Apply pep-8 formatting

Began using elpy's format code fn

4 files changed, 294 insertions, 268 deletions

diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index a341f62..d82f5a5 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -24,8 +24,7 @@ gemma = Blueprint("gemma", __name__)
 def get_version():
     """Display the installed version of gemma-wrapper"""
     gemma_cmd = current_app.config["GEMMA_WRAPPER_CMD"]
-    return jsonify(
-        run_cmd(f"{gemma_cmd} -v | head -n 1"))
+    return jsonify(run_cmd(f"{gemma_cmd} -v | head -n 1"))
 
 
 # This is basically extracted from genenetwork2
@@ -39,19 +38,21 @@ file output is returned.
     """
     data = request.get_json()
     app_defaults = current_app.config
-    __hash = generate_hash_of_string(
-        f"{data.get('genofile_name')}_"
-        ''.join(data.get("values", "")))
+    __hash = generate_hash_of_string(f"{data.get('genofile_name')}_"
+                                     ''.join(data.get("values", "")))
     gemma_kwargs = {
-        "geno_filename": os.path.join(app_defaults.get("GENODIR"), "bimbam",
-                                      f"{data.get('geno_filename')}"),
-        "trait_filename": generate_pheno_txt_file(
+        "geno_filename":
+        os.path.join(app_defaults.get("GENODIR"), "bimbam",
+                     f"{data.get('geno_filename')}"),
+        "trait_filename":
+        generate_pheno_txt_file(
             tmpdir=app_defaults.get("TMPDIR"),
             values=data.get("values"),
             # Generate this file on the fly!
             trait_filename=(f"{data.get('dataset_groupname')}_"
                             f"{data.get('trait_name')}_"
-                            f"{__hash}.txt"))}
+                            f"{__hash}.txt"))
+    }
     gemma_wrapper_kwargs = {}
     if data.get("loco"):
         gemma_wrapper_kwargs["loco"] = f"--input {data.get('loco')}"
@@ -74,14 +75,14 @@ file output is returned.
     if not all([k_computation_cmd, gwa_cmd]):
         return jsonify(status=128,
                        error="Unable to generate cmds for computation!"), 500
-    return jsonify(
-        unique_id=queue_cmd(conn=redis.Redis(),
-                            email=data.get("email"),
-                            job_queue=app_defaults.get("REDIS_JOB_QUEUE"),
-                            cmd=f"{k_computation_cmd} && {gwa_cmd}"),
-        status="queued",
-        output_file=(f"{data.get('dataset_name')}_GWA_"
-                     f"{__hash}.txt"))
+    return jsonify(unique_id=queue_cmd(
+        conn=redis.Redis(),
+        email=data.get("email"),
+        job_queue=app_defaults.get("REDIS_JOB_QUEUE"),
+        cmd=f"{k_computation_cmd} && {gwa_cmd}"),
+                   status="queued",
+                   output_file=(f"{data.get('dataset_name')}_GWA_"
+                                f"{__hash}.txt"))
 
 
 @gemma.route("/status/<unique_id>", methods=["GET"])
@@ -90,8 +91,7 @@ def check_cmd_status(unique_id):
 gemma endpoints, return the status of the command
 
