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| author | BonfaceKilz | 2021-03-01 11:47:21 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-03-08 21:09:58 +0300 |
| commit | 52e3569cca6b24d1318034f5ab004795e70135f5 (patch) | |
| tree | 8d65ba9802bc617b6b6936248aea426b1c5df3bd /gn3/api | |
| parent | b9d9ece5da00828fbe8c9984c8c43fd1659faeb9 (diff) | |
| download | genenetwork3-52e3569cca6b24d1318034f5ab004795e70135f5.tar.gz | |
Fix failing tests
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/gemma.py | 19 |
1 files changed, 12 insertions, 7 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index effae8a..7c76f2f 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -35,10 +35,12 @@ file output is returned. """ data = request.get_json() app_defaults = current_app.config.get('APP_DEFAULTS') - __hash = generate_hash_of_string("".join(data.get("values"))) + __hash = generate_hash_of_string( + f"{data.get('genofile_name')}_" + ''.join(data.get("values", ""))) gemma_kwargs = { "geno_filename": os.path.join(app_defaults.get("GENODIR"), "bimbam", - f"{data.get('genofile_name')}.txt"), + f"{data.get('geno_filename')}"), "trait_filename": generate_pheno_txt_file( tmpdir=app_defaults.get("TMPDIR"), values=data.get("values"), @@ -46,18 +48,21 @@ file output is returned. trait_filename=(f"{data.get('dataset_groupname')}_" f"{data.get('trait_name')}_" f"{__hash}.txt"))} + gemma_wrapper_kwargs = {} + if data.get("loco"): + gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}" k_computation_cmd = generate_gemma_computation_cmd( - gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), + gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD") + "_haha", + gemma_wrapper_kwargs={"loco": f"--input {data.get('loco')}"}, gemma_kwargs=gemma_kwargs, output_file=(f"{app_defaults.get('TMPDIR')}/gn2/" f"{data.get('dataset_name')}_K_" f"{__hash}.json")) - if data.get("covariates"): - gemma_kwargs["c"] = os.path.join(app_defaults.get("GENODIR"), - "bimbam", - data.get("covariates")) gemma_kwargs["lmm"] = data.get("lmm", 9) + gemma_wrapper_kwargs["input"] = (f"{data.get('dataset_name')}_K_" + f"{__hash}.json") gwa_cmd = generate_gemma_computation_cmd( + gemma_wrapper_kwargs=gemma_wrapper_kwargs, gemma_cmd=app_defaults.get("GEMMA_WRAPPER_CMD"), gemma_kwargs=gemma_kwargs, output_file=(f"{data.get('dataset_name')}_GWA_" |