diff options
| -rw-r--r-- | gn3/api/gemma.py | 402 | ||||
| -rw-r--r-- | gn3/computations/gemma.py | 7 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 133 | ||||
| -rw-r--r-- | tests/unit/computations/test_gemma.py | 20 |
4 files changed, 294 insertions, 268 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index a341f62..d82f5a5 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -24,8 +24,7 @@ gemma = Blueprint("gemma", __name__) def get_version(): """Display the installed version of gemma-wrapper""" gemma_cmd = current_app.config["GEMMA_WRAPPER_CMD"] - return jsonify( - run_cmd(f"{gemma_cmd} -v | head -n 1")) + return jsonify(run_cmd(f"{gemma_cmd} -v | head -n 1")) # This is basically extracted from genenetwork2 @@ -39,19 +38,21 @@ file output is returned. """ data = request.get_json() app_defaults = current_app.config - __hash = generate_hash_of_string( - f"{data.get('genofile_name')}_" - ''.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('geno_filename')}"), - "trait_filename": generate_pheno_txt_file( + "geno_filename": + os.path.join(app_defaults.get("GENODIR"), "bimbam", + f"{data.get('geno_filename')}"), + "trait_filename": + generate_pheno_txt_file( tmpdir=app_defaults.get("TMPDIR"), values=data.get("values"), # Generate this file on the fly! trait_filename=(f"{data.get('dataset_groupname')}_" f"{data.get('trait_name')}_" - f"{__hash}.txt"))} + f"{__hash}.txt")) + } gemma_wrapper_kwargs = {} if data.get("loco"): gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}" @@ -74,14 +75,14 @@ file output is returned. if not all([k_computation_cmd, gwa_cmd]): return jsonify(status=128, error="Unable to generate cmds for computation!"), 500 - return jsonify( - unique_id=queue_cmd(conn=redis.Redis(), - email=data.get("email"), - job_queue=app_defaults.get("REDIS_JOB_QUEUE"), - cmd=f"{k_computation_cmd} && {gwa_cmd}"), - status="queued", - output_file=(f"{data.get('dataset_name')}_GWA_" - f"{__hash}.txt")) + return jsonify(unique_id=queue_cmd( + conn=redis.Redis(), + email=data.get("email"), + job_queue=app_defaults.get("REDIS_JOB_QUEUE"), + cmd=f"{k_computation_cmd} && {gwa_cmd}"), + status="queued", + output_file=(f"{data.get('dataset_name')}_GWA_" + f"{__hash}.txt")) @gemma.route("/status/<unique_id>", methods=["GET"]) @@ -90,8 +91,7 @@ def check_cmd_status(unique_id): gemma endpoints, return the status of the command """ - status = redis.Redis().hget(name=unique_id, - key="status") + status = redis.Redis().hget(name=unique_id, key="status") if not status: return jsonify(status=128, error="The unique id you used does not exist!"), 500 @@ -105,39 +105,40 @@ and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile, traitfile, and snpsfile are extracted from a metadata.json file. """ - working_dir = os.path.join(current_app.config.get("TMPDIR"), - token) - _dict = jsonfile_to_dict(os.path.join(working_dir, - "metadata.json")) + working_dir = os.path.join(current_app.config.get("TMPDIR"), token) + _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: - genofile, phenofile, snpsfile = [os.path.join(working_dir, - _dict.get(x)) - for x in ["geno", "pheno", "snps"]] + genofile, phenofile, snpsfile = [ + os.path.join(working_dir, _dict.get(x)) + for x in ["geno", "pheno", "snps"] + ] 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" - 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}")])), - status="queued", - output_file=k_output_filename) + 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}") + ])), + status="queued", + output_file=k_output_filename) # pylint: disable=W0703 except Exception: - return jsonify(status=128, - # use better message - message="Metadata file non-existent!") + return jsonify( + status=128, + # use better message + message="Metadata file non-existent!") @gemma.route("/k-compute/loco/<chromosomes>/<token>", methods=["POST"]) @@ -146,39 +147,40 @@ def compute_k_loco(chromosomes, token): values. """ - working_dir = os.path.join(current_app.config.get("TMPDIR"), - token) - _dict = jsonfile_to_dict(os.path.join(working_dir, - "metadata.json")) + working_dir = os.path.join(current_app.config.get("TMPDIR"), token) + _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: - genofile, phenofile, snpsfile = [os.path.join(working_dir, - _dict.get(x)) - for x in ["geno", "pheno", "snps"]] + genofile, phenofile, snpsfile = [ + os.path.join(working_dir, _dict.get(x)) + for x in ["geno", "pheno", "snps"] + ] 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" - 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}")])), - status="queued", - output_file=k_output_filename) + 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}") + ])), + status="queued", + output_file=k_output_filename) # pylint: disable=W0703 except Exception: - return jsonify(status=128, - # use better message - message="Metadata file non-existent!") + return jsonify( + status=128, + # use better message + message="Metadata file non-existent!") @gemma.route("/gwa-compute/<k_filename>/<token>", methods=["POST"]) @@ -186,41 +188,46 @@ def compute_gwa(k_filename, token): """Compute GWA values. No loco no covariates provided. """ - working_dir = os.path.join(current_app.config.get("TMPDIR"), - token) - _dict = jsonfile_to_dict(os.path.join(working_dir, - "metadata.json")) + working_dir = os.path.join(current_app.config.get("TMPDIR"), token) + _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: genofile, phenofile, snpsfile = [ - os.path.join(working_dir, - _dict.get(x)) - for x in ["geno", "pheno", "snps"]] - gemma_kwargs = {"g": genofile, "p": phenofile, - "a": snpsfile, "lmm": _dict.get("lmm", 9)} + os.path.join(working_dir, _dict.get(x)) + for x in ["geno", "pheno", "snps"] + ] + gemma_kwargs = { + "g": genofile, + "p": phenofile, + "a": snpsfile, + "lmm": _dict.get("lmm", 9) + } _hash = get_hash_of_files([genofile, phenofile, snpsfile]) _output_filename = f"{_hash}-gwa-output.json" - 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={ - "input": os.path.join(working_dir, k_filename) - }, - gemma_kwargs=gemma_kwargs, - gemma_args=["gk", ">", - (f"{current_app.config.get('TMPDIR')}/" - f"{token}/{_output_filename}")])), - status="queued", - output_file=_output_filename) + 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={ + "input": + os.path.join(working_dir, k_filename) + }, + gemma_kwargs=gemma_kwargs, + gemma_args=[ + "gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}") + ])), + status="queued", + output_file=_output_filename) # pylint: disable=W0703 except Exception: - return jsonify(status=128, - # use better message - message="Metadata file non-existent!") + return jsonify( + status=128, + # use better message + message="Metadata file non-existent!") @gemma.route("/gwa-compute/covars/<k_filename>/<token>", methods=["POST"]) @@ -228,42 +235,47 @@ def compute_gwa_with_covar(k_filename, token): """Compute GWA values. Covariates provided. """ - working_dir = os.path.join(current_app.config.get("TMPDIR"), - token) - _dict = jsonfile_to_dict(os.path.join(working_dir, - "metadata.json")) + working_dir = os.path.join(current_app.config.get("TMPDIR"), token) + _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: genofile, phenofile, snpsfile, covarfile = [ - os.path.join(working_dir, - _dict.get(x)) - for x in ["geno", "pheno", "snps", "covar"]] - gemma_kwargs = {"g": genofile, "p": phenofile, - "a": snpsfile, "c": covarfile, - "lmm": _dict.get("lmm", 9)} + os.path.join(working_dir, _dict.get(x)) + for x in ["geno", "pheno", "snps", "covar"] + ] + gemma_kwargs = { + "g": genofile, + "p": phenofile, + "a": snpsfile, + "c": covarfile, + "lmm": _dict.get("lmm", 9) + } _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile]) _output_filename = f"{_hash}-gwa-output.json" - 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={ - "input": os.path.join(working_dir, k_filename) - }, - gemma_kwargs=gemma_kwargs, - gemma_args=["-gk", ">", - (f"{current_app.config.get('TMPDIR')}/" - f"{token}/{_output_filename}")])), - status="queued", - output_file=_output_filename) + 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={ + "input": + os.path.join(working_dir, k_filename) + }, + gemma_kwargs=gemma_kwargs, + gemma_args=[ + "-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}") + ])), + status="queued", + output_file=_output_filename) # pylint: disable=W0703 except Exception: - return jsonify(status=128, - # use better message - message="Metadata file non-existent!") + return jsonify( + status=128, + # use better message + message="Metadata file non-existent!") @gemma.route("/gwa-compute/<k_filename>/loco/maf/<maf>/<token>", @@ -272,45 +284,49 @@ def compute_gwa_with_loco_maf(k_filename, maf, token): """Compute GWA values. No Covariates provided. Only loco and maf vals given. """ - working_dir = os.path.join(current_app.config.get("TMPDIR"), - token) - _dict = jsonfile_to_dict(os.path.join(working_dir, - "metadata.json")) + working_dir = os.path.join(current_app.config.get("TMPDIR"), token) + _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: genofile, phenofile, snpsfile = [ - os.path.join(working_dir, - _dict.get(x)) - for x in ["geno", "pheno", "snps"]] + os.path.join(working_dir, _dict.get(x)) + for x in ["geno", "pheno", "snps"] + ] if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError - gemma_kwargs = {"g": genofile, "p": phenofile, - "a": snpsfile, "lmm": _dict.get("lmm", 9), - 'maf': float(maf)} + gemma_kwargs = { + "g": genofile, + "p": phenofile, + "a": snpsfile, + "lmm": _dict.get("lmm", 9), + 'maf': float(maf) + } _hash = get_hash_of_files([genofile, phenofile, snpsfile]) _output_filename = f"{_hash}-gwa-output.json" - 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": ("--input " - f"{os.path.join(working_dir, k_filename)}") - }, - gemma_kwargs=gemma_kwargs, - gemma_args=["-gk", ">", - (f"{current_app.config.get('TMPDIR')}/" - f"{token}/{_output_filename}")])), - status="queued", - output_file=_output_filename) + 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": ("--input " + f"{os.path.join(working_dir, k_filename)}") + }, + gemma_kwargs=gemma_kwargs, + gemma_args=[ + "-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}") + ])), + status="queued", + output_file=_output_filename) # pylint: disable=W0703 except Exception: - return jsonify(status=128, - # use better message - message="Metadata file non-existent!") + return jsonify( + status=128, + # use better message + message="Metadata file non-existent!") @gemma.route("/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>", @@ -319,43 +335,47 @@ def compute_gwa_with_loco_covar(k_filename, maf, token): """Compute GWA values. No Covariates provided. Only loco and maf vals given. """ - working_dir = os.path.join(current_app.config.get("TMPDIR"), - token) - _dict = jsonfile_to_dict(os.path.join(working_dir, - "metadata.json")) + working_dir = os.path.join(current_app.config.get("TMPDIR"), token) + _dict = jsonfile_to_dict(os.path.join(working_dir, "metadata.json")) try: genofile, phenofile, snpsfile, covarfile = [ - os.path.join(working_dir, - _dict.get(x)) - for x in ["geno", "pheno", "snps", "covar"]] + os.path.join(working_dir, _dict.get(x)) + for x in ["geno", "pheno", "snps", "covar"] + ] if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]): raise FileNotFoundError - gemma_kwargs = {"g": genofile, "p": phenofile, - "a": snpsfile, "c": covarfile, - "lmm": _dict.get("lmm", 9), - "maf": float(maf)} + gemma_kwargs = { + "g": genofile, + "p": phenofile, + "a": snpsfile, + "c": covarfile, + "lmm": _dict.get("lmm", 9), + "maf": float(maf) + } _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile]) _output_filename = f"{_hash}-gwa-output.json" - 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": ("--input " - f"{os.path.join(working_dir, k_filename)}") - }, - gemma_kwargs=gemma_kwargs, - gemma_args=["-gk", ">", - (f"{current_app.config.get('TMPDIR')}/" - f"{token}/{_output_filename}")])), - status="queued", - output_file=_output_filename) + 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": ("--input " + f"{os.path.join(working_dir, k_filename)}") + }, + gemma_kwargs=gemma_kwargs, + gemma_args=[ + "-gk", ">", + (f"{current_app.config.get('TMPDIR')}/" + f"{token}/{_output_filename}") + ])), + status="queued", + output_file=_output_filename) # pylint: disable=W0703 except Exception: - return jsonify(status=128, - # use better message - message="Metadata file