     """
-    status = redis.Redis().hget(name=unique_id,
-                                key="status")
+    status = redis.Redis().hget(name=unique_id, key="status")
     if not status:
         return jsonify(status=128,
                        error="The unique id you used does not exist!"), 500
@@ -105,39 +105,40 @@ and return <hash-of-inputs>.json with a UNIQUE-ID of the job. The genofile,
 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"))
+    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 = [os.path.join(working_dir,
-                                                      _dict.get(x))
-                                         for x in ["geno", "pheno", "snps"]]
+        genofile, phenofile, snpsfile = [
+            os.path.join(working_dir, _dict.get(x))
+            for x in ["geno", "pheno", "snps"]
+        ]
         if not do_paths_exist([genofile, phenofile, snpsfile]):
             raise FileNotFoundError
         gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
         _hash = get_hash_of_files([genofile, phenofile, snpsfile])
         k_output_filename = f"{_hash}-k-output.json"
-        return jsonify(
-            unique_id=queue_cmd(
-                conn=redis.Redis(),
-                email=(request.get_json() or {}).get('email'),
-                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
-                cmd=compose_gemma_cmd(
-                    gemma_wrapper_cmd=current_app.config.get("GEMMA_"
-                                                             "WRAPPER_CMD"),
-                    gemma_wrapper_kwargs=None,
-                    gemma_kwargs=gemma_kwargs,
-                    gemma_args=["-gk", ">",
-                                (f"{current_app.config.get('TMPDIR')}/"
-                                 f"{token}/{k_output_filename}")])),
-            status="queued",
-            output_file=k_output_filename)
+        return jsonify(unique_id=queue_cmd(
+            conn=redis.Redis(),
+            email=(request.get_json() or {}).get('email'),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            cmd=compose_gemma_cmd(gemma_wrapper_cmd=current_app.config.get(
+                "GEMMA_"
+                "WRAPPER_CMD"),
+                                  gemma_wrapper_kwargs=None,
+                                  gemma_kwargs=gemma_kwargs,
+                                  gemma_args=[
+                                      "-gk", ">",
+                                      (f"{current_app.config.get('TMPDIR')}/"
+                                       f"{token}/{k_output_filename}")
+                                  ])),
+                       status="queued",
+                       output_file=k_output_filename)
     # pylint: disable=W0703
     except Exception:
-        return jsonify(status=128,
-                       # use better message
-                       message="Metadata file non-existent!")
+        return jsonify(
+            status=128,
+            # use better message
+            message="Metadata file non-existent!")
 
 
 @gemma.route("/k-compute/loco/<chromosomes>/<token>", methods=["POST"])
@@ -146,39 +147,40 @@ def compute_k_loco(chromosomes, token):
 values.
 
     """
-    working_dir = os.path.join(current_app.config.get("TMPDIR"),
-                               token)
-    _dict = jsonfile_to_dict(os.path.join(working_dir,
-                                          "metadata.json"))
+    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 = [os.path.join(working_dir,
-                                                      _dict.get(x))
-                                         for x in ["geno", "pheno", "snps"]]
+        genofile, phenofile, snpsfile = [
+            os.path.join(working_dir, _dict.get(x))
+            for x in ["geno", "pheno", "snps"]
+        ]
         if not do_paths_exist([genofile, phenofile, snpsfile]):
             raise FileNotFoundError
         gemma_kwargs = {"g": genofile, "p": phenofile, "a": snpsfile}
         _hash = get_hash_of_files([genofile, phenofile, snpsfile])
         k_output_filename = f"{_hash}-k-output.json"
-        return jsonify(
-            unique_id=queue_cmd(
-                conn=redis.Redis(),
-                email=(request.get_json() or {}).get('email'),
-                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
-                cmd=compose_gemma_cmd(
-                    gemma_wrapper_cmd=current_app.config.get("GEMMA_"
-                                                             "WRAPPER_CMD"),
-                    gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"},
-                    gemma_kwargs=gemma_kwargs,
-                    gemma_args=["-gk", ">",
-                                (f"{current_app.config.get('TMPDIR')}/"
-                                 f"{token}/{k_output_filename}")])),
-            status="queued",
-            output_file=k_output_filename)
+        return jsonify(unique_id=queue_cmd(
+            conn=redis.Redis(),
+            email=(request.get_json() or {}).get('email'),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            cmd=compose_gemma_cmd(
+                gemma_wrapper_cmd=current_app.config.get("GEMMA_"
+                                                         "WRAPPER_CMD"),
+                gemma_wrapper_kwargs={"loco": f"--input {chromosomes}"},
+                gemma_kwargs=gemma_kwargs,
+                gemma_args=[
+                    "-gk", ">",
+                    (f"{current_app.config.get('TMPDIR')}/"
+                     f"{token}/{k_output_filename}")
+                ])),
+                       status="queued",
+                       output_file=k_output_filename)
     # pylint: disable=W0703
     except Exception:
-        return jsonify(status=128,
-                       # use better message
-                       message="Metadata file non-existent!")
+        return jsonify(
+            status=128,
+            # use better message
+            message="Metadata file non-existent!")
 
