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Fixes to the testing and app to bring it in line with the OAuth system
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@markmcdowall
markmcdowall committed Dec 20, 2017
1 parent 92aafec commit 62b9bb2
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Showing 2 changed files with 108 additions and 58 deletions.
120 changes: 72 additions & 48 deletions rest/app.py
View file
Expand Up @@ -15,15 +15,21 @@
limitations under the License.
"""

from __future__ import print_function

import os
import sys

from flask import Flask, make_response, request
from flask_restful import Api, Resource

from dmp import dmp
from reader.hdf5_adjacency import adjacency

from mg_rest_util.mg_auth import authorized

APP = Flask(__name__)
#app.config['DEBUG'] = False
# APP.config['DEBUG'] = True

REST_API = Api(APP)

Expand All @@ -42,7 +48,6 @@ def output_tsv(data, code, headers=None):
resp.headers.extend(headers or {})
return resp


def help_usage(error_message, status_code,
parameters_required, parameters_provided):
"""
Expand Down Expand Up @@ -74,24 +79,23 @@ def help_usage(error_message, status_code,
JSON formated status message to display to the user
"""
parameters = {
'user_id' : ['User ID', 'str', 'REQUIRED'],
'file_id' : ['File ID', 'str', 'REQUIRED'],
'chrom' : ['Chromosome', 'str', 'REQUIRED'],
'start' : ['Start', 'int', 'REQUIRED'],
'end' : ['End', 'int', 'REQUIRED'],
'res' : ['Resolution', 'int', 'REQUIRED'],
'limit_chr' : [
'Limit interactions to interacting with a specific chromosome',
'str', 'OPTIONAL'],
'limit_start' : [
'Limits interactions based on a region within the chromosome defined by the limit_chr parameter. REQUIRES that limit_chr and limit_end are defined',
'int', 'OPTIONAL'],
'limit_end' : [
'Limits interactions based on a region within the chromosome defined by the limit_chr parameter. REQUIRES that limit_chr and limit_start are defined',
'int', 'OPTIONAL'],
'pos_x' : ['Position i', 'int', 'REQUIRED'],
'pos_y' : ['Position j', 'int', 'REQUIRED'],
'type' : ['add_meta|remove_meta', 'str', 'REQUIRED']
"file_id" : ["File ID", "str", "REQUIRED"],
"chrom" : ["Chromosome", "str", "REQUIRED"],
"start" : ["Start", "int", "REQUIRED"],
"end" : ["End", "int", "REQUIRED"],
"res" : ["Resolution", "int", "REQUIRED"],
"limit_chr" : [
"Limit interactions to interacting with a specific chromosome",
"str", "OPTIONAL"],
"limit_start" : [
"Limits interactions based on a region within the chromosome defined by the limit_chr parameter. REQUIRES that limit_chr and limit_end are defined",
"int", "OPTIONAL"],
"limit_end" : [
"Limits interactions based on a region within the chromosome defined by the limit_chr parameter. REQUIRES that limit_chr and limit_start are defined",
"int", "OPTIONAL"],
"pos_x" : ["Position i", "int", "REQUIRED"],
"pos_y" : ["Position j", "int", "REQUIRED"],
"type" : ["add_meta|remove_meta", "str", "REQUIRED"]
}

used_param = {k : parameters[k] for k in parameters_required if k in parameters}
Expand Down Expand Up @@ -181,30 +185,33 @@ def get(self, user_id):
.. code-block:: none
:linenos:
curl -X GET http://localhost:5001/mug/api/adjacency/details?user_id=test&file_id=test_file
curl -X GET
-H "Authorization: Bearer teststring"
http://localhost:5001/mug/api/adjacency/details?file_id=test_file
"""
if user_id is not None:
file_id = request.args.get('file_id')

params_required = ['user_id', 'file_id']
params_required = ['file_id']
params = [user_id, file_id]

# Display the parameters available
if sum([x is None for x in params]) == len(params):
return help_usage(None, 200, params_required, {})
return {"usage": "test"}
#return help_usage(None, 200, params_required, {})

# ERROR - one of the required parameters is NoneType
if sum([x is not None for x in params]) != len(params):
return help_usage(
'MissingParameters', 400, params_required,
{'user_id' : user_id, 'file_id' : file_id}
{'file_id' : file_id}
)

#request_path = request.path
#rp = request_path.split("/")

hdf5_handle = adjacency(user_id, file_id)
hdf5_handle = adjacency(user_id["user_id"], file_id)
h5_data = hdf5_handle.get_details()
hdf5_handle.close()

