use basename of input JSON as default string label (-s, --str-label)

ENCODE-DCC · Jun 25, 2019 · ace9777 · ace9777
1 parent a302921
commit ace9777
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Showing 2 changed files with 11 additions and 25 deletions.
diff --git a/caper/caper.py b/caper/caper.py
@@ -67,7 +67,6 @@ class Caper(object):
     RE_PATTERN_WDL_COMMENT_DOCKER = r'^\s*\#\s*CAPER\s+docker\s(.+)'
     RE_PATTERN_WDL_COMMENT_SINGULARITY = \
         r'^\s*\#\s*CAPER\s+singularity\s(.+)'
-    RE_PATTERN_VALID_STR_LABEL = r'^[A-Za-z0-9\-\_]+$'
     RE_PATTERN_STARTED_WORKFLOW_ID = \
         r'started WorkflowActor-(\b[0-9a-f]{8}\b-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-\b[0-9a-f]{12}\b)'
     RE_PATTERN_FINISHED_WORKFLOW_ID = \
@@ -191,18 +190,9 @@ def run(self):
         """Run a workflow using Cromwell run mode
         """
         timestamp = Caper.__get_time_str()
-        if self._str_label is not None:
-            # check if str label is valid
-            r = re.findall(Caper.RE_PATTERN_VALID_STR_LABEL,
-                           self._str_label)
-            if len(r) != 1:
-                raise ValueError('Invalid str_label.')
-            suffix = os.path.join(
-                self._str_label, timestamp)
-        else:
-            # otherwise, use WDL basename
-            suffix = os.path.join(
-                self.__get_wdl_basename_wo_ext(), timestamp)
+        # otherwise, use WDL basename
+        suffix = os.path.join(
+            self.__get_wdl_basename_wo_ext(), timestamp)
         tmp_dir = self.__mkdir_tmp_dir(suffix)
 
         # all input files
@@ -346,18 +336,9 @@ def submit(self):
         """Submit a workflow to Cromwell server
         """
         timestamp = Caper.__get_time_str()
-        if self._str_label is not None:
-            # check if label is valid
-            r = re.findall(Caper.RE_PATTERN_VALID_STR_LABEL,
-                           self._str_label)
-            if len(r) != 1:
-                raise ValueError('Invalid str_label.')
-            suffix = os.path.join(
-                self._str_label, timestamp)
-        else:
-            # otherwise, use WDL basename
-            suffix = os.path.join(
-                self.__get_wdl_basename_wo_ext(), timestamp)
+        # otherwise, use WDL basename
+        suffix = os.path.join(
+            self.__get_wdl_basename_wo_ext(), timestamp)
         tmp_dir = self.__mkdir_tmp_dir(suffix)
 
         # all input files

diff --git a/caper/caper_args.py b/caper/caper_args.py
@@ -622,4 +622,9 @@ def parse_caper_arguments():
         args_d['singularity_cachedir'] = singularity_cachedir
         os.makedirs(singularity_cachedir, exist_ok=True)
 
+    if args_d.get('str_label') is None:
+        if args_d.get('inputs') is not None:
+            basename = os.path.basename(args_d['inputs'])
+            args_d['str_label'] = os.path.splitext(basename)[0]
+
     return args_d