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-rw-r--r--gn3/api/gemma.py1
-rw-r--r--gn3/computations/gemma.py30
-rw-r--r--tests/integration/test_gemma.py8
-rw-r--r--tests/unit/computations/test_gemma.py46
4 files changed, 81 insertions, 4 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index d82f5a5..d08c11b 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -12,6 +12,7 @@ from gn3.commands import queue_cmd
from gn3.commands import run_cmd
from gn3.file_utils import get_hash_of_files
from gn3.file_utils import jsonfile_to_dict
+from gn3.computations.gemma import compute_k_values
from gn3.computations.gemma import do_paths_exist
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 7b5f91d..3c6bd29 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -8,6 +8,7 @@ from typing import List
from typing import Optional
from typing import ValuesView
from gn3.commands import compose_gemma_cmd
+from gn3.file_utils import get_hash_of_files
def generate_hash_of_string(unhashed_str: str) -> str:
@@ -68,3 +69,32 @@ def generate_gemma_computation_cmd(
gemma_wrapper_kwargs=gemma_wrapper_kwargs,
gemma_kwargs=_kwargs,
gemma_args=["-gk", ">", output_file])
+
+
+# pylint: disable=R0913
+def generate_gemma_cmd(gemma_cmd: str,
+ output_dir: str,
+ token: str,
+ gemma_kwargs: Dict,
+ gemma_wrapper_kwargs: Dict = None,
+ chromosomes: str = None) -> Dict:
+ """Compute k values"""
+ _hash = get_hash_of_files(
+ [v for k, v in gemma_kwargs.items() if k in ["g", "p", "a", "c"]])
+ if chromosomes: # Only reached when calculating k-values
+ gemma_wrapper_kwargs = {"loco": f"--input {chromosomes}"}
+ _hash += f"-{generate_hash_of_string(chromosomes)[:6]}"
+ _output_filename = f"{_hash}-output.json"
+ return {
+ "output_file":
+ _output_filename,
+ "gemma_cmd":
+ compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd,
+ gemma_wrapper_kwargs=gemma_wrapper_kwargs,
+ gemma_kwargs=gemma_kwargs,
+ gemma_args=[
+ "-gk", ">",
+ (f"{output_dir}/"
+ f"{token}/{_output_filename}")
+ ])
+ }
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 822f088..f4ac685 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -162,7 +162,7 @@ class GemmaAPITest(unittest.TestCase):
self.assertEqual(response.get_json(), {"status": "test"})
@mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @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.redis.Redis")
@@ -195,7 +195,7 @@ class GemmaAPITest(unittest.TestCase):
})
@mock.patch("gn3.api.gemma.queue_cmd")
- @mock.patch("gn3.api.gemma.get_hash_of_files")
+ @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.redis.Redis")
@@ -223,9 +223,9 @@ class GemmaAPITest(unittest.TestCase):
"-g /tmp/test-data/genofile.txt "
"-p /tmp/test-data/phenofile.txt "
"-a /tmp/test-data/snpfile.txt "
- "-gk > /tmp/test-data/hash-k-output.json"))
+ "-gk > /tmp/test-data/hash-3R77Mz-k-output.json"))
self.assertEqual(response.get_json(), {
- "output_file": "hash-k-output.json",
+ "output_file": "hash-3R77Mz-k-output.json",
"status": "queued",
"unique_id": "my-unique-id"
})
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index 2d2fbf9..d3fb7aa 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -2,6 +2,7 @@
import unittest
from unittest import mock
+from gn3.computations.gemma import compute_k_values
from gn3.computations.gemma import generate_hash_of_string
from gn3.computations.gemma import generate_pheno_txt_file
from gn3.computations.gemma import generate_gemma_computation_cmd
@@ -50,3 +51,48 @@ class TestGemma(unittest.TestCase):
"test.txt -a genofile_snps.txt "
"-gk > /tmp/gn2/"
"k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))
+
+ @mock.patch("gn3.computations.gemma.get_hash_of_files")
+ def test_compute_k_values_without_loco(self, mock_get_hash):
+ """Test computing k valuse without loco"""
+ mock_get_hash.return_value = "my-hash"
+ self.assertEqual(
+ compute_k_values(gemma_cmd="gemma-wrapper",
+ output_dir="/tmp",
+ token="my-token",
+ gemma_kwargs={
+ "g": "genofile",
+ "p": "phenofile",
+ "a": "snpsfile"
+ }), {
+ "output_file":
+ "my-hash-k-output.json",
+ "gemma_cmd":
+ ("gemma-wrapper --json -- -g genofile "
+ "-p phenofile -a snpsfile "
+ "-gk > /tmp/my-token/my-hash-k-output.json")
+ })
+
+ @mock.patch("gn3.computations.gemma.get_hash_of_files")
+ def test_compute_k_values_with_loco(self, mock_get_hash):
+ """Test computing k valuse with loco"""
+ mock_get_hash.return_value = "my-hash"
+ self.assertEqual(
+ compute_k_values(gemma_cmd="gemma-wrapper",
+ output_dir="/tmp",
+ token="my-token",
+ chromosomes="1,2,3,4,5",
+ gemma_kwargs={
+ "g": "genofile",
+ "p": "phenofile",
+ "a": "snpsfile"
+ }), {
+ "output_file":
+ "my-hash-r+gF5a-k-output.json",
+ "gemma_cmd": ("gemma-wrapper --json "
+ "--loco --input 1,2,3,4,5 "
+ "-- -g genofile "
+ "-p phenofile -a snpsfile "
+ "-gk > /tmp/my-token/"
+ "my-hash-r+gF5a-k-output.json")
+ })