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| author | BonfaceKilz | 2021-05-13 10:58:19 +0300 |
|---|---|---|
| committer | BonfaceKilz | 2021-05-13 11:18:57 +0300 |
| commit | 7ab86429219a2ed5ad7b94f0ce9667dd4c38c56d (patch) | |
| tree | 609854b13e95958ee56bf55b91582afe4f234e88 | |
| parent | 378d0fc7f4ff5df5e8e77617c37bcef2b26ddf02 (diff) | |
| download | genenetwork3-7ab86429219a2ed5ad7b94f0ce9667dd4c38c56d.tar.gz | |
Add end-point for running an rQTL program
* gn3/api/general.py (run_r_qtl): New function.
* gn3/settings.py: New variable.
| -rw-r--r-- | gn3/api/general.py | 14 | ||||
| -rw-r--r-- | gn3/settings.py | 1 |
2 files changed, 15 insertions, 0 deletions
diff --git a/gn3/api/general.py b/gn3/api/general.py index a9a8da2..cebb2e3 100644 --- a/gn3/api/general.py +++ b/gn3/api/general.py @@ -6,6 +6,7 @@ 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__) @@ -50,3 +51,16 @@ TTL is set in the metadata file. If none is provided, the default is 1 week. 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 diff --git a/gn3/settings.py b/gn3/settings.py index 7b3ffb7..2057ce1 100644 --- a/gn3/settings.py +++ b/gn3/settings.py @@ -10,6 +10,7 @@ CACHEDIR = "" REDIS_URI = "redis://localhost:6379/0" REDIS_JOB_QUEUE = "GN3::job-queue" TMPDIR = os.environ.get("TMPDIR", tempfile.gettempdir()) +RQTL_WRAPPER = "rqtl_wrapper.R" # SQL confs SQL_URI = os.environ.get("SQL_URI", "mysql://webqtlout:webqtlout@localhost/db_webqtl") |