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-rw-r--r--wqflask/wqflask/api/router.py116
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 = """