simplify local webapp deployment

Author: ManuelTgn

.editorconfig

@@ -1371,10 +1371,10 @@ Epub 2022 Dec 15. PMID: 36522432; PMCID: PMC10272994.
 
 ## 5 Contacts
 
-- Luca Pinello, PhD 
+- Luca Pinello
   <br>[email protected]
 
-- Rosalba Giugno, PhD 
+- Rosalba Giugno
   <br>[email protected]
 
 - Daniel Bauer

README.md

@@ -34,7 +34,6 @@
     current_working_directory,
     cache,
 )
-from utils import check_directories
 
 from dash.dependencies import Input, Output, State
 from typing import Tuple
@@ -50,6 +49,15 @@
 HOST = "0.0.0.0"  # server host
 PORTWEB = 80  # website port
 PORTLOCAL = 8080  # local server port
+CRISPRME_DIRS = [
+    "Genomes",
+    "Results",
+    "Dictionaries",
+    "VCFs",
+    "Annotations",
+    "PAMs",
+    "samplesIDs",
+]  # crisprme directory tree
 
 # initialize the webpage
 server = app.server  # start server
@@ -65,6 +73,29 @@
 )
 
 
+def check_directories(basedir: str) -> None:
+    """Check and create necessary directories in the specified base directory.
+
+    This function verifies if the provided base directory exists and creates
+    any missing subdirectories defined in the CRISPRME_DIRS list.
+
+    Args:
+        basedir (str): The base directory to check and create subdirectories in.
+
+    Raises:
+        TypeError: If basedir is not a string.
+        FileNotFoundError: If the base directory does not exist.
+    """
+
+    if not isinstance(basedir, str):
+        raise TypeError(f"Expected {str.__name__}, got {type(basedir).__name__}")
+    if not os.path.exists(basedir):
+        raise FileNotFoundError(f"Unable to locate {basedir}")
+    for d in CRISPRME_DIRS:
+        if not os.path.exists(os.path.join(basedir, d)):
+            os.makedirs(os.path.join(basedir, d))
+
+
 # switch between the website pages
 @app.callback(
     [Output("page-content", "children"), Output("job-link", "children")],

TODO.txt

@@ -4,41 +4,6 @@
 import sys
 import os
 
-CRISPRME_DIRS = [
-    "Genomes",
-    "Results",
-    "Dictionaries",
-    "VCFs",
-    "Annotations",
-    "PAMs",
-    "samplesIDs",
-]
-
-
-def check_directories(basedir: str) -> None:
-    """The function checks the consistency of CRISPRme's directory tree.
-    If a directory is not found in the tree, it will be created.
-
-    ...
-
-    Parameters
-    ----------
-    basedir : str
-        Base directory
-
-    Returns
-    -------
-    None
-    """
-
-    if not isinstance(basedir, str):
-        raise TypeError(f"Expected {str.__name__}, got {type(basedir).__name__}")
-    if not os.path.exists(basedir):
-        raise FileNotFoundError(f"Unable to locate {basedir}")
-    for d in CRISPRME_DIRS:
-        if not os.path.exists(os.path.join(basedir, d)):
-            os.makedirs(os.path.join(basedir, d))
-
 
 def download_genome(chr: str, directory: str) -> None:
     if not isinstance(chr, str):