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| author | BonfaceKilz | 2021-03-05 12:54:05 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-03-08 21:09:58 +0300 |
| commit | a896c25bbe4f640665d547307efe389817f17848 (patch) | |
| tree | ae5595254e923cac8d3faaa3da8903ff11365933 | |
| parent | 8752937bc1e3cea84eefd3e363b429157f25acb5 (diff) | |
| download | genenetwork3-a896c25bbe4f640665d547307efe389817f17848.tar.gz | |
Use new "compute_k_values" procedure
| -rw-r--r-- | gn3/api/gemma.py | 43 |
1 files changed, 17 insertions, 26 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index d08c11b..1751530 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -116,24 +116,19 @@ traitfile, and snpsfile are extracted from a metadata.json file. if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} - _hash = get_hash_of_files([genofile, phenofile, snpsfile]) - k_output_filename = f"{_hash}-k-output.json" + results = compute_k_values(gemma_cmd=current_app.config.get( + "GEMMA_" + "WRAPPER_CMD"), + output_dir=current_app.config.get('TMPDIR'), + token=token, + gemma_kwargs=gemma_kwargs) return jsonify(unique_id=queue_cmd( conn=redis.Redis(), email=(request.get_json() or {}).get('email'), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), - cmd=compose_gemma_cmd(gemma_wrapper_cmd=current_app.config.get( - "GEMMA_" - "WRAPPER_CMD"), - gemma_wrapper_kwargs=None, - gemma_kwargs=gemma_kwargs, - gemma_args=[ - "-gk", ">", - (f"{current_app.config.get('TMPDIR')}/" - f"{token}/{k_output_filename}") - ])), + cmd=results.get("gemma_cmd")), status="queued", - output_file=k_output_filename) + output_file=results.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( @@ -158,24 +153,20 @@ values. if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} - _hash = get_hash_of_files([genofile, phenofile, snpsfile]) - k_output_filename = f"{_hash}-k-output.json" + results = compute_k_values(gemma_cmd=current_app.config.get( + "GEMMA_" + "WRAPPER_CMD"), + output_dir=current_app.config.get('TMPDIR'), + token=token, + gemma_kwargs=gemma_kwargs, + chromosomes=chromosomes) return jsonify(unique_id=queue_cmd( conn=redis.Redis(), email=(request.get_json() or {}).get('email'), job_queue=current_app.config.get("REDIS_JOB_QUEUE"), - cmd=compose_gemma_cmd( - gemma_wrapper_cmd=current_app.config.get("GEMMA_" - "WRAPPER_CMD"), - gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"}, - gemma_kwargs=gemma_kwargs, - gemma_args=[ - "-gk", ">", - (f"{current_app.config.get('TMPDIR')}/" - f"{token}/{k_output_filename}") - ])), + cmd=results.get("gemma_cmd")), status="queued", - output_file=k_output_filename) + output_file=results.get("output_file")) # pylint: disable=W0703 except Exception: return jsonify( |