Fix duplicated keys in metadata dict

PavlidisLab · Mar 13, 2024 · 71c0247 · 71c0247
1 parent 20a570d
commit 71c0247
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/rnaseq_pipeline/sources/geo.py b/rnaseq_pipeline/sources/geo.py
@@ -103,7 +103,9 @@ def run(self):
             raise RuntimeError('{} GEO record is not linked to SRA.'.format(self.gsm))
         platform, srx_url = samples_info[self.gsm]
         srx = parse_qs(urlparse(srx_url).query)['term'][0]
-        yield DownloadSraExperiment(srx, metadata=dict(**self.metadata, sample_id=self.sample_id))
+        metadata = dict(self.metadata)
+        metadata['sample_id'] = self.sample_id
+        yield DownloadSraExperiment(srx, metadata=metadata)
 
 class DownloadGeoSeriesMetadata(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task):
     """

diff --git a/rnaseq_pipeline/sources/sra.py b/rnaseq_pipeline/sources/sra.py
@@ -157,7 +157,9 @@ def run(self):
         # on the number of mates per spot
         is_paired = (self.sample_id in sra_cfg.paired_read_experiments) or (run.spots_with_mates > 0) or (run.LibraryLayout == 'PAIRED')
 
-        yield DumpSraRun(run.Run, self.srx, paired_reads=is_paired, metadata=dict(**self.metadata, sample_id=self.sample_id))
+        metadata = dict(self.metadata)
+        metadata['sample_id'] = self.sample_id
+        yield DumpSraRun(run.Run, self.srx, paired_reads=is_paired, metadata=metadata)
 
 class DownloadSraProjectRunInfo(TaskWithMetadataMixin, RerunnableTaskMixin, luigi.Task):
     """