update looper to reflect pipestat's refactor from sample_name to reco…

…rd_identifier
pepkit · Oct 5, 2023 · e45c0f6 · e45c0f6
1 parent b050268
commit e45c0f6
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/looper/conductor.py b/looper/conductor.py
@@ -430,7 +430,7 @@ def add_sample(self, sample, rerun=False):
         if self.prj.pipestat_configured:
             psms = self.prj.get_pipestat_managers(sample_name=sample.sample_name)
             sample_statuses = psms[self.pl_name].get_status(
-                sample_name=sample.sample_name
+                record_identifier=sample.sample_name
             )
             sample_statuses = [sample_statuses] if sample_statuses else []
         else:

diff --git a/looper/looper.py b/looper/looper.py
@@ -99,7 +99,7 @@ def __call__(self, args):
             for sample in self.prj.samples:
                 psms = self.prj.get_pipestat_managers(sample_name=sample.sample_name)
                 for pipeline_name, psm in psms.items():
-                    s = psm.get_status(sample_name=sample.sample_name)
+                    s = psm.get_status(record_identifier=sample.sample_name)
                     status.setdefault(pipeline_name, {})
                     status[pipeline_name][sample.sample_name] = s
                     _LOGGER.debug(f"{sample.sample_name} ({pipeline_name}): {s}")
@@ -578,7 +578,7 @@ def __call__(self, args):
         if project_level:
             psms = self.prj.get_pipestat_managers(project_level=True)
             for name, psm in psms.items():
-                results = psm.table(pipeline_type="project")
+                results = psm.table()
         else:
             for piface_source_samples in self.prj._samples_by_piface(
                 self.prj.piface_key
@@ -590,7 +590,7 @@ def __call__(self, args):
                     sample_name=first_sample_name, project_level=False
                 )
                 for name, psm in psms.items():
-                    results = psm.table(pipeline_type="sample")
+                    results = psm.table()
         # Results contains paths to stats and object summaries.
         return results