Merge pull request #241 from broadinstitute/upload-repo-update

update depmap_omics_upload

.github/workflows/pyright-ratchet.yaml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         python-version: [3.9]
-        poetry-version: ["1.3.2"]
+        poetry-version: ["1.8.3"]
 
     steps:
       - name: print branch

Dockerfile

@@ -3,7 +3,7 @@ FROM python:3.9-buster
 #RUN pip install pipx && \
 #  pipx install poetry==1.2.0
 
-RUN pip install poetry==1.2.2
+RUN pip install poetry==1.8.3
 
 RUN mkdir /install && mkdir /install/depmapomics && mkdir /install/mgenepy
 # first create these as if they are empty modules, 

depmapomics/dm_omics.py

@@ -145,8 +145,6 @@ async def expressionPostProcessing(
 
     pr_table = mytracker.read_pr_table()
 
-    mytracker.close_gumbo_client()
-
     renaming_dict = dict(list(zip(pr_table.MainSequencingID, pr_table.index)))
     h.dictToFile(renaming_dict, folder + "rna_seq2pr_renaming.json")
     pr_files = dict()
@@ -457,8 +455,6 @@ async def fusionPostProcessing(
         os.path.join(folder, "filteredfusions_latest_profile.csv"), index=False
     )
 
-    mytracker.close_gumbo_client()
-
     # taiga
     print("uploading to taiga")
     tc.update_dataset(
@@ -645,8 +641,6 @@ def cnPostProcessing(
     with open(masked_gene_list, "r") as f:
         genes_to_mask = f.read().splitlines()
 
-    mytracker.close_gumbo_client()
-
     renaming_dict = dict(list(zip(pr_table.MainSequencingID, pr_table.index)))
 
     # subset and rename to PR-indexed matrices
@@ -1027,7 +1021,6 @@ async def mutationPostProcessing(
     mytracker = track.SampleTracker()
     pr_table = mytracker.read_pr_table()
     renaming_dict = dict(list(zip(pr_table.MainSequencingID, pr_table.index)))
-    mytracker.close_gumbo_client()
 
     wesmutations_pr = wesmutations[
         wesmutations[constants.SAMPLEID].isin(renaming_dict.keys())