 
 @gemma.route("/gwa-compute/<k_filename>/<token>", methods=["POST"])
@@ -186,41 +188,46 @@ def compute_gwa(k_filename, token):
     """Compute GWA values. No loco no covariates provided.
 
     """
-    working_dir = os.path.join(current_app.config.get("TMPDIR"),
-                               token)
-    _dict = jsonfile_to_dict(os.path.join(working_dir,
-                                          "metadata.json"))
+    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 = [
-            os.path.join(working_dir,
-                         _dict.get(x))
-            for x in ["geno", "pheno", "snps"]]
-        gemma_kwargs = {"g": genofile, "p": phenofile,
-                        "a": snpsfile, "lmm": _dict.get("lmm", 9)}
+            os.path.join(working_dir, _dict.get(x))
+            for x in ["geno", "pheno", "snps"]
+        ]
+        gemma_kwargs = {
+            "g": genofile,
+            "p": phenofile,
+            "a": snpsfile,
+            "lmm": _dict.get("lmm", 9)
+        }
         _hash = get_hash_of_files([genofile, phenofile, snpsfile])
         _output_filename = f"{_hash}-gwa-output.json"
-        return jsonify(
-            unique_id=queue_cmd(
-                conn=redis.Redis(),
-                email=(request.get_json() or {}).get('email'),
-                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
-                cmd=compose_gemma_cmd(
-                    gemma_wrapper_cmd=current_app.config.get("GEMMA_"
-                                                             "WRAPPER_CMD"),
-                    gemma_wrapper_kwargs={
-                        "input": os.path.join(working_dir, k_filename)
-                    },
-                    gemma_kwargs=gemma_kwargs,
-                    gemma_args=["gk", ">",
-                                (f"{current_app.config.get('TMPDIR')}/"
-                                 f"{token}/{_output_filename}")])),
-            status="queued",
-            output_file=_output_filename)
+        return jsonify(unique_id=queue_cmd(
+            conn=redis.Redis(),
+            email=(request.get_json() or {}).get('email'),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            cmd=compose_gemma_cmd(gemma_wrapper_cmd=current_app.config.get(
+                "GEMMA_"
+                "WRAPPER_CMD"),
+                                  gemma_wrapper_kwargs={
+                                      "input":
+                                      os.path.join(working_dir, k_filename)
+                                  },
+                                  gemma_kwargs=gemma_kwargs,
+                                  gemma_args=[
+                                      "gk", ">",
+                                      (f"{current_app.config.get('TMPDIR')}/"
+                                       f"{token}/{_output_filename}")
+                                  ])),
+                       status="queued",
+                       output_file=_output_filename)
     # pylint: disable=W0703
     except Exception:
-        return jsonify(status=128,
-                       # use better message
-                       message="Metadata file non-existent!")
+        return jsonify(
+            status=128,
+            # use better message
+            message="Metadata file non-existent!")
 
 
 @gemma.route("/gwa-compute/covars/<k_filename>/<token>", methods=["POST"])
@@ -228,42 +235,47 @@ def compute_gwa_with_covar(k_filename, token):
     """Compute GWA values. Covariates provided.
 
