Skip to content

Commit

Permalink
Merge branch 'minimalInterface' of https://github.com/biocore/microse…
Browse files Browse the repository at this point in the history 
…tta-private-api into st_dh_issue_162
  • Loading branch information
@dhakim87
dhakim87 committed May 19, 2020
2 parents 8ecc37e + f0ae452 commit 3f3ca9a
Show file tree
Hide file tree
Showing 7 changed files with 274 additions and 193 deletions.
104 changes: 56 additions & 48 deletions microsetta_private_api/example/client.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -189,54 +189,6 @@ paths:
'302':
description: Redirecting to necessary action

'/claim_additional_kit':
post:
operationId: microsetta_private_api.example.client_impl.claim_additional_kit
requestBody:
content:
application/x-www-form-urlencoded:
schema:
type: object
additionalProperties: true
responses:
'200':
description: Error report
content:
text/html:
schema:
type: string
'302':
description: Redirecting to necessary action

'/workflow_claim_kit_samples':
get:
operationId: microsetta_private_api.example.client_impl.get_workflow_claim_kit_samples
responses:
'200':
description: Form to claim unassigned samples from a kit name to a human participant
content:
text/html:
schema:
type: string

post:
operationId: microsetta_private_api.example.client_impl.post_workflow_claim_kit_samples
requestBody:
content:
application/x-www-form-urlencoded:
schema:
type: object
additionalProperties: true
responses:
'200':
description: Error report
content:
text/html:
schema:
type: string
'302':
description: Redirecting to necessary action

'/error':
get:
operationId: microsetta_private_api.example.client_impl.generate_error_page
Expand Down Expand Up @@ -303,6 +255,38 @@ paths:
schema:
type: string

'/accounts/{account_id}/sources/{source_id}/claim_samples':
post:
operationId: microsetta_private_api.example.client_impl.claim_samples
tags:
- Samples
parameters:
- $ref: '#/components/parameters/account_id'
- $ref: '#/components/parameters/source_id'
requestBody:
content:
application/x-www-form-urlencoded:
schema:
type: object
properties:
sample_id:
type: array
items:
type: string
encoding:
sample_id:
style: form
explode: true
responses:
'302':
description: Return to view source page
'200':
description: Error report
content:
text/html:
schema:
type: string

'/accounts/{account_id}/sources/{source_id}/survey_templates/{survey_template_id}':
get:
operationId: microsetta_private_api.example.client_impl.show_source_survey
Expand Down Expand Up @@ -433,6 +417,19 @@ paths:
schema:
type: string

'/list_kit_samples':
get:
operationId: microsetta_private_api.example.client_impl.get_list_kit_samples
parameters:
- $ref: '#/components/parameters/kit_name'
responses:
'200':
description: Result of check
content:
application/json:
schema:
type: array

'/view_faq':
get:
operationId: microsetta_private_api.example.client_impl.render_faq
Expand Down Expand Up @@ -460,6 +457,13 @@ components:
type: string
example: "c442f31d-fa17-4fd1-85e2-1f251d13ec26"
required: true
kit_name:
name: kit_name
in: query
description: User-facing id of kit
schema:
$ref: '#/components/schemas/kit_name'
required: true
sample_id:
name: sample_id
in: path
Expand Down Expand Up @@ -521,3 +525,7 @@ components:
error_msg:
type: string
example: "%7B%0A%20%20%22detail%22%3A%20%22The%20browser%20(or%20proxy)%20sent%20a%20request%20that%20this%20server%20could%20not%20understand.%22%2C%0A%20%20%22status%22%3A%20400%2C%0A%20%20%22title%22%3A%20%22Bad%20Request%22%2C%0A%20%20%22type%22%3A%20%22about%3Ablank%22%0A%7D%0A"
kit_name:
type: string
example: "aaaaa"

