Change sbg:fa_icon to sbg:icon

Fix profile parsing
rabix · Sep 25, 2023 · 0580045 · 0580045
1 parent 8de94f2
commit 0580045
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/sbpack/noncwl/nextflow.py b/sbpack/noncwl/nextflow.py
@@ -60,7 +60,7 @@ def nf_cwl_port_map():
             'description': 'label',
             'help_text': 'doc',
             'mimetype': 'format',
-            'fa_icon': 'sbg:fa_icon',
+            'fa_icon': 'sbg:icon',
             'pattern': 'sbg:pattern',
             'hidden': 'sbg:hidden',
         }
@@ -74,7 +74,7 @@ def nf_cwl_category_map():
         return {
             'title': 'sbg:title',
             'description': 'sbg:doc',
-            'fa_icon': 'sbg:fa_icon',
+            'fa_icon': 'sbg:icon',
         }
 
     def nf_to_sb_input_mapper(self, port_id, port_data, category=None):

diff --git a/sbpack/noncwl/utils.py b/sbpack/noncwl/utils.py
@@ -344,10 +344,12 @@ def parse_config_file(file_path):
 
     # Extract profiles using regex
     profiles = {}
-    pattern = re.compile(r'^\s*(\w+)\s*{([^}]+)}', re.MULTILINE | re.DOTALL)
+    pattern = re.compile(r'\s*(\w+)\s*{([^}]+)}', re.MULTILINE | re.DOTALL)
     blocks = re.findall(pattern, profiles_text)
     for name, content in blocks:
-        settings = dict(re.findall(r'\s*([a-zA-Z.]+)\s*=\s*(.*)', content))
+        settings = dict(
+            re.findall(r'([a-zA-Z._]+)(?:\s+|)=(?:\s+|)([^\s]+)', content)
+        )
         profiles[name] = settings
         include_path = re.findall(
             r'includeConfig\s+[\'\"]([a-zA-Z_.\\/]+)[\'\"]', content)