     """
-    working_dir = os.path.join(current_app.config.get("TMPDIR"),
-                               token)
-    _dict = jsonfile_to_dict(os.path.join(working_dir,
-                                          "metadata.json"))
+    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 = [
-            os.path.join(working_dir,
-                         _dict.get(x))
-            for x in ["geno", "pheno", "snps", "covar"]]
-        gemma_kwargs = {"g": genofile, "p": phenofile,
-                        "a": snpsfile, "c": covarfile,
-                        "lmm": _dict.get("lmm", 9)}
+            os.path.join(working_dir, _dict.get(x))
+            for x in ["geno", "pheno", "snps", "covar"]
+        ]
+        gemma_kwargs = {
+            "g": genofile,
+            "p": phenofile,
+            "a": snpsfile,
+            "c": covarfile,
+            "lmm": _dict.get("lmm", 9)
+        }
         _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile])
         _output_filename = f"{_hash}-gwa-output.json"
-        return jsonify(
-            unique_id=queue_cmd(
-                conn=redis.Redis(),
-                email=(request.get_json() or {}).get('email'),
-                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
-                cmd=compose_gemma_cmd(
-                    gemma_wrapper_cmd=current_app.config.get("GEMMA_"
-                                                             "WRAPPER_CMD"),
-                    gemma_wrapper_kwargs={
-                        "input": os.path.join(working_dir, k_filename)
-                    },
-                    gemma_kwargs=gemma_kwargs,
-                    gemma_args=["-gk", ">",
-                                (f"{current_app.config.get('TMPDIR')}/"
-                                 f"{token}/{_output_filename}")])),
-            status="queued",
-            output_file=_output_filename)
+        return jsonify(unique_id=queue_cmd(
+            conn=redis.Redis(),
+            email=(request.get_json() or {}).get('email'),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            cmd=compose_gemma_cmd(gemma_wrapper_cmd=current_app.config.get(
+                "GEMMA_"
+                "WRAPPER_CMD"),
+                                  gemma_wrapper_kwargs={
+                                      "input":
+                                      os.path.join(working_dir, k_filename)
+                                  },
+                                  gemma_kwargs=gemma_kwargs,
+                                  gemma_args=[
+                                      "-gk", ">",
+                                      (f"{current_app.config.get('TMPDIR')}/"
+                                       f"{token}/{_output_filename}")
+                                  ])),
+                       status="queued",
+                       output_file=_output_filename)
     # pylint: disable=W0703
     except Exception:
-        return jsonify(status=128,
-                       # use better message
-                       message="Metadata file non-existent!")
+        return jsonify(
+            status=128,
+            # use better message
+            message="Metadata file non-existent!")
 
 
 @gemma.route("/gwa-compute/<k_filename>/loco/maf/<maf>/<token>",
@@ -272,45 +284,49 @@ def compute_gwa_with_loco_maf(k_filename, maf, token):
     """Compute GWA values. No Covariates provided. Only loco and maf vals given.
 
