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authorzsloan2019-11-26 13:51:30 -0600
committerzsloan2019-11-26 13:51:30 -0600
commit022180f032c7ff790dc0badf9458b959ac48ee8c (patch)
treefaaa6358da02d4a5d21c9a08b5064aae26c0e960
parent0ec99ac9e0315d4fda8decc0f509c08370119a70 (diff)
downloadgenenetwork2-022180f032c7ff790dc0badf9458b959ac48ee8c.tar.gz
Changed rqtl2 genotype download to export all datasets, not just phenotype ones + let user type in .zip extension
-rw-r--r--wqflask/wqflask/api/router.py15
1 files changed, 10 insertions, 5 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 4cd10b37..e371a24e 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -719,10 +719,12 @@ def get_mapping_results():
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
-@app.route("/api/v_{}/genotypes/<path:group_name>.<path:file_format>".format(version))
-@app.route("/api/v_{}/genotypes/<path:file_format>/<path:group_name>".format(version))
-@app.route("/api/v_{}/genotypes/<path:group_name>.<path:file_format>".format(version))
-def get_genotypes(group_name, file_format="csv"):
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version))
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version))
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version))
+@app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>".format(version))
+@app.route("/api/v_{}/genotypes/<string:group_name>.<string:file_format>".format(version))
+def get_genotypes(group_name, file_format="csv", dataset_name=None):
limit_num = None
if 'limit_to' in request.args:
if request.args['limit_to'].isdigit():
@@ -756,7 +758,10 @@ def get_genotypes(group_name, file_format="csv"):
config_file = open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))
geno_file = open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))
gmap_file = open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))
- phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish")
+ if dataset_name:
+ phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name)
+ else:
+ phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish")
with ZipFile(memory_file, 'w', compression=ZIP_DEFLATED) as zf:
for this_file in [config_file, geno_file, gmap_file]: