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oestebanoesteban
authored
Merge branch 'master' into shutdown
2 parents a51035c + 2d992b9 commit c372332

25 files changed

+427
-203
lines changed

‎.circleci/config.yml

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version: 2.1
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orbs:
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docker: circleci/docker@2.1.4
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jobs:
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build_and_test:
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working_directory: /home/circleci/mriqcwebapi
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machine:
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image: ubuntu-2004:202104-01
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docker_layer_caching: true
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environment:
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- SECRET_KEY: CI
16+
- MONGODB_HOST: mongodb
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- MONGODB_PORT: 27017
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- API_TOKEN: <secret_token>
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- API_URL: "http://localhost/docs/api"
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steps:
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- docker/install-docker-credential-helper
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- run:
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name: Docker authentication
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command: |
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if [[ -n $DOCKER_PAT ]]; then
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echo "$DOCKER_PAT" | docker login -u $DOCKER_USER --password-stdin
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fi
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- checkout
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- run:
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name: Install dependencies
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command: |
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python3 -m pip install --upgrade pip
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python3 -m pip install docker-compose
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python3 -m pip install requests
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- run:
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name: Set-up dockereve
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command: |
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mkdir -p dockereve-master/nginx/.ssl
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touch dockereve-master/nginx/.ssl/mriqcep.crt
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touch dockereve-master/nginx/.ssl/mriqcep.key
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docker pull mongo:latest
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docker pull swaggerapi/swagger-ui:latest
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docker pull nginx:latest
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docker-compose -f dockereve-master/docker-compose.yml build
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- run:
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name: Start server
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command: docker-compose -f dockereve-master/docker-compose.yml up -d
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- run:
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name: Test MRIQC WebAPI
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command: python3 test/testGetPost.py
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workflows:
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version: 2
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webapi:
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jobs:
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- build_and_test:
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context:
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- nipreps-common
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filters:
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tags:
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only: /.*/

‎circle.yml

-25
This file was deleted.

‎dockereve-master/docker-compose.yml

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@@ -16,7 +16,7 @@ nginx:
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- swagger_ui:swagger_ui
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swagger_ui:
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image: swaggerapi/swagger-ui:v3.0.12
19+
image: swaggerapi/swagger-ui:latest
2020
env_file: .env
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eve:

‎dockereve-master/eve-app/Dockerfile

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1-
FROM python:3.4-onbuild
1+
FROM python:3.6-onbuild
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33
WORKDIR /usr/src/app
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ADD . /usr/src/app
66

77
RUN pip3 install -r requirements.txt
88
RUN pip3 install pytest
9-
RUN sed -i 's/\[scheme\]/\["https"\]/' /usr/local/lib/python3.4/site-packages/eve_swagger/objects.py
9+
RUN sed -i 's/\[scheme\]/\["https"\]/' /usr/local/lib/python3.6/site-packages/eve_swagger/objects.py
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#EXPOSE 5000
1212
#CMD ["python3", "server.py"]

‎dockereve-master/eve-app/app.py

+7-3
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@@ -6,24 +6,28 @@
66

77
from eve import Eve
88
from eve.auth import TokenAuth
9-
from eve_swagger import swagger
9+
from eve_swagger import get_swagger_blueprint
1010
from settings import settings
1111

1212
API_TOKEN = os.environ.get("API_TOKEN")
1313

14+
1415
class TokenAuth(TokenAuth):
1516
def check_auth(self, token, allowed_roles, resource, method):
1617
return token == API_TOKEN
1718

19+
1820
app = Eve(settings=settings, auth=TokenAuth)
21+
swagger = get_swagger_blueprint()
1922
app.register_blueprint(swagger, url_prefix='/docs/api')
2023
app.add_url_rule('/docs/api', 'eve_swagger.index')
2124

