db'):

cleanup.py

@@ -4,14 +4,15 @@
 
 # Define the path for the log file
 primary_log_directory = "/var/log/reform"
+local_log_dirs = "./cleanuplog" # If not, use the local log directory
 
-if not os.path.exists(primary_log_directory):
-    local_log_dirs = "./cleanuplog" # If not, use the local log directory
+if os.path.exists(primary_log_directory) and os.access(primary_log_directory, os.W_OK):
+    log_file_path = os.path.join(primary_log_directory, "cleanup.log")
+else:
+    # If the primary log directory does not exist or is not writable, use the local log directory
     if not os.path.exists(local_log_dirs):
         os.makedirs(local_log_dirs)
-    log_file_path = os.path.join(local_log_dirs, "cleanup.log")
-else:
-    log_file_path = os.path.join(primary_log_directory, "cleanup.log") # create cleanup.log in /var/log/reform
+    log_file_path = os.path.join(local_log_dirs, "cleanup.log") # create cleanup.log in /var/log/reform
 
 # Configure logging
 logging.basicConfig(

corn-cleanup.md

@@ -0,0 +1,9 @@
+touch mycron
+
+'''
+0 * * * * /home/reform/venv/bin/python /home/reform/reformWeb/cleanup.py
+'''
+
+crontab mycron
+
+crontab -l

mycorn

@@ -0,0 +1 @@
+# 0 * * * * /home/reform/venv/bin/python /home/reform/reformWeb/cleanup.py

run.sh

@@ -45,6 +45,7 @@ download_and_decompress() {
 }
 
 # Create the upload directories
+echo "mkdir -p ./$target_dir"
 mkdir -p "./$target_dir"
 
 # Variables to hold the final paths to be used in the reform.py command
@@ -55,6 +56,9 @@ ref_gff_path="$ref_gff"
 if is_url "$ref_fasta"; then
     download_and_decompress "$ref_fasta" "./$target_dir"
     ref_fasta_path="./$target_dir/$(basename "$ref_fasta")"
+    if [[ ${ref_fasta_path: -3} == ".gz" ]]; then
+        ref_fasta_path="${ref_fasta_path::-3}"
+    fi
 else
     echo "Using local file: $ref_fasta"
     ref_fasta_path="$ref_fasta"
@@ -63,7 +67,10 @@ fi
 # Check and process the reference gff file
 if is_url "$ref_gff"; then
     download_and_decompress "$ref_gff" "./$target_dir"
-    ref_fasta_path="./$target_dir/$(basename "$ref_gff")"
+    ref_gff_path="./$target_dir/$(basename "$ref_gff")"
+    if [[ ${ref_gff_path: -3} == ".gz" ]]; then
+        ref_gff_path="${ref_gff_path::-3}"
+    fi
 else
     echo "Using local file: $ref_gff"
     ref_gff_path="$ref_gff"