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"""General API endpoints. Put endpoints that can't be grouped together nicely
here."""
import os
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
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 = 'scripts/rqtl_wrapper.R' # This is a stub
cmd = (f"Rscript {rqtl_wrapper} "
f"{geno_filestr} {pheno_filestr}")
return jsonify(run_cmd(cmd)), 201
@general.route("/stream ", methods=["GET"])
def stream():
"""
This endpoint streams the stdout content from a file.
It expects an identifier to be passed as a query parameter.
Example: `/stream?id=<identifier>`
The `id` will be used to locate the corresponding file.
You can also pass an optional `peak` parameter
to specify the file position to start reading from.
Query Parameters:
- `id` (required): The identifier used to locate the file.
- `peak` (optional): The position in the file to start reading from.
Returns:
- dict with data(stdout), run_id unique id for file,
pointer last read position for file
"""
run_id = request.args.get("id", "")
output_file = os.path.join(current_app.config.get("TMPDIR"),
f"{run_id}.txt")
seek_position = int(request.args.get("peak", 0))
with open(output_file, encoding="utf-8") as file_handler:
# read to the last position default to 0
file_handler.seek(seek_position)
return jsonify({"data": file_handler.readlines(),
"run_id": run_id,
"pointer": file_handler.tell()})
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