2225
# required. See http://swagger.io/specification/#infoObject for details.
2326
app.config['SWAGGER_INFO'] = {
2427
'title': 'MRIQC Web API',
2528
'version': 'v1',
26-
'description': """<p>####################################################<br />
29+
'description': """\
30+
<p>####################################################<br />
2731
Because of a lapse in government funding, the information on this website
2832
may not be up to date, transactions submitted via the website may not be
2933
processed, and the agency may not be able to respond to inquiries until
@@ -35,7 +39,7 @@ def check_auth(self, token, allowed_roles, resource, method):
3539
no-reference image quality metrics from structural and
3640
functional MRI data developed by the <a href="http://poldracklab.stanford.edu">
3741
Poldrack Lab</a> at <a href="http://www.stanford.edu">Stanford University</a>.
38-
This website provides an api to a crowdsourced repository of MRI quality
42+
This website provides an API to a crowdsourced repository of MRI quality
3943
metrics contributed by users of MRIQC and hosted by
4044
the <a href="http://cmn.nimh.nih.gov">Data Science and Sharing Team</a>
4145
at the <a href="http://nimh.nih.gov">National Institute of Mental Health</a>.</p>""",

‎dockereve-master/eve-app/requirements.txt

+3-3
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1-
gunicorn==19.3.0
2-
eve==0.7.4
3-
eve-swagger==0.0.7
1+
gunicorn
2+
eve
3+
eve-swagger>=0.1

‎dockereve-master/eve-app/settings.py

+76-6
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,4 @@
11
import os
2-
import re
32
from copy import deepcopy
43

54
bids_schema = {
@@ -43,7 +42,7 @@
4342
'InversionTime': {'type': 'float'},
4443
'MRAcquisitionType': {'type': 'string'},
4544
'MRTransmitCoilSequence': {'type': 'string'},
46-
'MagneticFieldStrength': {'type': 'integer'},
45+
'MagneticFieldStrength': {'type': 'float'},
4746
'Manufacturer': {'type': 'string'},
4847
'ManufacturersModelName': {'type': 'string'},
4948
'MatrixCoilMode': {'type': 'string'},
@@ -553,13 +552,14 @@
553552
'API_VERSION': 'v1',
554553
'ALLOWED_FILTERS': ['*'],
555554
'MONGO_HOST': os.environ.get('MONGODB_HOST', ''),
556-
'MONGO_PORT': os.environ.get('MONGODB_PORT', ''),
555+
'MONGO_PORT': int(os.environ.get('MONGODB_PORT', 27017)),
557556
'MONGO_DBNAME': 'mriqc_api',
558557
'PUBLIC_METHODS': ['GET'],
559558
'PUBLIC_ITEM_METHODS': ['GET'],
560559
'RESOURCE_METHODS': ['GET', 'POST'],
561560
'ITEM_METHODS': ['GET'],
562561
'X_DOMAINS': '*',
562+
'X_HEADERS': ['Authorization', 'Content-Type'],
563563
'DOMAIN': {
564564
'bold': {
565565
'item_title': 'bold',
@@ -574,6 +574,72 @@
574574
}
575575
}
576576

577+
rating_schema = {
578+
'rating': {
579+
'type': 'string',
580+
'required': True
581+
},
582+
'name': {
583+
'type': 'string',
584+
'required': False
585+
},
586+
'comment': {
587+
'type': 'string',
588+
'required': False
589+
},
590+
'md5sum': {
591+
'type': 'string',
592+
'required': True
593+
}
594+
}
595+
596+
nipype_schema = {
597+
'interface_class_name': {
598+
'type': 'string',
599+
'required': True
600+
},
601+
'version': {
602+
'type': 'string',
603+
'required': True
604+
},
605+
'mem_peak_gb': {
606+
'type': 'float',
607+
'required': True
608+
},
609+
'duration_sec': {
610+
'type': 'float',
611+
'required': True
612+
},
613+
'inputs': {
614+
'type': 'dict',
615+
'required': True
616+
}
617+
}
618+
619+
settings['DOMAIN']['nipype_telemetry'] = {
620+
'type': 'dict',
621+
'required': False,
622+
'schema': deepcopy(nipype_schema)
623+
}
624+
625+
settings['DOMAIN']['rating'] ={
626+
'type': 'dict',
627+
'required': False,
628+
'schema': deepcopy(rating_schema)
629+
}
630+
631+
settings['DOMAIN']['rating_counts'] = {
632+
'datasource': {
633+
'source': 'rating',
634+
'aggregation': {
635+
'pipeline': [
636+
{"$match": {"md5sum": "$value"}},
637+
{"$unwind": "$rating"},
638+
{"$group": {"_id": "$rating", "count": {"$sum": 1}}},
639+
],
640+
}
641+
}
642+
}
577643

