diff options
| -rw-r--r-- | wqflask/wqflask/api/router.py | 30 |
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" |