     """
-    working_dir = os.path.join(current_app.config.get("TMPDIR"),
-                               token)
-    _dict = jsonfile_to_dict(os.path.join(working_dir,
-                                          "metadata.json"))
+    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 = [
-            os.path.join(working_dir,
-                         _dict.get(x))
-            for x in ["geno", "pheno", "snps"]]
+            os.path.join(working_dir, _dict.get(x))
+            for x in ["geno", "pheno", "snps"]
+        ]
         if not do_paths_exist([genofile, phenofile, snpsfile]):
             raise FileNotFoundError
-        gemma_kwargs = {"g": genofile, "p": phenofile,
-                        "a": snpsfile, "lmm": _dict.get("lmm", 9),
-                        'maf': float(maf)}
+        gemma_kwargs = {
+            "g": genofile,
+            "p": phenofile,
+            "a": snpsfile,
+            "lmm": _dict.get("lmm", 9),
+            'maf': float(maf)
+        }
         _hash = get_hash_of_files([genofile, phenofile, snpsfile])
         _output_filename = f"{_hash}-gwa-output.json"
-        return jsonify(
-            unique_id=queue_cmd(
-                conn=redis.Redis(),
-                email=(request.get_json() or {}).get('email'),
-                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
-                cmd=compose_gemma_cmd(
-                    gemma_wrapper_cmd=current_app.config.get("GEMMA_"
-                                                             "WRAPPER_CMD"),
-                    gemma_wrapper_kwargs={
-                        "loco": ("--input "
-                                 f"{os.path.join(working_dir, k_filename)}")
-                    },
-                    gemma_kwargs=gemma_kwargs,
-                    gemma_args=["-gk", ">",
-                                (f"{current_app.config.get('TMPDIR')}/"
-                                 f"{token}/{_output_filename}")])),
-            status="queued",
-            output_file=_output_filename)
+        return jsonify(unique_id=queue_cmd(
+            conn=redis.Redis(),
+            email=(request.get_json() or {}).get('email'),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            cmd=compose_gemma_cmd(
+                gemma_wrapper_cmd=current_app.config.get("GEMMA_"
+                                                         "WRAPPER_CMD"),
+                gemma_wrapper_kwargs={
+                    "loco": ("--input "
+                             f"{os.path.join(working_dir, k_filename)}")
+                },
+                gemma_kwargs=gemma_kwargs,
+                gemma_args=[
+                    "-gk", ">",
+                    (f"{current_app.config.get('TMPDIR')}/"
+                     f"{token}/{_output_filename}")
+                ])),
+                       status="queued",
+                       output_file=_output_filename)
     # pylint: disable=W0703
     except Exception:
-        return jsonify(status=128,
-                       # use better message
-                       message="Metadata file non-existent!")
+        return jsonify(
+            status=128,
+            # use better message
+            message="Metadata file non-existent!")
 
 
 @gemma.route("/gwa-compute/<k_filename>/loco/covariates/maf/<maf>/<token>",
@@ -319,43 +335,47 @@ def compute_gwa_with_loco_covar(k_filename, maf, token):
     """Compute GWA values. No Covariates provided. Only loco and maf vals given.
 
     """
-    working_dir = os.path.join(current_app.config.get("TMPDIR"),
-                               token)
-    _dict = jsonfile_to_dict(os.path.join(working_dir,
-                                          "metadata.json"))
+    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 = [
-            os.path.join(working_dir,
-                         _dict.get(x))
-            for x in ["geno", "pheno", "snps", "covar"]]
+            os.path.join(working_dir, _dict.get(x))
+            for x in ["geno", "pheno", "snps", "covar"]
+        ]
         if not do_paths_exist([genofile, phenofile, snpsfile, covarfile]):
             raise FileNotFoundError
-        gemma_kwargs = {"g": genofile, "p": phenofile,
-                        "a": snpsfile, "c": covarfile,
-                        "lmm": _dict.get("lmm", 9),
-                        "maf": float(maf)}
+        gemma_kwargs = {
+            "g": genofile,
+            "p": phenofile,
+            "a": snpsfile,
+            "c": covarfile,
+            "lmm": _dict.get("lmm", 9),
+            "maf": float(maf)
+        }
         _hash = get_hash_of_files([genofile, phenofile, snpsfile, covarfile])
         _output_filename = f"{_hash}-gwa-output.json"
-        return jsonify(
-            unique_id=queue_cmd(
-                conn=redis.Redis(),
-                email=(request.get_json() or {}).get('email'),
-                job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
-                cmd=compose_gemma_cmd(
-                    gemma_wrapper_cmd=current_app.config.get("GEMMA_"
-                                                             "WRAPPER_CMD"),
-                    gemma_wrapper_kwargs={
-                        "loco": ("--input "
-                                 f"{os.path.join(working_dir, k_filename)}")
-                    },
-                    gemma_kwargs=gemma_kwargs,
-                    gemma_args=["-gk", ">",
-                                (f"{current_app.config.get('TMPDIR')}/"
-                                 f"{token}/{_output_filename}")])),
-            status="queued",
-            output_file=_output_filename)
+        return jsonify(unique_id=queue_cmd(
+            conn=redis.Redis(),
+            email=(request.get_json() or {}).get('email'),
+            job_queue=current_app.config.get("REDIS_JOB_QUEUE"),
+            cmd=compose_gemma_cmd(
+                gemma_wrapper_cmd=current_app.config.get("GEMMA_"
+                                                         "WRAPPER_CMD"),
+                gemma_wrapper_kwargs={
+                    "loco": ("--input "
+                             f"{os.path.join(working_dir, k_filename)}")
+                },
+                gemma_kwargs=gemma_kwargs,
+                gemma_args=[
+                    "-gk", ">",
+                    (f"{current_app.config.get('TMPDIR')}/"
+                     f"{token}/{_output_filename}")
+                ])),
+                       status="queued",
+                       output_file=_output_filename)
     # pylint: disable=W0703
     except Exception:
-        return jsonify(status=128,
-                       # use better message
-                       message="Metadata file non-existent!")
+        return jsonify(
+            status=128,
+            # use better message
+            message="Metadata file non-existent!")
diff --git a/gn3/computations/gemma.py b/gn3/computations/gemma.py
index 7ee70b0..7b5f91d 100644
--- a/gn3/computations/gemma.py
+++ b/gn3/computations/gemma.py
@@ -49,9 +49,7 @@ def do_paths_exist(paths: ValuesView) -> bool:
 
