Change behavior of do_paths_exist to actually throw useful error

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,