minor refactor to use pipestat properties instead of cfg dict

pypiper/manager.py

@@ -329,7 +329,7 @@ def __init__(
         signal.signal(signal.SIGTERM, self._signal_term_handler)
 
         # pipestat setup
-        self.pipestat_sample_name = pipestat_sample_name or DEFAULT_SAMPLE_NAME
+        self.pipestat_record_identifier = pipestat_sample_name or DEFAULT_SAMPLE_NAME
 
         # don't force default pipestat_results_file value unless
         # pipestat config not provided
@@ -343,7 +343,7 @@ def _get_arg(args_dict, arg_name):
             return None if arg_name not in args_dict else args_dict[arg_name]
 
         self._pipestat_manager = PipestatManager(
-            record_identifier=self.pipestat_sample_name
+            record_identifier=self.pipestat_record_identifier
             or _get_arg(args_dict, "pipestat_sample_name")
             or DEFAULT_SAMPLE_NAME,
             pipeline_name=self.name,
@@ -436,7 +436,7 @@ def _completed(self):
         :return bool: Whether the managed pipeline is in a completed state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            self.pipestat.get_status(self._pipestat_manager.record_identifier)
             == COMPLETE_FLAG
         )
 
@@ -448,7 +448,7 @@ def _failed(self):
         :return bool: Whether the managed pipeline is in a failed state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            self.pipestat.get_status(self._pipestat_manager.record_identifier)
             == FAIL_FLAG
         )
 
@@ -459,7 +459,7 @@ def halted(self):
         :return bool: Whether the managed pipeline is in a paused/halted state.
         """
         return (
-            self.pipestat.get_status(self._pipestat_manager.cfg["record_identifier"])
+            self.pipestat.get_status(self._pipestat_manager.record_identifier)
             == PAUSE_FLAG
         )
 
@@ -723,11 +723,11 @@ def start_pipeline(self, args=None, multi=False):
         results = self._pipestat_manager.__str__().split("\n")
         for i in results:
             self.info("* " + i)
-        self.info("* Sample name: " + self.pipestat_sample_name + "\n")
+        self.info("* Sample name: " + self.pipestat_record_identifier + "\n")
         self.info("\n----------------------------------------\n")
         self.status = "running"
         self.pipestat.set_status(
-            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            record_identifier=self._pipestat_manager.record_identifier,
             status_identifier="running",
         )
 
@@ -774,7 +774,7 @@ def _set_status_flag(self, status):
         prev_status = self.status
         self.status = status
         self.pipestat.set_status(
-            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            record_identifier=self._pipestat_manager.record_identifier,
             status_identifier=status,
         )
         self.debug("\nChanged status from {} to {}.".format(prev_status, self.status))
@@ -791,8 +791,8 @@ def _flag_file_path(self, status=None):
         """
 
         flag_file_name = "{}_{}_{}".format(
-            self._pipestat_manager.cfg["pipeline_name"],
-            self.pipestat_sample_name,
+            self._pipestat_manager.pipeline_name,
+            self.pipestat_record_identifier,
             flag_name(status or self.status),
         )
         return pipeline_filepath(self, filename=flag_file_name)
@@ -1424,7 +1424,7 @@ def _wait_for_lock(self, lock_file):
                 )
                 # self._set_status_flag(WAIT_FLAG)
                 self.pipestat.set_status(
-                    record_identifier=self._pipestat_manager.cfg["record_identifier"],
+                    record_identifier=self._pipestat_manager.record_identifier,
                     status_identifier="waiting",
                 )
                 first_message_flag = True
@@ -1448,7 +1448,7 @@ def _wait_for_lock(self, lock_file):
             self.timestamp("File unlocked.")
             # self._set_status_flag(RUN_FLAG)
             self.pipestat.set_status(
-                record_identifier=self._pipestat_manager.cfg["record_identifier"],
+                record_identifier=self._pipestat_manager.record_identifier,
                 status_identifier="running",
             )
 
@@ -1607,7 +1607,7 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
 
         reported_result = self.pipestat.report(
             values={key: value},
-            record_identifier=self.pipestat_sample_name,
+            record_identifier=self.pipestat_record_identifier,
             result_formatter=rf,
         )
 
@@ -1689,7 +1689,9 @@ def report_object(
         val = {key: message_raw.replace("\t", " ")}
 
         reported_result = self.pipestat.report(
-            values=val, record_identifier=self.pipestat_sample_name, result_formatter=rf
+            values=val,
+            record_identifier=self.pipestat_record_identifier,
+            result_formatter=rf,
         )
         if not nolog:
             for r in reported_result:
@@ -1856,12 +1858,12 @@ def _refresh_stats(self):
             _, data = read_yaml_data(path=self.pipeline_stats_file, what="stats_file")
             print(data)
             pipeline_key = list(
-                data[self._pipestat_manager.cfg["pipeline_name"]][
+                data[self._pipestat_manager.pipeline_name][
                     self.pipestat["_pipeline_type"]
                 ]
             )[0]
             if self.name == pipeline_key:
-                for key, value in data[self._pipestat_manager.cfg["pipeline_name"]][
+                for key, value in data[self._pipestat_manager.pipeline_name][
                     self.pipestat["_pipeline_type"]
                 ][pipeline_key].items():
                     self.stats_dict[key] = value.strip()
@@ -2032,7 +2034,7 @@ def fail_pipeline(self, exc: Exception, dynamic_recover: bool = False):
             self.info("Total time: " + str(total_time))
             self.info("Failure reason: " + str(exc))
             self.pipestat.set_status(
-                record_identifier=self._pipestat_manager.cfg["record_identifier"],
+                record_identifier=self._pipestat_manager.record_identifier,
                 status_identifier="failed",
             )
 
@@ -2093,7 +2095,7 @@ def stop_pipeline(self, status=COMPLETE_FLAG):
         """
         # self._set_status_flag(status)
         self.pipestat.set_status(
-            record_identifier=self._pipestat_manager.cfg["record_identifier"],
+            record_identifier=self._pipestat_manager.record_identifier,
             status_identifier=status,
         )
         self._cleanup()
@@ -2464,8 +2466,8 @@ def _cleanup(self, dry_run=False):
                 for fn in glob.glob(self.outfolder + flag_name("*"))
                 if COMPLETE_FLAG not in os.path.basename(fn)
                 and not "{}_{}_{}".format(
-                    self._pipestat_manager.cfg["pipeline_name"],
-                    self.pipestat_sample_name,
+                    self._pipestat_manager.pipeline_name,
+                    self.pipestat_record_identifier,
                     run_flag,
                 )
                 == os.path.basename(fn)