Checking md5 of workflow and parameters files (#28)

* Added saving md5 of workflow and parameters files inside of ExecutionState class
* Added comparison of new and previous md5's

run_galaxy_workflow.py

@@ -134,7 +134,9 @@ def main():
         gi = GalaxyInstance(ins['url'], key=ins['key'])
         validate_dataset_id_exists(gi, inputs_data)
 
-        state = ExecutionState.start(path=args.state_file)
+        state = ExecutionState.start(path=args.state_file,
+                                     workflow_path=args.workflow,
+                                     parameters_path=args.parameters)
 
         # Create new history to run workflow
         if state.input_history is None:

wfexecutor/__init__.py

@@ -8,6 +8,7 @@
 import yaml
 import json
 import pickle
+from hashlib import md5
 
 
 def get_instance(conf, name='__default'):
@@ -402,6 +403,7 @@ def process_allowed_errors(allowed_errors_dict, wf_from_json):
 
     return allowed_errors_state
 
+
 def produce_versions_file(gi, workflow_from_json, table_path, tools_dict=[]):
     """
     Produces a tool versions file for the workflow run.
@@ -449,24 +451,38 @@ class ExecutionState(object):
     results = None
     input_history = None
 
-    def __init__(self, path):
-        self.path = path
+    def __init__(self, state_path, workflow_path, parameters_path):
+        self.state_path = state_path
+        self.workflow_hex = self.get_file_md5(workflow_path)
+        self.parameters_hex = self.get_file_md5(parameters_path)
+
+    @staticmethod
+    def get_file_md5(file_path):
+        with open(file_path, 'rb') as f:
+            return md5(f.read()).hexdigest()
 
     @staticmethod
-    def start(path):
-        if os.path.isfile(path):
+    def start(state_path, workflow_path, parameters_path):
+        if os.path.isfile(state_path):
             try:
-                with open(path, mode='rb') as d:
+                with open(state_path, mode='rb') as d:
                     es = pickle.load(d)
                     if type(es) is ExecutionState:
+                        # Check if there are any changes in the parameters and workflow files
+                        if ExecutionState.get_file_md5(workflow_path) != es.workflow_hex:
+                            logging.warning(f"The workflow file's ({workflow_path}) changed from the previous run. "
+                                            "Delete .pickle file if you want to run workflow from the beginning.")
+                        if ExecutionState.get_file_md5(parameters_path) != es.parameters_hex:
+                            logging.warning(f"The para file's ({parameters_path}) changed from the previous run. "
+                                            "Delete .pickle file if you want to run workflow from the beginning.")
                         return es
                     else:
-                        logging.warning("The provided file {} does not have an ExecutionState object serialised".format(path))
+                        logging.warning("The provided file {} does not have an ExecutionState object serialised".format(state_path))
             except Exception:
-                logging.warning("Could not read serialized file {}.".format(path))
-        return ExecutionState(path)
+                logging.warning("Could not read serialized file {}.".format(state_path))
+        return ExecutionState(state_path, workflow_path, parameters_path)
 
     def save_state(self):
-        with open(self.path, mode='wb') as d:
+        with open(self.state_path, mode='wb') as d:
             pickle.dump(self, d)