Added default configuration for modules and rewrote the profiles collection

bin/PSOT

@@ -42,20 +42,17 @@ def generate_execution(config, args):
     execution['fasta'] = os.path.abspath(args.fasta)
     execution['output'] = os.path.abspath(args.output)
     execution['directory'] = 'tmp' # TODO replace by random tmp directory or make it configurable (cli option)
-    modules = generate_execution_modules_for_profile(config, args.profile)
-    execution['modules'] = modules
+    execution['modules'] = generate_execution_modules_for_profile(config, args.profile)
     return execution
     
 def generate_execution_modules_for_profile(config, profile):
     # find profile by name
     p = [x for x in config['profiles'] if x['name'] == profile][0]
-    # find all modules for profile from modules config section
-    m = [x for x in config['modules'] if x['name'] in p['modules']]
-    modules = copy.deepcopy(m)
+    modules = copy.deepcopy(p['modules'])
     # generate unique ids for each module
     for module in modules:
         module['id'] = module['name']
-        module['params'] = generate_params_string(p['modules'][module['name']])
+        module['params'] = generate_params_string(module['parameters'])
     return modules
 
 def generate_params_string(options):

bin/config.py

 import os
 import yaml
+import copy
 
 def get_install_location():
     """Finds the location directory of the tool"""
@@ -40,16 +41,45 @@ def create_app_config():
     return config
         
 def load_modules():
-    modules = []
+    modules = {}
     for manifest in get_module_manifests():
         with (open(manifest)) as f:
-            modules.append(yaml.load(f))
+            module = yaml.load(f)
+            modules[module['name']] = module
+            if 'parameters' not in module:
+                module['parameters'] = {}
     return modules
 
+def normalize_profiles(profiles):
+    """take care that all keys of the profile map exist"""
+    for profile in profiles:
+        if 'modules' not in profile:
+            profile['modules'] = []
+        for module in profile['modules']:
+            if profile['modules'][module] is None:
+                profile['modules'][module] = {}
+
+def merge_modules_in_profiles(config):
+    """Merge the module configuration and the profile configuration. Profile has precedence over module."""
+    profiles = config['profiles']
+    modules = config['modules']
+    for profile in profiles:
+        resolved_modules = []
+        for module_name in profile['modules']:
+            profile_module_config = profile['modules'][module_name]
+            resolved_module = modules[module_name]
+            copied_module = copy.deepcopy(resolved_module)
+            resolved_modules.append(copied_module)
+            for c in profile_module_config:
+                copied_module[c] = profile_module_config[c]
+        profile['modules'] = resolved_modules
+
 def load_config():
     config = load_config_file()
     config['modules'] = load_modules()
     config['app'] = create_app_config()
+    normalize_profiles(config['profiles'])
+    merge_modules_in_profiles(config)
     return config
 
 if __name__ == "__main__":