578644
settings['DOMAIN']['bold']['schema'] = deepcopy(bold_iqms_schema)
579645
settings['DOMAIN']['bold']['schema'].update(
@@ -588,7 +654,12 @@
588654
'type': 'dict',
589655
'required': True,
590656
'schema': deepcopy(prov_schema)
591-
}
657+
},
658+
'rating': {
659+
'type': 'dict',
660+
'required': False,
661+
'schema': deepcopy(rating_schema)
662+
},
592663
}
593664
)
594665

@@ -613,9 +684,8 @@
613684
'type': 'dict',
614685
'required': True,
615686
'schema': deepcopy(prov_schema)
616-
}
687+
},
617688
}
618689
)
619690

620691
settings['DOMAIN']['T2w']['schema'] = deepcopy(settings['DOMAIN']['T1w']['schema'])
621-

‎dockereve-master/eve-app/test_settings.py

+32-31
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@@ -1,45 +1,46 @@
11
from eve.tests import TestMinimal
22
import os
3-
import re
43
from flask_pymongo import MongoClient
54

65
url = 'mriqc_api'
76
MONGO_HOST = os.environ.get("MONGODB_HOST", 'mongodb'),
87
MONGO_PORT = int(os.environ.get("MONGODB_PORT", 27017))
98
MONGO_DBNAME = 'test_DB'
9+
10+
1011
class settingsTestCase(TestMinimal):
11-
def setUp(self):
12-
return super().setUp(settings_file = './settings.py')
13-
def dropDB(self):
14-
self.connection = MongoClient(MONGO_HOST,MONGO_PORT)
15-
self.connection.drop_database(MONGO_DBNAME)
16-
self.connection.close()
17-
def setupDB(self):
18-
self.connection = MongoClient(MONGO_HOST,MONGO_PORT)
19-
self.connection.drop_database(MONGO_DBNAME)
20-
def testGet(self):
21-
return_json,return_code = self.get(url)
22-
self.assert200(return_code)
23-
def testPost(self):
24-
return_json, return_code = self.post(url, {"cjv": 0.1231231})
25-
self.assertFalse(self.domain)
26-
self.assertFalse(return_json)
27-
# self.assert200(return_code)
28-
29-
# class settingsTestCase(TestMinimal):
30-
# def dropDB(self):
31-
# self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
32-
# self.connection.drop_database(MONGO_DBNAME)
33-
# self.connection.close()
12+
def setUp(self):
13+
return super().setUp(settings_file='./settings.py')
3414

35-
# def setupDB(self):
36-
# self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
37-
# self.connection.drop_database(MONGO_DBNAME)
38-
# def testPost():
39-
# return_json, return_code = self.post(url,{"cjg":0.123123})
40-
# print(return_json)
41-
# print(return_code)
15+
def dropDB(self):
16+
self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
17+
self.connection.drop_database(MONGO_DBNAME)
18+
self.connection.close()
4219

20+
def setupDB(self):
21+
self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
22+
self.connection.drop_database(MONGO_DBNAME)
4323

24+
def testGet(self):
25+
return_json, return_code = self.get(url)
26+
self.assert200(return_code)
4427

28+
def testPost(self):
29+
return_json, return_code = self.post(url, {"cjv": 0.1231231})
30+
self.assertFalse(self.domain)
31+
self.assertFalse(return_json)
32+
# self.assert200(return_code)
33+
34+
# class settingsTestCase(TestMinimal):
35+
# def dropDB(self):
36+
# self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
37+
# self.connection.drop_database(MONGO_DBNAME)
38+
# self.connection.close()
4539

40+
# def setupDB(self):
41+
# self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
42+
# self.connection.drop_database(MONGO_DBNAME)
43+
# def testPost():
44+
# return_json, return_code = self.post(url,{"cjg":0.123123})
45+
# print(return_json)
46+
# print(return_code)

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