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-rw-r--r--gn3/api/gemma.py158
1 files changed, 84 insertions, 74 deletions
diff --git a/gn3/api/gemma.py b/gn3/api/gemma.py
index 2bdaf26..0f4b8e3 100644
--- a/gn3/api/gemma.py
+++ b/gn3/api/gemma.py
@@ -60,13 +60,14 @@ traitfile, and snpsfile are extracted from a metadata.json file.
output_dir=current_app.config.get('TMPDIR'),
token=token,
gemma_kwargs=gemma_kwargs)
- 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=results.get("gemma_cmd")),
- status="queued",
- output_file=results.get("output_file"))
+ 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=results.get("gemma_cmd")),
+ status="queued",
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -98,13 +99,14 @@ values.
token=token,
gemma_kwargs=gemma_kwargs,
chromosomes=chromosomes)
- 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=results.get("gemma_cmd")),
- status="queued",
- output_file=results.get("output_file"))
+ 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=results.get("gemma_cmd")),
+ status="queued",
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -140,13 +142,14 @@ def compute_gwa(k_filename, token):
gemma_wrapper_kwargs={
"input": os.path.join(working_dir, k_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=results.get("gemma_cmd")),
- status="queued",
- output_file=results.get("output_file"))
+ 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=results.get("gemma_cmd")),
+ status="queued",
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -183,13 +186,14 @@ def compute_gwa_with_covar(k_filename, token):
gemma_wrapper_kwargs={
"input": os.path.join(working_dir, k_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=results.get("gemma_cmd")),
- status="queued",
- output_file=results.get("output_file"))
+ 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=results.get("gemma_cmd")),
+ status="queued",
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -229,13 +233,14 @@ def compute_gwa_with_loco_maf(k_filename, maf, token):
gemma_wrapper_kwargs={
"loco": f"--input {os.path.join(working_dir, k_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=results.get("gemma_cmd")),
- status="queued",
- output_file=results.get("output_file"))
+ 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=results.get("gemma_cmd")),
+ status="queued",
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -276,13 +281,14 @@ def compute_gwa_with_loco_covar(k_filename, maf, token):
gemma_wrapper_kwargs={
"loco": f"--input {os.path.join(working_dir, k_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=results.get("gemma_cmd")),
- status="queued",
- output_file=results.get("output_file"))
+ 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=results.get("gemma_cmd")),
+ status="queued",
+ output_file=results.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -326,14 +332,15 @@ covars; lmm defaults to 9!
"input": os.path.join(working_dir,
gemma_k_cmd.get("output_file"))
})
- 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
- f"{gemma_gwa_cmd.get('gemma_cmd')}")),
- status="queued",
- output_file=gemma_gwa_cmd.get("output_file"))
+ 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -378,14 +385,15 @@ covars; lmm defaults to 9!
"input": os.path.join(working_dir,
gemma_k_cmd.get("output_file"))
})
- 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
- f"{gemma_gwa_cmd.get('gemma_cmd')}")),
- status="queued",
- output_file=gemma_gwa_cmd.get("output_file"))
+ 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -431,14 +439,15 @@ def compute_k_gwa_with_loco_only(chromosomes, maf, token):
f"{os.path.join(working_dir, gemma_k_cmd.get('output_file'))}"
)
})
- 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
- f"{gemma_gwa_cmd.get('gemma_cmd')}")),
- status="queued",
- output_file=gemma_gwa_cmd.get("output_file"))
+ 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
@@ -485,14 +494,15 @@ def compute_k_gwa_with_loco_and_cavar(chromosomes, maf, token):
f"{os.path.join(working_dir, gemma_k_cmd.get('output_file'))}"
)
})
- 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
- f"{gemma_gwa_cmd.get('gemma_cmd')}")),
- status="queued",
- output_file=gemma_gwa_cmd.get("output_file"))
+ 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=(f"{gemma_k_cmd.get('gemma_cmd')} && "
+ f"{gemma_gwa_cmd.get('gemma_cmd')}")),
+ status="queued",
+ output_file=gemma_gwa_cmd.get("output_file"))
# pylint: disable=W0703
except Exception:
return jsonify(
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 13:34:54 +0000