 
 def generate_gemma_computation_cmd(
-        gemma_cmd: str,
-        gemma_kwargs: Dict[str, str],
-        output_file: str,
+        gemma_cmd: str, gemma_kwargs: Dict[str, str], output_file: str,
         gemma_wrapper_kwargs: Dict[str, str]) -> Optional[str]:
     """Create a computation cmd"""
     geno_filename = gemma_kwargs.get("geno_filename", "")
@@ -69,5 +67,4 @@ def generate_gemma_computation_cmd(
     return compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd,
                              gemma_wrapper_kwargs=gemma_wrapper_kwargs,
                              gemma_kwargs=_kwargs,
-                             gemma_args=["-gk", ">",
-                                         output_file])
+                             gemma_args=["-gk", ">", output_file])
diff --git a/tests/integration/test_gemma.py b/tests/integration/test_gemma.py
index 6d2116b..822f088 100644
--- a/tests/integration/test_gemma.py
+++ b/tests/integration/test_gemma.py
@@ -21,19 +21,21 @@ class GemmaAPITest(unittest.TestCase):
     """Test cases for the Gemma API"""
     def setUp(self):
         self.app = create_app({
-            "GENODIR": os.path.abspath(
-                os.path.join(os.path.dirname(__file__),
-                             "test_data/")),
-            "REDIS_JOB_QUEUE": "GN3::job-queue",
-            "GEMMA_WRAPPER_CMD": "gemma-wrapper"}).test_client()
+            "GENODIR":
+            os.path.abspath(
+                os.path.join(os.path.dirname(__file__), "test_data/")),
+            "REDIS_JOB_QUEUE":
+            "GN3::job-queue",
+            "GEMMA_WRAPPER_CMD":
+            "gemma-wrapper"
+        }).test_client()
 
     @mock.patch("gn3.api.gemma.run_cmd")
     def test_get_version(self, mock_run_cmd):
         """Test that the correct response is returned"""
         mock_run_cmd.return_value = {"status": 0, "output": "v1.9"}
         response = self.app.get("/api/gemma/version", follow_redirects=True)
-        self.assertEqual(response.get_json(),
-                         {"status": 0, "output": "v1.9"})
+        self.assertEqual(response.get_json(), {"status": 0, "output": "v1.9"})
         self.assertEqual(response.status_code, 200)
 
