PEP8 format

galaxyproject · Jul 28, 2024 · d44f112 · d44f112
1 parent ea90041
commit d44f112
Showing 1 changed file with 31 additions and 22 deletions.
diff --git a/subdomains/scripts/parse_tools_to_produce_yml_files.py b/subdomains/scripts/parse_tools_to_produce_yml_files.py
@@ -1,15 +1,22 @@
-# coding: utf-8
+"""Parse tools from a toolkit.yaml file to produce yml files for tool
+installation.
+"""
+
 import yaml
-import io
 import os
-import re 
+import re
 import argparse
 
 import tools_au
 
-parser = argparse.ArgumentParser(description='Create installation yaml files from a Yaml file containing the panel_view/Toolkit data')
-parser.add_argument('--tk', action="store", dest='toolkit', help='Path of the toolkit.yaml file') # Toolkit.yaml file
-parser.add_argument('--yml-folder', action="store", dest='dest', help='Folder containing the yml files with tool installed in the target instance') # Folder containing the .yml and yml.lock containing the tools installed in the target instance
+parser = argparse.ArgumentParser(
+    description='Create installation yaml files from a Yaml file containing'
+    ' the panel_view/Toolkit data')
+parser.add_argument('--tk', action="store", dest='toolkit',
+                    help='Path of the toolkit.yaml file')
+parser.add_argument('--yml-folder', action="store", dest='dest',
+                    help='Folder containing the yml files with tool installed'
+                    ' in the target instance')
 args = parser.parse_args()
 
 print(args.toolkit)
@@ -18,22 +25,24 @@
 with open(args.toolkit, 'r') as stream:
     data_loaded = yaml.safe_load(stream)
 
-for i in range(3,len(data_loaded['items'])-2):
-    section=data_loaded['items'][i]['id']
-    name=data_loaded['items'][i]['name']
-    f = open(section+".yml", "w")
-    f.write("tool_panel_section_label: "+name+"\ntools:\n")
-    for j in data_loaded['items'][i]['items']: #for loop on toolkit sections
-        path=j['id']
-        infos=path.replace('toolshed.g2.bx.psu.edu/repos/',"")
-        pattern=re.compile(r"([^\/]+)\/([^\/]+)\/") # extract the owner (group1) and the name of the tool (group2)
-        for match in pattern.finditer(infos): #for each tool in the seection
-            owner=match.group(1)
-            tool=match.group(2)
-            installed = os.popen('grep -r "'+tool+'" '+args.dest).read() #verify the tool is not already installed
-            if installed=='': ## if tool not installed
-                f.write("- name: "+tool+"\n")
-                f.write("  owner: "+owner+"\n")
+for i in range(3, len(data_loaded['items']) - 2):
+    section = data_loaded['items'][i]['id']
+    name = data_loaded['items'][i]['name']
+    f = open(section + ".yml", "w")
+    f.write("tool_panel_section_label: " + name + "\ntools:\n")
+    for j in data_loaded['items'][i]['items']:  # for loop on toolkit sections
+        path = j['id']
+        infos = path.replace('toolshed.g2.bx.psu.edu/repos/', "")
+        # extract the owner (group1) and the name of the tool (group2)
+        pattern = re.compile(r"([^\/]+)\/([^\/]+)\/")
+        for match in pattern.finditer(infos):  # for each tool in the seection
+            owner = match.group(1)
+            tool = match.group(2)
+            # verify the tool is not already installed
+            installed = os.popen('grep -r "' + tool + '" ' + args.dest).read()
+            if installed == '':  # if tool not installed
+                f.write("- name: " + tool + "\n")
+                f.write("  owner: " + owner + "\n")
     f.close()
 
 tools_au.parse()