diff options
| -rw-r--r-- | wqflask/wqflask/api/router.py | 116 |
1 files changed, 105 insertions, 11 deletions
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py index 845873a0..4ecd6699 100644 --- a/wqflask/wqflask/api/router.py +++ b/wqflask/wqflask/api/router.py @@ -290,6 +290,106 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"): else: return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") +@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=('GET',)) +@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=('GET',)) +def fetch_traits(dataset_name, file_format = "csv"): + trait_ids, _trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name) + if ('ids_only' in request.args) and (len(trait_ids) > 0): + if file_format == "json": + filename = dataset_name + "_trait_ids.json" + return flask.jsonify(trait_ids) + else: + filename = dataset_name + "_trait_ids.csv" + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows([[trait_id] for trait_id in trait_ids]) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + else: + if len(trait_ids) > 0: + if data_type == "ProbeSet": + query = """ + SELECT + ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias, + ProbeSetXRef.mean, ProbeSetXRef.se, ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.additive, ProbeSetXRef.h2 + FROM + ProbeSet, ProbeSetXRef + WHERE + ProbeSetXRef.ProbeSetFreezeId = '{0}' AND + ProbeSetXRef.ProbeSetId = ProbeSet.Id + ORDER BY + ProbeSet.Id + """ + + field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"] + elif data_type == "Geno": + query = """ + SELECT + Geno.Id, Geno.Name, Geno.Marker_Name, Geno.Chr, Geno.Mb, Geno.Sequence, Geno.Source + FROM + Geno, GenoXRef + WHERE + GenoXRef.GenoFreezeId = '{0}' AND + GenoXRef.GenoId = Geno.Id + ORDER BY + Geno.Id + """ + + field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"] + else: + query = """ + SELECT + PublishXRef.Id, PublishXRef.PhenotypeId, PublishXRef.PublicationId, PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive, PublishXRef.Sequence + FROM + PublishXRef + WHERE + PublishXRef.InbredSetId = {0} + ORDER BY + PublishXRef.Id + """ + + field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"] + + if file_format == "json": + filename = dataset_name + "_traits.json" + + final_query = query.format(dataset_id) + + result_list = [] + for result in g.db.execute(final_query).fetchall(): + trait_dict = {} + for i, field in enumerate(field_list): + if result[i]: + trait_dict[field] = result[i] + result_list.append(trait_dict) + + return flask.jsonify(result_list) + elif file_format == "csv": + filename = dataset_name + "_traits.csv" + + results_list = [] + header_list = [] + header_list += field_list + results_list.append(header_list) + + final_query = query.format(dataset_id) + for result in g.db.execute(final_query).fetchall(): + results_list.append(result) + + si = StringIO.StringIO() + csv_writer = csv.writer(si) + csv_writer.writerows(results_list) + output = make_response(si.getvalue()) + output.headers["Content-Disposition"] = "attachment; filename=" + filename + output.headers["Content-type"] = "text/csv" + return output + else: + return return_error(code=400, source=request.url_rule.rule, title="Invalid Output Format", details="Current formats available are JSON and CSV, with CSV as default") + else: + return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") @app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version)) @app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version)) @@ -528,8 +628,6 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"): PublishXRef.Id = '{0}' AND PublishXRef.InbredSetId = '{1}' """.format(trait_name, group_id) - - logger.debug("QUERY:", pheno_query) pheno_results = g.db.execute(pheno_query) @@ -612,13 +710,6 @@ def get_genotypes(group_name, file_format="csv"): return output -@app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=('GET',)) -@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=('GET',)) -def get_traits(dataset_name, file_format = "json"): - #ZS: Need to check about the "start" and "stop" stuff since it seems to just limit the number of results to stop - start + 1 in Pjotr's elixir code - - NotImplemented - def return_error(code, source, title, details): json_ob = {"errors": [ { @@ -652,7 +743,7 @@ def get_dataset_trait_ids(dataset_name): dataset_id = results[0][2] return trait_ids, trait_names, data_type, dataset_id - elif "Publish" in dataset_name: + elif "Publish" in dataset_name or get_group_id(dataset_name): data_type = "Publish" dataset_name = dataset_name.replace("Publish", "") dataset_id = get_group_id(dataset_name) @@ -743,7 +834,10 @@ def get_group_id_from_dataset(dataset_name): result = g.db.execute(query).fetchone() - return result[0] + if len(result) > 0: + return result[0] + else: + return None def get_group_id(group_name): query = """ |