     @mock.patch("gn3.api.gemma.redis.Redis")
@@ -59,60 +61,69 @@ class GemmaAPITest(unittest.TestCase):
              "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt")
         ]
         mock_queue_cmd.return_value = "my-unique-id"
-        response = self.app.post("/api/gemma/k-gwa-computation", json={
-            "trait_filename": "BXD.txt",
-            "geno_filename": "BXD_geno",
-            "values": ["X", "N/A", "X"],
-            "dataset_groupname": "BXD",
-            "trait_name": "Height",
-            "email": "me@me.com",
-            "dataset_name": "BXD"
-        })
-        mock_queue_cmd.assert_has_calls(
-            [mock.call(conn=_redis_conn,
-                       email="me@me.com",
-                       job_queue="GN3::job-queue",
-                       cmd=("gemma-wrapper --json -- -g "
-                            "genofile.txt -p test.txt "
-                            "-a genofile_snps.txt -gk > "
-                            "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
-                            "&& gemma-wrapper --json --input "
-                            "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
-                            " -- -a genofile_snps.txt -lmm 9 -g "
-                            "genofile.txt -p test.txt "
-                            "-a genofile_snps.txt "
-                            "-gk > "
-                            "/tmp/gn2/"
-                            "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))]
-        )
+        response = self.app.post("/api/gemma/k-gwa-computation",
+                                 json={
+                                     "trait_filename": "BXD.txt",
+                                     "geno_filename": "BXD_geno",
+                                     "values": ["X", "N/A", "X"],
+                                     "dataset_groupname": "BXD",
+                                     "trait_name": "Height",
+                                     "email": "me@me.com",
+                                     "dataset_name": "BXD"
+                                 })
+        mock_queue_cmd.assert_has_calls([
+            mock.call(conn=_redis_conn,
+                      email="me@me.com",
+                      job_queue="GN3::job-queue",
+                      cmd=("gemma-wrapper --json -- -g "
+                           "genofile.txt -p test.txt "
+                           "-a genofile_snps.txt -gk > "
+                           "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt "
+                           "&& gemma-wrapper --json --input "
+                           "/tmp/gn2/bxd_K_gUFhGu4rLG7k+CXLPk1OUg.txt"
+                           " -- -a genofile_snps.txt -lmm 9 -g "
+                           "genofile.txt -p test.txt "
+                           "-a genofile_snps.txt "
+                           "-gk > "
+                           "/tmp/gn2/"
+                           "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
+        ])
         # mock_pheno_txt_file.return_value = "/tmp/gn2/BXD_6OBEPW."
         self.assertEqual(
-            response.get_json(),
-            {"unique_id": 'my-unique-id',
-             "status": "queued",
-             "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"})
+            response.get_json(), {
+                "unique_id": 'my-unique-id',
+                "status": "queued",
+                "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
+            })
 
     @mock.patch("gn3.api.gemma.redis.Redis")
     @mock.patch("gn3.api.gemma.queue_cmd")
-    def test_run_gemma_with_loco(self,
-                                 mock_queue_cmd, mock_redis):
+    def test_run_gemma_with_loco(self, mock_queue_cmd, mock_redis):
         """Test that gemma composes the command correctly with loco"""
         _redis_conn = MockRedis(redis=mock.MagicMock(), hget=mock.MagicMock())
         mock_redis.return_value = _redis_conn
         mock_queue_cmd.return_value = "my-unique-id"
-        response = self.app.post("/api/gemma/k-gwa-computation", json={
-            "trait_filename": os.path.abspath(os.path.join(
-                os.path.dirname(__file__),
-                "test_data/"
-            )),
-            "geno_filename": "BXD_geno.txt.gz",
-            "values": ["X", "N/A", "X"],
-            "dataset_groupname": "BXD",
-            "trait_name": "Height",
-            "email": "me@me.com",
-            "dataset_name": "BXD",
-            "loco": "1,2,3,4,5,6"
-        })
+        response = self.app.post("/api/gemma/k-gwa-computation",
+                                 json={
+                                     "trait_filename":
+                                     os.path.abspath(
+                                         os.path.join(
+                                             os.path.dirname(__file__),
+                                             "test_data/")),
+                                     "geno_filename":
+                                     "BXD_geno.txt.gz",
+                                     "values": ["X", "N/A", "X"],
+                                     "dataset_groupname":
+                                     "BXD",
+                                     "trait_name":
+                                     "Height",
+                                     "email":
+                                     "me@me.com",
+                                     "dataset_name":
+                                     "BXD",
+                                     "loco":
+                                     "1,2,3,4,5,6"
+                                 })
         mock_queue_cmd.called_with(
             conn=_redis_conn,
             email="me@me.com",
@@ -130,10 +141,11 @@ class GemmaAPITest(unittest.TestCase):
                  "/tmp/gn2/"
                  "bxd_GWA_gUFhGu4rLG7k+CXLPk1OUg.txt"))
         self.assertEqual(
-            response.get_json(),
-            {"unique_id": 'my-unique-id',
-             "status": "queued",
-             "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"})
+            response.get_json(), {
+                "unique_id": 'my-unique-id',
+                "status": "queued",
+                "output_file": "BXD_GWA_WzxVcfhKAn4fJnSWpsBq0g.txt"
+            })
 
