version 0.13.3a1 for pipestat 0.6.0a1

databio · Oct 4, 2023 · 0b430c7 · 0b430c7
1 parent 8aaede5
commit 0b430c7
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Showing 5 changed files with 24 additions and 17 deletions.
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,5 +1,9 @@
 # Changelog
 
+## [0.13.3a1] -- 2023-10-04
+### Fixed
+- refactor for pipestat 0.6.0a1
+
 ## [0.13.2] -- 2023-08-02
 ### Fixed
 - fixed self.new_start overriding checkpoints.

diff --git a/pypiper/_version.py b/pypiper/_version.py
@@ -1 +1 @@
-__version__ = "0.13.2"
+__version__ = "0.13.3a1"
diff --git a/pypiper/manager.py b/pypiper/manager.py
@@ -344,7 +344,7 @@ 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(
-            sample_name=self.pipestat_sample_name
+            record_identifier=self.pipestat_sample_name
             or _get_arg(args_dict, "pipestat_sample_name")
             or DEFAULT_SAMPLE_NAME,
             pipeline_name=self.name,
@@ -724,7 +724,8 @@ def start_pipeline(self, args=None, multi=False):
         self.info("\n----------------------------------------\n")
         self.status = "running"
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier="running"
+            record_identifier=self._pipestat_manager.sample_name,
+            status_identifier="running",
         )
 
         # Record the start in PIPE_profile and PIPE_commands output files so we
@@ -770,7 +771,8 @@ def _set_status_flag(self, status):
         prev_status = self.status
         self.status = status
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier=status
+            record_identifier=self._pipestat_manager.sample_name,
+            status_identifier=status,
         )
         self.debug("\nChanged status from {} to {}.".format(prev_status, self.status))
 
@@ -1419,7 +1421,7 @@ def _wait_for_lock(self, lock_file):
                 )
                 # self._set_status_flag(WAIT_FLAG)
                 self.pipestat.set_status(
-                    sample_name=self._pipestat_manager.sample_name,
+                    record_identifier=self._pipestat_manager.sample_name,
                     status_identifier="waiting",
                 )
                 first_message_flag = True
@@ -1443,7 +1445,7 @@ def _wait_for_lock(self, lock_file):
             self.timestamp("File unlocked.")
             # self._set_status_flag(RUN_FLAG)
             self.pipestat.set_status(
-                sample_name=self._pipestat_manager.sample_name,
+                record_identifier=self._pipestat_manager.sample_name,
                 status_identifier="running",
             )
 
@@ -1602,7 +1604,7 @@ def report_result(self, key, value, nolog=False, result_formatter=None):
 
         reported_result = self.pipestat.report(
             values={key: value},
-            sample_name=self.pipestat_sample_name,
+            record_identifier=self.pipestat_sample_name,
             result_formatter=rf,
         )
 
@@ -1684,7 +1686,7 @@ def report_object(
         val = {key: message_raw.replace("\t", " ")}
 
         reported_result = self.pipestat.report(
-            values=val, sample_name=self.pipestat_sample_name, result_formatter=rf
+            values=val, record_identifier=self.pipestat_sample_name, result_formatter=rf
         )
         if not nolog:
             for r in reported_result:
@@ -2026,7 +2028,7 @@ def fail_pipeline(self, exc, dynamic_recover=False):
             self.info("Failure reason: " + str(exc))
             # self._set_status_flag(FAIL_FLAG)
             self.pipestat.set_status(
-                sample_name=self._pipestat_manager.sample_name,
+                record_identifier=self._pipestat_manager.sample_name,
                 status_identifier="failed",
             )
 
@@ -2087,7 +2089,8 @@ def stop_pipeline(self, status=COMPLETE_FLAG):
         """
         # self._set_status_flag(status)
         self.pipestat.set_status(
-            sample_name=self._pipestat_manager.sample_name, status_identifier=status
+            record_identifier=self._pipestat_manager.sample_name,
+            status_identifier=status,
         )
         self._cleanup()
         elapsed_time_this_run = str(

diff --git a/pypiper/utils.py b/pypiper/utils.py
@@ -387,20 +387,20 @@ def split_by_pipes(cmd):
     cmdlist = []
     newcmd = str()
     for char in cmd:
-        if char is "{":
+        if char == "{":
             stack_brace.append("{")
-        elif char is "}":
+        elif char == "}":
             stack_brace.pop()
-        elif char is "(":
+        elif char == "(":
             stack_paren.append("(")
-        elif char is ")":
+        elif char == ")":
             stack_paren.pop()
 
         if len(stack_brace) > 0 or len(stack_paren) > 0:
             # We are inside a parenthetic of some kind; emit character
             # no matter what it is
             newcmd += char
-        elif char is "|":
+        elif char == "|":
             # if it's a pipe, finish the command and start a new one
             cmdlist.append(newcmd)
             newcmd = str()
@@ -1110,7 +1110,7 @@ def _add_args(parser, args, required):
     return parser
 
 
-def result_formatter_markdown(pipeline_name, sample_name, res_id, value) -> str:
+def result_formatter_markdown(pipeline_name, record_identifier, res_id, value) -> str:
     """
     Returns Markdown formatted value as string
     """

diff --git a/requirements/requirements-pypiper.txt b/requirements/requirements-pypiper.txt
@@ -4,4 +4,4 @@ psutil
 pandas
 ubiquerg>=0.4.5
 yacman
-pipestat>=0.4.0
+pipestat>=0.6.0a1