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"""General API endpoints. Put endpoints that can't be grouped together nicely
here."""
from flask import Blueprint
from flask import current_app
from flask import jsonify
from flask import request
from gn3.fs_helpers import extract_uploaded_file
from gn3.commands import run_cmd
from gn3.db import datasets
general = Blueprint("general", __name__)
@general.route("/version")
def version():
"""Get API version."""
return jsonify("1.0")
@general.route("/metadata/upload/", methods=["POST"],
strict_slashes=False)
def upload_metadata_with_no_token():
"""Extract uploaded file to a some TMPDIR/TOKEN/ with a TTL(Time To Live). The
TTL is set in the metadata file. If none is provided, the default is 1
week. Generate a TOKEN
"""
file_ = request.files.get("file")
if not file_:
return jsonify(status=128, error="Please provide a file!"), 400
status = 201
results = extract_uploaded_file(
gzipped_file=file_,
target_dir=current_app.config["TMPDIR"],
token=None)
if results.get("status") > 0:
status = 500
return jsonify(results), status
@general.route("/metadata/upload/<token>", methods=["POST"],
strict_slashes=False)
def upload_metadata(token):
"""Extract uploaded file to a some TMPDIR/TOKEN/ with a TTL(Time To Live). The
TTL is set in the metadata file. If none is provided, the default is 1 week.
"""
file_ = request.files.get("file")
if not file_:
return jsonify(status=128, error="Please provide a file!"), 400
status = 201
results = extract_uploaded_file(
gzipped_file=file_,
target_dir=current_app.config["TMPDIR"],
token=token)
if results.get("status") > 0:
status = 500
return jsonify(results), status
@general.route("/qtl/run/<geno_filestr>/<pheno_filestr>",
methods=["POST"],
strict_slashes=False)
def run_r_qtl(geno_filestr, pheno_filestr):
"""Run r_qtl command using the written rqtl_wrapper program
"""
rqtl_wrapper = current_app.config["RQTL_WRAPPER"]
cmd = (f"Rscript {rqtl_wrapper} "
f"{geno_filestr} {pheno_filestr}")
return jsonify(run_cmd(cmd)), 201
@general.route("/dataset/<accession_id>")
def dataset_metadata(accession_id):
"""Return info as JSON for dataset with ACCESSION_ID."""
return jsonify(datasets.dataset_metadata(accession_id))
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