     @mock.patch("gn3.api.gemma.redis.Redis")
     def test_check_cmd_status(self, mock_redis):
@@ -146,18 +158,15 @@ class GemmaAPITest(unittest.TestCase):
                                  "cmd%3A%3A2021-02-1217-3224-3224-1234"),
                                 follow_redirects=True)
         mock_hget.assert_called_once_with(
-            name="cmd::2021-02-1217-3224-3224-1234",
-            key="status")
-        self.assertEqual(response.get_json(),
-                         {"status": "test"})
+            name="cmd::2021-02-1217-3224-3224-1234", key="status")
+        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.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,
+    def test_k_compute(self, mock_redis, mock_path_exist, mock_json, mock_hash,
                        mock_queue_cmd):
         """Test /gemma/k-compute/<token>"""
         mock_path_exist.return_value, _redis_conn = True, mock.MagicMock()
diff --git a/tests/unit/computations/test_gemma.py b/tests/unit/computations/test_gemma.py
index b5ffbfd..2d2fbf9 100644
--- a/tests/unit/computations/test_gemma.py
+++ b/tests/unit/computations/test_gemma.py
@@ -12,8 +12,7 @@ class TestGemma(unittest.TestCase):
     def test_generate_pheno_txt_file(self):
         """Test that the pheno text file is generated correctly"""
         open_mock = mock.mock_open()
-        with mock.patch("gn3.computations.gemma.open",
-                        open_mock, create=True):
+        with mock.patch("gn3.computations.gemma.open", open_mock, create=True):
             _file = generate_pheno_txt_file(tmpdir="/tmp",
                                             trait_filename="phenotype.txt",
                                             values=["x", "x", "BXD07 438.700"])
@@ -24,7 +23,8 @@ class TestGemma(unittest.TestCase):
         open_mock.return_value.write.assert_has_calls([
             mock.call("NA\n"),
             mock.call("NA\n"),
-            mock.call("BXD07 438.700\n")])
+            mock.call("BXD07 438.700\n")
+        ])
 
     def test_generate_hash_of_string(self):
         """Test that a string is hashed correctly"""
@@ -42,11 +42,11 @@ class TestGemma(unittest.TestCase):
                 gemma_kwargs={
                     "geno_filename": "genofile.txt",
                     "trait_filename": "test.txt",
-                    "covar_filename": "genofile_snps.txt"},
+                    "covar_filename": "genofile_snps.txt"
+                },
                 output_file="/tmp/gn2/k_output_gUFhGu4rLG7k+CXLPk1OUg.txt",
-            ),
-            ("gemma-wrapper --json -- "
-             "-g genofile.txt -p "
-             "test.txt -a genofile_snps.txt "
-             "-gk > /tmp/gn2/"
-             "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))
+            ), ("gemma-wrapper --json -- "
+                "-g genofile.txt -p "
+                "test.txt -a genofile_snps.txt "
+                "-gk > /tmp/gn2/"
+                "k_output_gUFhGu4rLG7k+CXLPk1OUg.txt"))