Expand All @@ -213,11 +220,13 @@ def get(self, user_id):
'_self': request.base_url,
'_parent': request.url_root + 'mug/api/adjacency'
},
'chromosomes' : [{'chromosome' : c[0], 'length' : c[1]} for c in h5_data["chromosomes"]],
'chromosomes' : [
{'chromosome' : c[0], 'length' : c[1]} for c in h5_data["chromosomes"]
],
'resolutions' : h5_data['resolutions']
}

return help_usage('Forbidden', 403, ['file_id'], {})
return help_usage('Forbidden', 403, params_required, {})


class GetInteractions(Resource):
Expand Down Expand Up @@ -289,7 +298,9 @@ def get(self, user_id):
.. code-block:: none
:linenos:
curl -X GET http://localhost:5001/mug/api/adjacency/getInteractions?user_id=test&file_id=test_file&chr=<chr_id>&res=<res>
curl -X GET
-H "Authorization: Bearer teststring"
http://localhost:5001/mug/api/adjacency/getInteractions?file_id=test_file&chr=<chr_id>&res=<res>
Notes
-----
Expand All @@ -300,7 +311,10 @@ def get(self, user_id):
.. code-block:: none
:linenos:
curl -X GET --header "Accept: application/tsv" http://localhost:5001/mug/api/adjacency/getInteractions?user_id=test&file_id=test_file&chr=<chr_id>&res=<res>
curl -X GET
-H "Accept: application/tsv"
-H "Authorization: Bearer teststring"
http://localhost:5001/mug/api/adjacency/getInteractions?file_id=test_file&chr=<chr_id>&res=<res>
This will return the values from the JSON format in the following order
Expand Down Expand Up @@ -337,7 +351,7 @@ def get(self, user_id):
return help_usage(
'MissingParameters', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'chr' : chr_id, 'start' : start, 'end' : end,
'res' : resolution, 'limit_chr' : limit_chr,
'limit_start' : limit_start, 'limit_end' : limit_end
Expand All @@ -353,13 +367,13 @@ def get(self, user_id):
return help_usage(
'IncorrectParameterType', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'chr' : chr_id, 'start' : start, 'end' : end,
'res' : resolution, 'limit_chr' : limit_chr
}
)

hdf5_handle = adjacency(user_id, file_id, resolution)
hdf5_handle = adjacency(user_id["user_id"], file_id, resolution)
details = hdf5_handle.get_details()
#print("Details:", details)

Expand All @@ -368,7 +382,7 @@ def get(self, user_id):
return help_usage(
'Resolution Not Available', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'chr' : chr_id, 'start' : start, 'end' : end,
'res' : resolution, 'limit_chr' : limit_chr,
'limit_start' : limit_start, 'limit_end' : limit_end
Expand All @@ -380,7 +394,7 @@ def get(self, user_id):
return help_usage(
'MissingParameters', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'chr' : chr_id, 'start' : start, 'end' : end,
'res' : resolution, 'limit_chr' : limit_chr,
'limit_start' : limit_start, 'limit_end' : limit_end
Expand All @@ -394,7 +408,7 @@ def get(self, user_id):
return help_usage(
'IncorrectParameterType', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'chr' : chr_id, 'start' : start, 'end' : end,
'res' : resolution, 'limit_chr' : limit_chr,
'limit_start' : limit_start, 'limit_end' : limit_end
Expand Down Expand Up @@ -482,7 +496,9 @@ def get(self, user_id):
.. code-block:: none
:linenos:
curl -X GET http://localhost:5001/mug/api/adjacency/getValue?user_id=test&file_id=test_file&chr=<chr_id>&res=<res>
curl -X GET
-H "Authorization: Bearer teststring"
http://localhost:5001/mug/api/adjacency/getValue?file_id=test_file&chr=<chr_id>&res=<res>
"""
if user_id is not None:
file_id = request.args.get('file_id')
Expand All @@ -502,7 +518,7 @@ def get(self, user_id):
return help_usage(
'MissingParameters', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'resolution' : resolution, 'pos_x' : pos_x, 'pos_y' : pos_y
}
)
Expand All @@ -516,12 +532,12 @@ def get(self, user_id):
return help_usage(
'IncorrectParameterType', 400, params_required,
{
'user_id' : user_id, 'file_id' : file_id,
'file_id' : file_id,
'resolution' : resolution, 'pos_x' : pos_x, 'pos_y' : pos_y
}
)

h5_handle = adjacency(user_id, file_id, resolution)
h5_handle = adjacency(user_id["user_id"], file_id, resolution)
#meta_data = h5.get_details()
#print("chr_param:", meta_data["chr_param"])
value = h5_handle.get_value(pos_x, pos_y)
Expand All @@ -532,18 +548,18 @@ def get(self, user_id):
h5_handle.close()

return {
'_links': {
'_self': request.url_root + 'mug/api/adjacency/getValue?user_id=' + str(user_id) + "&file_id=" + str(file_id) + "&res=" + str(resolution) + "&pos_x=" + str(pos_x) + "&pos_y=" + str(pos_y)
"_links": {
"_self": request.url_root + "mug/api/adjacency/getValue?file_id=" + str(file_id) + "&res=" + str(resolution) + "&pos_x=" + str(pos_x) + "&pos_y=" + str(pos_y)
},
'chrA': chr_a_id,
'chrB': chr_b_id,
'resolution': resolution,
'pos_x': pos_x,
'pos_y': pos_y,
'value': int(value)
"chrA": chr_a_id,
"chrB": chr_b_id,
"resolution": resolution,
"pos_x": pos_x,
"pos_y": pos_y,
"value": int(value)
}

return help_usage('Forbidden', 403, ['file_id', 'res', 'pos_x', 'pos_y'], {})
return help_usage("Forbidden", 403, ["file_id", "res", "pos_x", "pos_y"], {})

class Ping(Resource):
"""
Expand Down Expand Up @@ -581,6 +597,14 @@ def get():
}
return res

