Avoid overriding metadata in DownloadGeoSample and DownloadSraExperiment

PavlidisLab · Aug 13, 2024 · 16f249d · 16f249d
1 parent ae02f56
commit 16f249d
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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
@@ -104,7 +104,9 @@ def run(self):
         platform, srx_url = samples_info[self.gsm]
         srx = parse_qs(urlparse(srx_url).query)['term'][0]
         metadata = dict(self.metadata)
-        metadata['sample_id'] = self.sample_id
+        # do not override the sample_id when invoked from DownloadGemmaExperiment
+        if 'sample_id' not in 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
@@ -151,7 +151,9 @@ def run(self):
         is_paired = run.LibraryLayout == 'PAIRED'
 
         metadata = dict(self.metadata)
-        metadata['sample_id'] = self.sample_id
+        # do not override the sample_id when invoked from DownloadGeoSample or DownloadGemmaExperiment
+        if 'sample_id' not in 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):