diff options
| -rw-r--r-- | wqflask/wqflask/api/router.py | 27 |
1 files changed, 18 insertions, 9 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index eb6880f6..6324cabe 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -2,7 +2,7 @@ from __future__ import absolute_import, division, print_function -import os, io, csv, json, datetime, requests +import os, io, csv, json, datetime, requests, yaml import zlib from zipfile import ZipFile, ZIP_DEFLATED @@ -754,25 +754,34 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None): 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 dataset_name: + filename = dataset_name + else: + filename = group_name 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)) + yaml_file = json.load(open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name))) + yaml_file["geno"] = filename + "_geno.csv" + yaml_file["gmap"] = filename + "_gmap.csv" + yaml_file["pheno"] = filename + "_pheno.csv" + config_file = [filename + ".json", json.dumps(yaml_file)] + #config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))] + geno_file = [filename + "_geno.csv", open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))] + gmap_file = [filename + "_gmap.csv", open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))] 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]: - zf.writestr(this_file.name.split("/")[-1], this_file.read()) - zf.writestr("{0}_pheno.csv".format(group_name), phenotypes.content) + zf.writestr(config_file[0], config_file[1]) + for this_file in [geno_file, gmap_file]: + zf.writestr(this_file[0], this_file[1].read()) + zf.writestr(filename + "_pheno.csv", phenotypes.content) memory_file.seek(0) - return send_file(memory_file, attachment_filename=filename, as_attachment=True) + return send_file(memory_file, attachment_filename=filename + ".zip", as_attachment=True) else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") else: |