Added rewrite option to pass to module_generators. Updated module generators...

Added rewrite option to pass to module_generators.  Updated module generators to allow module yaml to specify db saving & prefix type.

chipathlon/module_generator.py

@@ -80,7 +80,15 @@ class ModuleGenerator(object):
             all_jobs.append(self.workflow_jobs[job_name])
             for output_info in job_info["outputs"]:
                 logical_name = output_info.keys()[0]
-                result = Result(logical_name, final_result.control_samples, final_result.signal_samples, all_markers, all_jobs, should_save=False)
+                result = Result(
+                    logical_name,
+                    final_result.control_samples,
+                    final_result.signal_samples,
+                    all_markers,
+                    all_jobs,
+                    should_save=output_info[logical_name]["save_result"] if "save_result" in output_info[logical_name] else False,
+                    prefix_join=output_info[logical_name].get("prefix_join")
+                )
                 results.append(result)
             run.add_result(self.module.name, result)
         results.append(final_result)
@@ -163,10 +171,12 @@ class ModuleGenerator(object):
                 self._download_from_gridfs(run, result)
         return
 
-    def generate(self, run):
+    def generate(self, run, rewrite=False):
         """
         :param run: The target run to generate jobs for.
         :type run: :py:class:chipathlon.run.Run
+        :param rewrite: Whether or not to rewrite data even if it exists.
+        :type rewrite: bool
 
         Generates actual workflow jobs for a particular run.  The logic for
         job generation is based on the fact that all output files are unique,
@@ -184,9 +194,9 @@ class ModuleGenerator(object):
         """
         final_results = self.create_final_results(run)
         for result in final_results:
-            if not result.exists_in_db(self.mdb, run.genome):
+            if rewrite or not result.exists_in_db(self.mdb, run.genome):
                 for prev_result in self.get_prev_results(run, result):
-                    if prev_result.exists_in_encode() or prev_result.exists_in_db(self.mdb, run.genome):
+                    if prev_result.exists_in_encode() or (not rewrite and prev_result.exists_in_db(self.mdb, run.genome)):
                         self.add_download_job(run, prev_result)
                 self.add_jobs(run, result)
         return
@@ -276,4 +286,3 @@ class ModuleGenerator(object):
         will be used to get a target result.
         This should be overriden by the actual generators.
         """
-        return

chipathlon/result.py

@@ -10,7 +10,7 @@ class Result(object):
     run on the result file up to this point.
     """
 
-    def __init__(self, logical_name, control_samples, signal_samples, all_markers, all_jobs, should_save=False):
+    def __init__(self, logical_name, control_samples, signal_samples, all_markers, all_jobs, should_save=False, prefix_join=None):
         """
         :param logical_name: The unique name of the file as presented in the module yaml
         :type logical_name: string
@@ -43,7 +43,7 @@ class Result(object):
         self.should_save = should_save
 
         self.prefix = self._get_prefix()
-        self.full_name = self.prefix + "_" + self.logical_name
+        self.full_name = self.prefix + ("_" if prefix_join is None else prefix_join) + self.logical_name
         self.file_type = os.path.splitext(self.logical_name)[1][1:]
         self.pegasus_file = File(self.full_name)
         return