diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/api/gemma.py | 80 | ||||
| -rw-r--r-- | gn3/settings.py | 2 |
2 files changed, 61 insertions, 21 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py index 0f4b8e3..81e185d 100644 --- a/gn3/api/gemma.py +++ b/gn3/api/gemma.py @@ -9,6 +9,7 @@ from flask import request from gn3.commands import queue_cmd from gn3.commands import run_cmd +from gn3.file_utils import cache_ipfs_file from gn3.file_utils import jsonfile_to_dict from gn3.computations.gemma import generate_gemma_cmd from gn3.computations.gemma import do_paths_exist @@ -47,10 +48,13 @@ 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")) try: - genofile, phenofile, snpsfile = [ + phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps"] + for x in ["pheno", "snps"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR')) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} @@ -85,10 +89,14 @@ values. 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 = [ + phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps"] + for x in ["pheno", "snps"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} @@ -123,10 +131,14 @@ def compute_gwa(k_filename, token): 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 = [ + phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps"] + for x in ["pheno", "snps"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) gemma_kwargs = { "g": genofile, "p": phenofile, @@ -166,10 +178,14 @@ def compute_gwa_with_covar(k_filename, token): 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 = [ + phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps", "covar"] + for x in ["pheno", "snps", "covar"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) gemma_kwargs = { "g": genofile, "p": phenofile, @@ -211,10 +227,14 @@ def compute_gwa_with_loco_maf(k_filename, maf, token): 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 = [ + phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps"] + for x in ["pheno", "snps"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = { @@ -258,10 +278,14 @@ def compute_gwa_with_loco_covar(k_filename, maf, token): 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 = [ + phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps", "covar"] + for x in ["pheno", "snps", "covar"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]): raise FileNotFoundError gemma_kwargs = { @@ -308,10 +332,14 @@ covars; lmm defaults to 9! 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 = [ + phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps"] + for x in ["pheno", "snps"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} @@ -360,10 +388,14 @@ covars; lmm defaults to 9! 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 = [ + phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps", "covar"] + for x in ["pheno", "snps", "covar"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} @@ -411,10 +443,14 @@ def compute_k_gwa_with_loco_only(chromosomes, maf, token): 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 = [ + phenofile, snpsfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps"] + for x in ["pheno", "snps"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} @@ -465,10 +501,14 @@ def compute_k_gwa_with_loco_and_cavar(chromosomes, maf, token): 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 = [ + phenofile, snpsfile, covarfile = [ os.path.join(working_dir, _dict.get(x)) - for x in ["geno", "pheno", "snps", "covar"] + for x in ["pheno", "snps", "covar"] ] + genofile = cache_ipfs_file( + ipfs_file=_dict.get("geno"), + cache_dir=current_app.config.get('CACHEDIR') + ) if not do_paths_exist([genofile, phenofile, snpsfile]): raise FileNotFoundError gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile} diff --git a/gn3/settings.py b/gn3/settings.py index c09e6e0..2836581 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -6,7 +6,7 @@ import os BCRYPT_SALT = "$2b$12$mxLvu9XRLlIaaSeDxt8Sle" # Change this! DATA_DIR = "" GEMMA_WRAPPER_CMD = os.environ.get("GEMMA_WRAPPER", "gemma-wrapper") -GENODIR = "" +CACHEDIR = "" REDIS_URI = "redis://localhost:6379/0" REDIS_JOB_QUEUE = "GN3::job-queue" TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) |