non-existent!") + return jsonify( + status=128, + # use better message + message="Metadata file non-existent!") diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py index 7ee70b0..7b5f91d 100644 --- a/gn3/computations/gemma.py +++ b/gn3/computations/gemma.py @@ -49,9 +49,7 @@ def do_paths_exist(paths: ValuesView) -> bool: def generate_gemma_computation_cmd( - gemma_cmd: str, - gemma_kwargs: Dict[str, str], - output_file: str, + gemma_cmd: str, gemma_kwargs: Dict[str, str], output_file: str, gemma_wrapper_kwargs: Dict[str, str]) -> Optional[str]: """Create a computation cmd""" geno_filename = gemma_kwargs.get("geno_filename", "") @@ -69,5 +67,4 @@ def generate_gemma_computation_cmd( return compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd, gemma_wrapper_kwargs=gemma_wrapper_kwargs, gemma_kwargs=_kwargs, - gemma_args=["-gk", ">", - output_file]) + gemma_args=["-gk", ">", output_file]) diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py index 6d2116b..822f088 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -21,19 +21,21 @@ class GemmaAPITest(unittest.TestCase): """Test cases for the Gemma API""" def setUp(self): self.app = create_app({ - "GENODIR": os.path.abspath( - os.path.join(os.path.dirname(__file__), - "test_data/")), - "REDIS_JOB_QUEUE": "GN3::job-queue", - "GEMMA_WRAPPER_CMD": "gemma-wrapper"}).test_client() + "GENODIR": + os.path.abspath( + os.path.join(os.path.dirname(__file__), "test_data/")), + "REDIS_JOB_QUEUE": + "GN3::job-queue", + "GEMMA_WRAPPER_CMD": + "gemma-wrapper" + }).test_client() @mock.patch("gn3.api.gemma.run_cmd") def test_get_version(self, mock_run_cmd): """Test that the correct response is returned""" mock_run_cmd.return_value = {"status": 0, "output": "v1.9"} response = self.app.get("/api/gemma/version", follow_redirects=True) - self.assertEqual(response.get_json(), - {"status": 0, "output": "v1.9"}) + self.assertEqual(response.get_json(), {"status": 0, "output": "v1.9"}) self.assertEqual(response.status_code, 200) @mock.patch("gn3.api.gemma.redis.Redis") @@ -59,60 +61,69 @@ class GemmaAPITest(unittest.TestCase): "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt") ] mock_queue_cmd.return_value = "my-unique-id" - response = self.app.post("/api/gemma/k-gwa-computation", json={ - "trait_filename": "BXD.txt", - "geno_filename": "BXD_geno", - "values": ["X", "N/A", "X"], - "dataset_groupname": "BXD", - "trait_name": "Height", - "email": "me@me.com", - "dataset_name": "BXD" - }) - mock_queue_cmd.assert_has_calls( - [mock.call(conn=_redis_conn, - email="me@me.com", - job_queue="GN3::job-queue", - cmd=("gemma-wrapper --json -- -g " - "genofile.txt -p test.txt " - "-a genofile_snps.txt -gk > " - "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt " - "&& gemma-wrapper --json --input " - "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt" - " -- -a genofile_snps.txt -lmm 9 -g " - "genofile.txt -p test.txt " - "-a genofile_snps.txt " - "-gk > " - "/tmp/gn2/" - "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))] - ) + response = self.app.post("/api/gemma/k-gwa-computation", + json={ + "trait_filename": "BXD.txt", + "geno_filename": "BXD_geno", + "values": ["X", "N/A", "X"], + "dataset_groupname": "BXD", + "trait_name": "Height", + "email": "me@me.com", + "dataset_name": "BXD" + }) + mock_queue_cmd.assert_has_calls([ + mock.call(conn=_redis_conn, + email="me@me.com", + job_queue="GN3::job-queue", + cmd=("gemma-wrapper --json -- -g " + "genofile.txt -p test.txt " + "-a genofile_snps.txt -gk > " + "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt " + "&& gemma-wrapper --json --input " + "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt" + " -- -a genofile_snps.txt -lmm 9 -g " + "genofile.txt -p test.txt " + "-a genofile_snps.txt " + "-gk > " + "/tmp/gn2/" + "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")) + ]) # mock_pheno_txt_file.return_value = "/tmp/gn2/BXD_6OBEPW." self.assertEqual( - response.get_json(), - {"unique_id": 'my-unique-id', - "status": "queued", - "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"}) + response.get_json(), { + "unique_id": 