diff options
| -rw-r--r-- | gn3/api/gemma.py | 80 | ||||
| -rw-r--r-- | gn3/settings.py | 2 | ||||
| -rw-r--r-- | tests/integration/test_gemma.py | 171 |
3 files changed, 191 insertions, 62 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()) diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py index a04b0df..1eef3f9 100644 --- a/tests/integration/test_gemma.py +++ b/tests/integration/test_gemma.py @@ -19,6 +19,7 @@ class MockRedis: class GemmaAPITest(unittest.TestCase): """Test cases for the Gemma API""" + def setUp(self): self.app = create_app({ "GENODIR": @@ -57,9 +58,16 @@ class GemmaAPITest(unittest.TestCase): @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, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_k_compute(self, mock_ipfs_cache, + mock_redis, + mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/k-compute/<token>""" + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" @@ -75,7 +83,8 @@ class GemmaAPITest(unittest.TestCase): email=None, job_queue='GN3::job-queue', cmd=("gemma-wrapper --json -- " - "-g /tmp/test-data/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/test-data/phenofile.txt " "-a /tmp/test-data/snpfile.txt " "-gk > /tmp/test-data/hash-output.json")) @@ -91,9 +100,15 @@ class GemmaAPITest(unittest.TestCase): @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_loco(self, mock_redis, mock_path_exist, mock_json, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_k_compute_loco(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/k-compute/loco/<chromosomes>/<token>""" + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" @@ -111,7 +126,8 @@ class GemmaAPITest(unittest.TestCase): job_queue='GN3::job-queue', cmd=("gemma-wrapper --json --loco " "1,2,3,4,5,6 -- " - "-g /tmp/test-data/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/test-data/phenofile.txt " "-a /tmp/test-data/snpfile.txt " "-gk > /tmp/test-data/hash-3R77Mz-output.json")) @@ -127,9 +143,15 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute(self, mock_redis, mock_path_exist, mock_json, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_gwa_compute(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/gwa-compute/<k-inputfile>/<token>""" + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" @@ -142,7 +164,9 @@ class GemmaAPITest(unittest.TestCase): response = self.app.post(("/api/gemma/gwa-compute/hash-k-output.json/" "my-token")) mock_hash.assert_called_once_with([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8' + 'G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]) mock_queue_cmd.assert_called_once_with( @@ -151,7 +175,9 @@ class GemmaAPITest(unittest.TestCase): job_queue='GN3::job-queue', cmd=("gemma-wrapper --json " "--input /tmp/my-token/hash-k-output.json" - " -- -g /tmp/my-token/genofile.txt " + " -- " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-lmm 9 -gk > /tmp/my-token/hash-output.json")) @@ -167,9 +193,15 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_with_covars(self, mock_redis, mock_path_exist, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_gwa_compute_with_covars(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/gwa-compute/covars/<k-inputfile>/<token>""" + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" @@ -185,7 +217,9 @@ class GemmaAPITest(unittest.TestCase): "covars/hash-k-output.json/" "my-token")) mock_hash.assert_called_once_with([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8' + 'G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt', '/tmp/my-token/covarfile.txt' ]) mock_queue_cmd.assert_called_once_with( @@ -194,7 +228,8 @@ class GemmaAPITest(unittest.TestCase): job_queue="GN3::job-queue", cmd=("gemma-wrapper --json --input " "/tmp/my-token/hash-k-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-c /tmp/my-token/covarfile.txt -lmm 9 " @@ -211,16 +246,21 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_with_loco_only(self, mock_redis, mock_path_exist, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_gwa_compute_with_loco_only(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/gwa-compute/<k-inputfile>/loco/maf/<maf>/<token> """ + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { - "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", } @@ -229,7 +269,9 @@ class GemmaAPITest(unittest.TestCase): "hash-output.json/loco/" "maf/21/my-token")) mock_hash.assert_called_once_with([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]) mock_queue_cmd.assert_called_once_with( @@ -238,7 +280,8 @@ class GemmaAPITest(unittest.TestCase): job_queue='GN3::job-queue', cmd=("gemma-wrapper --json --loco --input " "/tmp/my-token/hash-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-lmm 9 -maf 21.0 " @@ -255,17 +298,22 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_with_loco_covars(self, mock_redis, mock_path_exist, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_gwa_compute_with_loco_covars(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/gwa-compute/<k-inputfile>/loco/covars/maf/<maf>/<token> """ + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { - "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", "covar": "covarfile.txt", @@ -275,7 +323,8 @@ class GemmaAPITest(unittest.TestCase): "hash-output.json/loco/" "covars/maf/21/my-token")) mock_hash.assert_called_once_with([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt', "/tmp/my-token/covarfile.txt" ]) mock_queue_cmd.assert_called_once_with( @@ -284,7 +333,8 @@ class GemmaAPITest(unittest.TestCase): job_queue='GN3::job-queue', cmd=("gemma-wrapper --json --loco --input " "/tmp/my-token/hash-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-c /tmp/my-token/covarfile.txt " @@ -302,24 +352,30 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_without_loco_covars(self, mock_redis, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_k_gwa_compute_without_loco_covars(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/k-gwa-compute/<token> """ + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { - "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", } mock_hash.return_value = "hash" response = self.app.post(("/api/gemma/k-gwa-compute/" "my-token")) mock_hash.assert_called_with([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]) mock_queue_cmd.assert_called_once_with( @@ -327,13 +383,15 @@ class GemmaAPITest(unittest.TestCase): email=None, job_queue='GN3::job-queue', cmd=("gemma-wrapper --json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-gk > /tmp/my-token/hash-output.json " "&& gemma-wrapper --json " "--input /tmp/my-token/hash-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt -lmm 9 " "-gk > /tmp/my-token/hash-output.json")) @@ -349,17 +407,22 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_with_covars_only(self, mock_redis, mock_path_exist, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_k_gwa_compute_with_covars_only(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/k-gwa-compute/covars/<token> """ + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { - "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", "covar": "covarfile.txt", @@ -368,11 +431,13 @@ class GemmaAPITest(unittest.TestCase): response = self.app.post("/api/gemma/k-gwa-compute/covars/my-token") mock_hash.assert_has_calls([ mock.call([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]), mock.call([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt', "/tmp/my-token/covarfile.txt" ]) ]) @@ -381,13 +446,15 @@ class GemmaAPITest(unittest.TestCase): email=None, job_queue='GN3::job-queue', cmd=("gemma-wrapper --json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-gk > /tmp/my-token/hash-output.json " "&& gemma-wrapper --json " "--input /tmp/my-token/hash-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-c /tmp/my-token/covarfile.txt -lmm 9 " @@ -404,17 +471,22 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_with_loco_only(self, mock_redis, mock_path_exist, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_k_gwa_compute_with_loco_only(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /gemma/k-gwa-compute/loco/<chromosomes>/maf/<maf>/<token> """ + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { - "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", } @@ -423,11 +495,15 @@ class GemmaAPITest(unittest.TestCase): "/api/gemma/k-gwa-compute/loco/1%2C2%2C3%2C4/maf/9/my-token") mock_hash.assert_has_calls([ mock.call([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]), mock.call([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]), ]) @@ -436,13 +512,15 @@ class GemmaAPITest(unittest.TestCase): email=None, job_queue='GN3::job-queue', cmd=("gemma-wrapper --json --loco 1,2,3,4 -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-gk > /tmp/my-token/hash-+O9bus-output.json " "&& gemma-wrapper --json --loco " "--input /tmp/my-token/hash-+O9bus-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt -maf 9.0 -lmm 9 " "-gk > /tmp/my-token/hash-output.json")) @@ -458,17 +536,22 @@ class GemmaAPITest(unittest.TestCase): @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_gwa_compute_with_loco_and_covar(self, mock_redis, + @mock.patch("gn3.api.gemma.cache_ipfs_file") + def test_k_gwa_compute_with_loco_and_covar(self, mock_ipfs_cache, + mock_redis, mock_path_exist, mock_json, mock_hash, mock_queue_cmd): """Test /k-gwa-compute/covars/loco/<chromosomes>/maf/<maf>/<token> """ + mock_ipfs_cache.return_value = ("/tmp/cache/" + "QmQPeNsJPyVWPFDVHb" + "77w8G42Fvo15z4bG2X8D2GhfbSXc/" + "genotype.txt") mock_path_exist.return_value, _redis_conn = True, mock.MagicMock() mock_redis.return_value = _redis_conn mock_queue_cmd.return_value = "my-unique-id" mock_json.return_value = { - "geno": "genofile.txt", "pheno": "phenofile.txt", "snps": "snpfile.txt", "covar": "covarfile.txt", @@ -478,11 +561,15 @@ class GemmaAPITest(unittest.TestCase): "loco/1%2C2%2C3%2C4/maf/9/my-token")) mock_hash.assert_has_calls([ mock.call([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt' ]), mock.call([ - '/tmp/my-token/genofile.txt', '/tmp/my-token/phenofile.txt', + ('/tmp/cache/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc/' + 'genotype.txt'), + '/tmp/my-token/phenofile.txt', '/tmp/my-token/snpfile.txt', '/tmp/my-token/covarfile.txt' ]), ]) @@ -491,13 +578,15 @@ class GemmaAPITest(unittest.TestCase): email=None, job_queue='GN3::job-queue', cmd=("gemma-wrapper --json --loco 1,2,3,4 -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-gk > /tmp/my-token/hash-+O9bus-output.json " "&& gemma-wrapper --json --loco " "--input /tmp/my-token/hash-+O9bus-output.json -- " - "-g /tmp/my-token/genofile.txt " + "-g /tmp/cache/QmQPeNsJPyVWPFD" + "VHb77w8G42Fvo15z4bG2X8D2GhfbSXc/genotype.txt " "-p /tmp/my-token/phenofile.txt " "-a /tmp/my-token/snpfile.txt " "-c /tmp/my-token/covarfile.txt -maf 9.0 -lmm 9 " |