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authorBonfaceKilz2021-03-05 12:06:22 +0300
committerBonfaceKilz2021-03-08 21:09:58 +0300
commit5c56425d51ab6a6b4ffd6ec8f86121bd91ff5e63 (patch)
tree4bb947a5f3775cdefc492adede41e018694c654d /gn3/api/gemma.py
parent4cf5c29a06001577054b3548a24d895cf1911e13 (diff)
downloadgenenetwork3-5c56425d51ab6a6b4ffd6ec8f86121bd91ff5e63.tar.gz
Apply pep-8 formatting
Began using elpy's format code fn
Diffstat (limited to 'gn3/api/gemma.py')
-rw-r--r--gn3/api/gemma.py402
1 files changed, 211 insertions, 191 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!")