#
# For the services where there needs to be an extra layer (adjacency lists),
# then there needs to be a way of forwarding for this. But the majority of
# things can be redirected to the raw files for use as a track.
#

sys._auth_meta_json = os.path.dirname(os.path.realpath(__file__)) + '/auth_meta.json'

# Define the URIs and their matching methods

# List the available end points for this service
Expand Down
46 changes: 36 additions & 10 deletions tests/test_rest.py
View file
Expand Up @@ -63,17 +63,22 @@ def test_details(client):
"""
Test the details endpoint to ensure it returns the usage element
"""
rest_value = client.get('/mug/api/adjacency/details')
rest_value = client.get(
'/mug/api/adjacency/details',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print(details)
assert 'usage' in details

def test_details_00(client):
"""
Test that details endpoint includes a resolution value when a test user and
file are specified
"""
rest_value = client.get('/mug/api/adjacency/details?user_id=test&file_id=test')
rest_value = client.get(
'/mug/api/adjacency/details?file_id=test',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print(details)
assert 'resolutions' in details
Expand All @@ -83,7 +88,10 @@ def test_details_01(client):
Test that details endpoint includes 3 resolution values when a test user and
file are specified
"""
rest_value = client.get('/mug/api/adjacency/details?user_id=test&file_id=test')
rest_value = client.get(
'/mug/api/adjacency/details?file_id=test',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print(details)
assert len(details['resolutions']) == 3
Expand All @@ -92,7 +100,10 @@ def test_getinteractions(client):
"""
Test the interactions endpoint to ensure it returns the usage element
"""
rest_value = client.get('/mug/api/adjacency/getInteractions')
rest_value = client.get(
'/mug/api/adjacency/getInteractions',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print(details)
assert 'usage' in details
Expand All @@ -102,7 +113,10 @@ def test_getinteractions_00(client):
Test that interactions returns a values block when test parameters are
provided
"""
rest_value = client.get('/mug/api/adjacency/getInteractions?user_id=test&file_id=test&chr=chr1&res=10000&start=100000&end=200000')
rest_value = client.get(
'/mug/api/adjacency/getInteractions?file_id=test&chr=chr1&res=10000&start=100000&end=200000',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print('TEST - getinteractions_00:', details.keys())
assert 'values' in details
Expand All @@ -112,7 +126,10 @@ def test_getinteractions_01(client):
Test that interactions returns a known number of values when test parameters
are provided
"""
rest_value = client.get('/mug/api/adjacency/getInteractions?user_id=test&file_id=test&chr=chr1&res=10000&start=100000&end=200000')
rest_value = client.get(
'/mug/api/adjacency/getInteractions?file_id=test&chr=chr1&res=10000&start=100000&end=200000',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print('TEST - getinteractions_01:', details.keys())
value_count = len(details['values'])
Expand All @@ -122,7 +139,10 @@ def test_getvalue(client):
"""
Test the values endpoint to ensure it returns the usage element
"""
rest_value = client.get('/mug/api/adjacency/getValue')
rest_value = client.get(
'/mug/api/adjacency/getValue',
headers=dict(Authorization='Authorization: Bearer teststring')
)
details = json.loads(rest_value.data)
print(details)
assert 'usage' in details
Expand All @@ -132,13 +152,19 @@ def test_getvalue_00(client):
Test that values returns with a value element when test parameters are
provided
"""
rest_interactions = client.get('/mug/api/adjacency/getInteractions?user_id=test&file_id=test&chr=chr1&res=10000&start=100000&end=200000')
rest_interactions = client.get(
'/mug/api/adjacency/getInteractions?file_id=test&chr=chr1&res=10000&start=100000&end=200000',
headers=dict(Authorization='Authorization: Bearer teststring')
)
interaction_details = json.loads(rest_interactions.data)
print(interaction_details['values'][0])
pos_x = interaction_details['values'][0]['pos_x']
pos_y = interaction_details['values'][0]['pos_y']

rest_value = client.get('/mug/api/adjacency/getValue?user_id=test&file_id=test&res=10000&pos_x=' + str(pos_x) + '&pos_y=' + str(pos_y))
rest_value = client.get(
'/mug/api/adjacency/getValue?file_id=test&res=10000&pos_x=' + str(pos_x) + '&pos_y=' + str(pos_y),
headers=dict(Authorization='Authorization: Bearer teststring')
)
value_details = json.loads(rest_value.data)
print(value_details)
assert 'value' in value_details
Expand Down

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