'my-unique-id', + "status": "queued", + "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt" + }) @mock.patch("gn3.api.gemma.redis.Redis") @mock.patch("gn3.api.gemma.queue_cmd") - def test_run_gemma_with_loco(self, - mock_queue_cmd, mock_redis): + def test_run_gemma_with_loco(self, mock_queue_cmd, mock_redis): """Test that gemma composes the command correctly with loco""" _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock()) mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" - response = self.app.post("/api/gemma/k-gwa-computation", json={ - "trait_filename": os.path.abspath(os.path.join( - os.path.dirname(__file__), - "test_data/" - )), - "geno_filename": "BXD_geno.txt.gz", - "values": ["X", "N/A", "X"], - "dataset_groupname": "BXD", - "trait_name": "Height", - "email": "me@me.com", - "dataset_name": "BXD", - "loco": "1,2,3,4,5,6" - }) + response = self.app.post("/api/gemma/k-gwa-computation", + json={ + "trait_filename": + os.path.abspath( + os.path.join( + os.path.dirname(__file__), + "test_data/")), + "geno_filename": + "BXD_geno.txt.gz", + "values": ["X", "N/A", "X"], + "dataset_groupname": + "BXD", + "trait_name": + "Height", + "email": + "me@me.com", + "dataset_name": + "BXD", + "loco": + "1,2,3,4,5,6" + }) mock_queue_cmd.called_with( conn=_redis_conn, email="me@me.com", @@ -130,10 +141,11 @@ class GemmaAPITest(unittest.TestCase): "/tmp/gn2/" "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")) self.assertEqual( - response.get_json(), - {"unique_id": 'my-unique-id', - "status": "queued", - "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"}) + response.get_json(), { + "unique_id": 'my-unique-id', + "status": "queued", + "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt" + }) @mock.patch("gn3.api.gemma.redis.Redis") def test_check_cmd_status(self, mock_redis): @@ -146,18 +158,15 @@ class GemmaAPITest(unittest.TestCase): "cmd%3A%3A2021-02-1217-3224-3224-1234"), follow_redirects=True) mock_hget.assert_called_once_with( - name="cmd::2021-02-1217-3224-3224-1234", - key="status") - self.assertEqual(response.get_json(), - {"status": "test"}) + name="cmd::2021-02-1217-3224-3224-1234", key="status") + self.assertEqual(response.get_json(), {"status": "test"}) @mock.patch("gn3.api.gemma.queue_cmd") @mock.patch("gn3.api.gemma.get_hash_of_files") @mock.patch("gn3.api.gemma.jsonfile_to_dict") @mock.patch("gn3.api.gemma.do_paths_exist") @mock.patch("gn3.api.gemma.redis.Redis") - def test_k_compute(self, mock_redis, mock_path_exist, - mock_json, mock_hash, + def test_k_compute(self, mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/k-compute/<token>""" mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py index b5ffbfd..2d2fbf9 100644 --- a/tests/unit/computations/test_gemma.py +++ b/tests/unit/computations/test_gemma.py @@ -12,8 +12,7 @@ class TestGemma(unittest.TestCase): def test_generate_pheno_txt_file(self): """Test that the pheno text file is generated correctly""" open_mock = mock.mock_open() - with mock.patch("gn3.computations.gemma.open", - open_mock, create=True): + with mock.patch("gn3.computations.gemma.open", open_mock, create=True): _file = generate_pheno_txt_file(tmpdir="/tmp", trait_filename="phenotype.txt", values=["x", "x", "BXD07 438.700"]) @@ -24,7 +23,8 @@ class TestGemma(unittest.TestCase): open_mock.return_value.write.assert_has_calls([ mock.call("NA\n"), mock.call("NA\n"), - mock.call("BXD07 438.700\n")]) + mock.call("BXD07 438.700\n") + ]) def test_generate_hash_of_string(self): """Test that a string is hashed correctly""" @@ -42,11 +42,11 @@ class TestGemma(unittest.TestCase): gemma_kwargs={ "geno_filename": "genofile.txt", "trait_filename": "test.txt", - "covar_filename": "genofile_snps.txt"}, + "covar_filename": "genofile_snps.txt" + }, output_file="/tmp/gn2/k_output_gUFhGu4rLG7k+CXLPk1OUg.txt", - ), - ("gemma-wrapper --json -- " - "-g genofile.txt -p " - "test.txt -a genofile_snps.txt " - "-gk > /tmp/gn2/" - "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt")) + ), ("gemma-wrapper --json -- " + "-g genofile.txt -p " + "test.txt -a genofile_snps.txt " + "-gk > /tmp/gn2/" + "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt")) |