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-rw-r--r--gn3/api/gemma.py26
-rw-r--r--gn3/api/rqtl.py5
-rw-r--r--gn3/computations/gemma.py10
-rw-r--r--tests/integration/test_gemma.py20
4 files changed, 28 insertions, 33 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 6b0b20e..c862d91 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -12,7 +12,7 @@ from gn3.commands import run_cmd
from gn3.fs_helpers import cache_ipfs_file
from gn3.fs_helpers import jsonfile_to_dict
from gn3.computations.gemma import generate_gemma_cmd
-from gn3.computations.gemma import do_paths_exist
+from gn3.computations.gemma import assert_paths_exist
gemma = Blueprint("gemma", __name__)
@@ -55,8 +55,7 @@ traitfile, and snpsfile are extracted from a metadata.json file.
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
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
results = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
@@ -97,8 +96,7 @@ values.
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
results = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
@@ -235,8 +233,7 @@ def compute_gwa_with_loco_maf(k_filename, maf, token):
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {
"g": genofile,
"p": phenofile,
@@ -286,8 +283,7 @@ def compute_gwa_with_loco_covar(k_filename, maf, token):
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile, covarfile])
gemma_kwargs = {
"g": genofile,
"p": phenofile,
@@ -340,8 +336,7 @@ covars; lmm defaults to 9!
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
gemma_k_cmd = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
@@ -396,8 +391,7 @@ covars; lmm defaults to 9!
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
gemma_k_cmd = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
@@ -451,8 +445,7 @@ def compute_k_gwa_with_loco_only(chromosomes, maf, token):
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
gemma_k_cmd = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
@@ -509,8 +502,7 @@ def compute_k_gwa_with_loco_and_cavar(chromosomes, maf, token):
ipfs_file=_dict.get("geno"),
cache_dir=current_app.config.get('CACHEDIR')
)
- if not do_paths_exist([genofile, phenofile, snpsfile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile, snpsfile])
gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
gemma_k_cmd = generate_gemma_cmd(
gemma_cmd=current_app.config.get("GEMMA_"
diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index ae0110d..bfb191e 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -8,7 +8,7 @@ from flask import request
from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_mapping, \
process_rqtl_pairscan, process_perm_output
-from gn3.computations.gemma import do_paths_exist
+from gn3.computations.gemma import assert_paths_exist
rqtl = Blueprint("rqtl", __name__)
@@ -21,8 +21,7 @@ run the rqtl_wrapper script and return the results as JSON
genofile = request.form['geno_file']
phenofile = request.form['pheno_file']
- if not do_paths_exist([genofile, phenofile]):
- raise FileNotFoundError
+ assert_paths_exist([genofile, phenofile])
# Split kwargs by those with values and boolean ones that just convert to True/False
kwargs = ["covarstruct", "model", "method", "nperm", "scale", "control"]
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 03e1a76..5a2616b 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -1,4 +1,5 @@
"""Procedures related gemma computations"""
+import errno
import os
from base64 import b64encode
@@ -40,11 +41,14 @@ def generate_pheno_txt_file(trait_filename: str,
return f"{tmpdir}/gn2/{trait_filename}"
-def do_paths_exist(paths: ValuesView) -> bool:
- """Given a list of PATHS, return False if any of them do not exist."""
+def assert_paths_exist(paths: ValuesView) -> bool:
+ """Given a list of PATHS, throw error if any of them do not exist."""
for path in paths:
if not os.path.isfile(path):
- return False
+ if throw_error:
+ raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), path)
+ else:
+ return False
return True
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 79ddaca..53a1596 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -60,7 +60,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_k_compute(self, mock_ipfs_cache,
@@ -103,7 +103,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_k_compute_loco(self, mock_ipfs_cache,
@@ -147,7 +147,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_gwa_compute(self, mock_ipfs_cache,
@@ -198,7 +198,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_gwa_compute_with_covars(self, mock_ipfs_cache,
@@ -252,7 +252,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_gwa_compute_with_loco_only(self, mock_ipfs_cache,
@@ -305,7 +305,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_gwa_compute_with_loco_covars(self, mock_ipfs_cache,
@@ -360,7 +360,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_k_gwa_compute_without_loco_covars(self, mock_ipfs_cache,
@@ -416,7 +416,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_k_gwa_compute_with_covars_only(self, mock_ipfs_cache,
@@ -481,7 +481,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_k_gwa_compute_with_loco_only(self, mock_ipfs_cache,
@@ -547,7 +547,7 @@ class GemmaAPITest(unittest.TestCase):
@mock.patch("gn3.api.gemma.queue_cmd")
@mock.patch("gn3.computations.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.assert_paths_exist")
@mock.patch("gn3.api.gemma.redis.Redis")
@mock.patch("gn3.api.gemma.cache_ipfs_file")
def test_k_gwa_compute_with_loco_and_covar(self, mock_ipfs_cache,
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-21 22:29:07 +0000