diff options
Diffstat (limited to 'gn3/api')
| -rw-r--r-- | gn3/api/datasets.py | 20 | ||||
| -rw-r--r-- | gn3/api/traits.py | 27 |
2 files changed, 29 insertions, 18 deletions
diff --git a/gn3/api/datasets.py b/gn3/api/datasets.py index 70ee3a1..eb4097d 100644 --- a/gn3/api/datasets.py +++ b/gn3/api/datasets.py @@ -32,19 +32,19 @@ def create_dataset_api(dataset_name, dataset_type=None): @dataset.route("/fetch_traits_data/<dataset_name>/<dataset_type>") def fetch_traits_data(dataset_name, dataset_type): - """endpoints fetches sample for each trait in\ - a dataset""" + """test fetch_traits_data/dataset_name/dataset_type""" # what actually brings speed issues in correlation - sample_ids = [4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, - 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, - 35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115, - 116, 117, 118, 119, 120, 919, 147, - 121, 40, 41, 124, 125, 128, 135, 129, 130, 131, - 132, 134, 138, 139, 140, 141, 142, 144, - 145, 148, 149, 920, 922, 2, 3, 1, 1100] + # should fetch this + trait_sample_ids = [4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, + 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, + 35, 36, 37, 39, 98, 99, 100, 103, 487, 105, 106, 110, 115, + 116, 117, 118, 119, 120, 919, 147, + 121, 40, 41, 124, 125, 128, 135, 129, 130, 131, + 132, 134, 138, 139, 140, 141, 142, 144, + 145, 148, 149, 920, 922, 2, 3, 1, 1100] conn, _cursor = database_connector() - results = get_traits_data(sample_ids=sample_ids, database_instance=conn, + results = get_traits_data(sample_ids=trait_sample_ids, database_instance=conn, dataset_name=dataset_name, dataset_type=dataset_type) conn.close() diff --git a/gn3/api/traits.py b/gn3/api/traits.py index a9ff906..758dcca 100644 --- a/gn3/api/traits.py +++ b/gn3/api/traits.py @@ -7,6 +7,8 @@ from flask import request from gn3.computations.traits import fetch_trait from gn3.computations.traits import get_trait_info_data +from gn3.experimental_db import database_connector + trait = Blueprint("trait", __name__) @@ -18,14 +20,23 @@ def home(): @trait.route("/<string:trait_name>/<string:dataset_name>") def create_trait(trait_name, dataset_name): - """endpoints for creating trait first should\ - call the endpoint for creating the trait only\ - also acts as endpoints for fetching trait data""" - - trait_dataset = mock.Mock() # xtodo should replace this with calling epoints - trait_dataset.name = dataset_name - - trait_results = fetch_trait(dataset=trait_dataset, trait_name=trait_name) + """/test:trait_name/dataset_name/type :retrieve sample\ + data for trait""" + + # xtodo replace the object at most this endpoint + # requires dataset_type,dataset_name ,dataset_id + trait_dataset = { + "name": dataset_name, + "id": 12, + "type": "ProbeSet" # temp values + } + conn, _cursor = database_connector() + + trait_results = fetch_trait(dataset=trait_dataset, + trait_name=trait_name, + database=conn) + + conn.close() return jsonify(trait_results) |