164 changes: 105 additions & 59 deletions microsetta_private_api/example/client_impl.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,6 @@
https://github.com/realpython/materials/blob/master/flask-connexion-rest/version_3/people.py # noqa: E501
"""

import json
import flask
from flask import render_template, session, redirect
import jwt
Expand Down Expand Up @@ -62,7 +61,6 @@
NEEDS_EMAIL_CHECK = "NeedsEmailCheck"
NEEDS_HUMAN_SOURCE = "NeedsHumanSource"
TOO_MANY_HUMAN_SOURCES = "TooManyHumanSources"
NEEDS_SAMPLE = "NeedsSample"
NEEDS_PRIMARY_SURVEY = _NEEDS_SURVEY_PREFIX + "1"
NEEDS_COVID_SURVEY = _NEEDS_SURVEY_PREFIX + "6"
ALL_DONE = "AllDone"
Expand Down Expand Up @@ -365,25 +363,47 @@ def post_source(account_id, body):
return redirect('/accounts/%s' % acct_id)


def get_workflow_claim_kit_samples():
next_state, current_state = determine_workflow_state()
if next_state != NEEDS_SAMPLE:
return redirect(WORKFLOW_URL)
def _claim_kit_samples_helper(acct_id,
source_id,
sample_ids_to_claim,
answered_survey_ids_to_associate):

if KIT_NAME_KEY in session:
mock_body = {KIT_NAME_KEY: session[KIT_NAME_KEY]}
return post_workflow_claim_kit_samples(mock_body)
else:
return render_template("kit_sample_association.jinja2")
# TODO: Any of these requests may fail independently, but we don't have
# a good policy to deal with partial failures. Currently, we abort early
# but that will result in some set of associations being already made,
# one association failing, and the remaining associations not attempted.

for curr_sample_id in sample_ids_to_claim:
# Claim sample
do_return, sample_output, _ = ApiRequest.post(
'/accounts/{0}/sources/{1}/samples'.format(acct_id, source_id),
json={"sample_id": curr_sample_id}
)

if do_return:
return sample_output

# Associate the input answered surveys with this sample.
for survey_id in answered_survey_ids_to_associate:
do_return, sample_survey_output, _ = ApiRequest.post(
'/accounts/{0}/sources/{1}/samples/{2}/surveys'.format(
acct_id, source_id, curr_sample_id
), json={"survey_id": survey_id}
)

if do_return:
return sample_output

return None


def claim_kit_samples(expected_state, body):
next_state, current_state = determine_workflow_state()
if next_state == expected_state:
acct_id = current_state["account_id"]
source_id = current_state["human_source_id"]
answered_survey_id = current_state["answered_primary_survey_id"]
answered_covid_survey_id = current_state["answered_covid_survey_id"]
primary_survey_id = current_state["answered_primary_survey_id"]
covid_survey_id = current_state["answered_covid_survey_id"]

# get all the unassociated samples in the provided kit
kit_name = body[KIT_NAME_KEY]
Expand All @@ -395,45 +415,19 @@ def claim_kit_samples(expected_state, body):
# for each sample, associate it to the human source
# and ALSO to the (single) primary and COVID survey for this human
# source
for curr_sample_obj in sample_output:
curr_sample_id = curr_sample_obj["sample_id"]
do_return, sample_output, _ = ApiRequest.post(
'/accounts/{0}/sources/{1}/samples'.format(acct_id, source_id),
json={"sample_id": curr_sample_id}
)

if do_return:
return sample_output

do_return, sample_survey_output, _ = ApiRequest.post(
'/accounts/{0}/sources/{1}/samples/{2}/surveys'.format(
acct_id, source_id, curr_sample_id
), json={"survey_id": answered_survey_id}
)

if do_return:
return sample_output
error = _claim_kit_samples_helper(
acct_id,
source_id,
[x["sample_id"] for x in sample_output],
[primary_survey_id, covid_survey_id]
)

