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-rw-r--r--wqflask/wqflask/api/router.py30
1 files changed, 26 insertions, 4 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index a6e56962..3708401b 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -2,12 +2,13 @@
from __future__ import absolute_import, division, print_function
-import os, io, csv, json, datetime
+import os, io, csv, json, datetime, requests
+from zipfile import ZipFile
import StringIO
import flask
-from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect
+from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, send_file
import sqlalchemy
from wqflask import app
@@ -497,7 +498,7 @@ def all_sample_data(dataset_name, file_format = "csv"):
results_list = []
header_list = []
- header_list.append("Trait ID")
+ header_list.append("id")
header_list += sample_list
results_list.append(header_list)
for i, trait_id in enumerate(trait_ids):
@@ -717,7 +718,8 @@ 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>".format(version))
+@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"):
limit_num = None
@@ -745,6 +747,26 @@ def get_genotypes(group_name, file_format="csv"):
csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+ elif file_format == "rqtl2":
+ memory_file = io.BytesIO()
+ filename = group_name + "_rqtl.zip"
+
+ if os.path.isfile("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name)):
+ 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")
+
+ with ZipFile(memory_file, 'w') as zf:
+ for this_file in [config_file, geno_file, gmap_file]:
+ zf.writestr(this_file.name.split("/")[-1], this_file.read())
+ zf.writestr("{0}_pheno.csv".format(group_name), phenotypes.content)
+
+ memory_file.seek(0)
+
+ return send_file(memory_file, attachment_filename=filename, as_attachment=True)
+ else:
+ return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
else:
filename = group_name + ".bimbam"