do_return, sample_survey_output, _ = ApiRequest.post(
'/accounts/{0}/sources/{1}/samples/{2}/surveys'.format(
acct_id, source_id, curr_sample_id
), json={"survey_id": answered_covid_survey_id}
)

if do_return:
return sample_output
if error:
return error

return redirect(WORKFLOW_URL)


def claim_additional_kit(body):
return claim_kit_samples(ALL_DONE, body)


def post_workflow_claim_kit_samples(body):
return claim_kit_samples(NEEDS_SAMPLE, body)


def get_workflow_fill_survey(survey_template_id):
next_state, current_state = determine_workflow_state()
if next_state != _NEEDS_SURVEY_PREFIX + str(survey_template_id):
Expand Down Expand Up @@ -659,7 +653,7 @@ def get_sample(account_id, source_id, sample_id):
return sample_output

source_type = source_output['source_type']
is_environmental = source_type == Source.SOURCE_TYPE_ENVIRONMENTAL
is_environmental = source_type == Source.SOURCE_TYPE_ENVIRONMENT
is_human = source_type == Source.SOURCE_TYPE_HUMAN

if is_human:
Expand Down Expand Up @@ -724,32 +718,84 @@ def put_sample(account_id, source_id, sample_id):
(account_id, source_id))


def post_check_acct_inputs(body):
def _get_kit(kit_name):
unable_to_validate_msg = "Unable to validate the kit name; please " \
"reload the page."
response_info = True
error_msg = None
try:
kit_name = body[KIT_NAME_KEY]

# call api and find out if kit name has unclaimed samples.
# NOT doing this through ApiRequest.get bc in this case
# DON'T want the automated error-handling

response = requests.get(
ApiRequest.API_URL + '/kits',
ApiRequest.API_URL + '/kits/', # appending slash saves a 308 redir
auth=BearerAuth(session[TOKEN_KEY_NAME]),
verify=ApiRequest.CAfile,
params=ApiRequest.build_params({KIT_NAME_KEY: kit_name}))

if response.status_code == 404:
response_info = ("The provided kit id is not valid or has "
"already been used; please re-check your entry.")
error_msg = ("The provided kit id is not valid or has "
"already been used; please re-check your entry.")
elif response.status_code > 200:
response_info = unable_to_validate_msg
error_msg = unable_to_validate_msg
except: # noqa
response_info = unable_to_validate_msg
finally:
return json.dumps(response_info)
error_msg = unable_to_validate_msg

if error_msg is not None:
return None, error_msg, response.status_code
return response.json(), None, response.status_code


def post_check_acct_inputs(body):
kit, error, _ = _get_kit(body[KIT_NAME_KEY])
if error is None:
return flask.jsonify(True)
else:
return flask.jsonify(error)


def get_list_kit_samples(kit_name):
kit, error, code = _get_kit(kit_name)
if error is None:
return flask.jsonify(kit), code
else:
return flask.jsonify({"error": error}), code


def claim_samples(account_id, source_id, body):
# TODO: they could theoretically successfully claim some samples and
# fail out when trying to claim others. And I have no transaction support
# here. Boo...

if "sample_id" not in body:
# User claimed no samples...?
return redirect("/accounts/%s/sources/%s" % (account_id, source_id))

do_return, survey_output, _ = ApiRequest.get(
'/accounts/{0}/sources/{1}/surveys'.format(account_id, source_id)
)

if do_return:
return survey_output

sample_ids_to_claim = body['sample_id']

# Grab all primary and covid surveys from the source and associate with
# newly claimed samples
survey_ids_to_associate_with_samples = [
x['survey_id'] for x in survey_output
if x['survey_template_id'] in [1, 6]
]

error = _claim_kit_samples_helper(
account_id,
source_id,
sample_ids_to_claim,
survey_ids_to_associate_with_samples)
if error:
return error

return redirect("/accounts/%s/sources/%s" % (account_id, source_id))


def generate_error_page(error_msg):
Expand Down

0 comments on commit 3f3ca9a

Please sign in to comment.