Merge pull request #40 from poldracklab/oesteban-patch-1

[FIX] Do not pin versions

.circleci/config.yml

@@ -5,7 +5,7 @@ jobs:
     working_directory: /home/circleci/mriqcwebapi
 
     machine:
-      image: circleci/classic:201711-01
+      image: circleci/classic:latest
 
     environment:
       - SECRET_KEY: CI
@@ -28,7 +28,7 @@ jobs:
             touch dockereve-master/nginx/.ssl/mriqcep.crt
             touch dockereve-master/nginx/.ssl/mriqcep.key
             docker pull mongo:latest 
-            docker pull swaggerapi/swagger-ui:v3.0.12 
+            docker pull swaggerapi/swagger-ui:latest 
             docker pull nginx:latest
             docker-compose -f dockereve-master/docker-compose.yml build
       - run:

dockereve-master/docker-compose.yml

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

dockereve-master/eve-app/Dockerfile

@@ -1,12 +1,12 @@
-FROM python:3.4-onbuild
+FROM python:3.6-onbuild
 
 WORKDIR /usr/src/app
 
 ADD . /usr/src/app
 
 RUN pip3 install -r requirements.txt
 RUN pip3 install pytest
-RUN sed -i 's/\[scheme\]/\["https"\]/' /usr/local/lib/python3.4/site-packages/eve_swagger/objects.py
+RUN sed -i 's/\[scheme\]/\["https"\]/' /usr/local/lib/python3.6/site-packages/eve_swagger/objects.py
 
 #EXPOSE 5000
 #CMD ["python3", "server.py"]

dockereve-master/eve-app/app.py

@@ -11,10 +11,12 @@
 
 API_TOKEN = os.environ.get("API_TOKEN")
 
+
 class TokenAuth(TokenAuth):
     def check_auth(self, token, allowed_roles, resource, method):
         return token == API_TOKEN
 
+
 app = Eve(settings=settings, auth=TokenAuth)
 app.register_blueprint(swagger, url_prefix='/docs/api')
 app.add_url_rule('/docs/api', 'eve_swagger.index')
@@ -23,13 +25,14 @@ def check_auth(self, token, allowed_roles, resource, method):
 app.config['SWAGGER_INFO'] = {
     'title': 'MRIQC Web API',
     'version': 'v1',
-    'description': """<a href="http://mriqc.org">MRIQC</a> is an open-source tool that extracts 
-no-reference image quality metrics from structural and 
-functional MRI data developed by the <a href="http://poldracklab.stanford.edu"> 
-Poldrack Lab</a> at <a href="http://www.stanford.edu">Stanford University</a>. 
-This website provides an api to a crowdsourced repository of MRI quality 
-metrics contributed by users of MRIQC and hosted by 
-the <a href="http://cmn.nimh.nih.gov">Data Science and Sharing Team</a> 
+    'description': """\
+<a href="http://mriqc.org">MRIQC</a> is an open-source tool that extracts
+no-reference image quality metrics from structural and
+functional MRI data developed by the <a href="http://poldracklab.stanford.edu">
+Poldrack Lab</a> at <a href="http://www.stanford.edu">Stanford University</a>.
+This website provides an api to a crowdsourced repository of MRI quality
+metrics contributed by users of MRIQC and hosted by
+the <a href="http://cmn.nimh.nih.gov">Data Science and Sharing Team</a>
 at the <a href="http://nimh.nih.gov">National Institute of Mental Health</a>.""",
 }
 

dockereve-master/eve-app/requirements.txt

@@ -1,3 +1,3 @@
-gunicorn==19.3.0
-eve==0.7.4
-eve-swagger==0.0.7
+gunicorn
+eve
+eve-swagger

dockereve-master/eve-app/settings.py

@@ -1,5 +1,4 @@
 import os
-import re
 from copy import deepcopy
 
 bids_schema = {
@@ -553,7 +552,7 @@
     'API_VERSION': 'v1',
     'ALLOWED_FILTERS': ['*'],
     'MONGO_HOST': os.environ.get('MONGODB_HOST', ''),
-    'MONGO_PORT': os.environ.get('MONGODB_PORT', ''),
+    'MONGO_PORT': int(os.environ.get('MONGODB_PORT', '')),
     'MONGO_DBNAME': 'mriqc_api',
     'PUBLIC_METHODS': ['GET'],
     'PUBLIC_ITEM_METHODS': ['GET'],

dockereve-master/eve-app/test_settings.py

@@ -1,45 +1,46 @@
 from eve.tests import TestMinimal
 import os
-import re
 from flask_pymongo import MongoClient
 
 url = 'mriqc_api'
 MONGO_HOST = os.environ.get("MONGODB_HOST", 'mongodb'),
 MONGO_PORT = int(os.environ.get("MONGODB_PORT", 27017))
 MONGO_DBNAME = 'test_DB'
+
+
 class settingsTestCase(TestMinimal):
-	def setUp(self):
-		return super().setUp(settings_file = './settings.py') 
-	def dropDB(self):
-		self.connection = MongoClient(MONGO_HOST,MONGO_PORT)
-		self.connection.drop_database(MONGO_DBNAME)
-		self.connection.close()
-	def setupDB(self):
-		self.connection = MongoClient(MONGO_HOST,MONGO_PORT)
-		self.connection.drop_database(MONGO_DBNAME)
-	def testGet(self):
-		return_json,return_code = self.get(url)
-		self.assert200(return_code)
-	def testPost(self):
-	 	return_json, return_code = self.post(url, {"cjv": 0.1231231})
-	 	self.assertFalse(self.domain)
-	 	self.assertFalse(return_json)
-	 	# self.assert200(return_code)
-
-# class settingsTestCase(TestMinimal):
-# 	def dropDB(self):
-# 		self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
-# 		self.connection.drop_database(MONGO_DBNAME)
-# 		self.connection.close()
+    def setUp(self):
+        return super().setUp(settings_file='./settings.py')
 
-# 	def setupDB(self):
-# 		self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
-# 		self.connection.drop_database(MONGO_DBNAME)
-# 	def testPost():
-#     	return_json, return_code = self.post(url,{"cjg":0.123123}) 
-# 		print(return_json)
-# 		print(return_code)
+    def dropDB(self):
+        self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
+        self.connection.drop_database(MONGO_DBNAME)
+        self.connection.close()
 
+    def setupDB(self):
+        self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
+        self.connection.drop_database(MONGO_DBNAME)
 
+    def testGet(self):
+        return_json, return_code = self.get(url)
+        self.assert200(return_code)
 
+    def testPost(self):
+        return_json, return_code = self.post(url, {"cjv": 0.1231231})
+        self.assertFalse(self.domain)
+        self.assertFalse(return_json)
+        # self.assert200(return_code)
+
+# class settingsTestCase(TestMinimal):
+#   def dropDB(self):
+#       self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
+#       self.connection.drop_database(MONGO_DBNAME)
+#       self.connection.close()
 
+#   def setupDB(self):
+#       self.connection = MongoClient(MONGO_HOST, MONGO_PORT)
+#       self.connection.drop_database(MONGO_DBNAME)
+#   def testPost():
+#       return_json, return_code = self.post(url,{"cjg":0.123123})
+#       print(return_json)
+#       print(return_code)

test/T1w/missingField/sub-10159_T1w.json

@@ -37,8 +37,7 @@
   "icvs_csf": 0.2430190456707652, 
   "PatientPosition": "HFS", 
   "SequenceName": "*tfl3d1_ns", 
-  "summary_bg_p05": 0.0, 
-  "ImageType": "ORIGINAL/PRIMARY/M/ND/NORM", 
+  "summary_bg_p05": 0.0,
   "qi_2": 0.0042996791690604694, 
   "qi_1": 5.289201412128623e-06, 
   "ImagingFrequency": 123249959, 

test/T1w/validData/sub-50785_T1w.json

@@ -1,16 +1,7 @@
 {
   "bids_meta": {
     "modality": "T1w",
-    "subject_id": "50785",
-    "ImageType": [
-        "ORIGINAL",
-        "PRIMARY",
-        "M",
-        "MB",
-        "ND",
-        "NORM",
-        "MOSAIC"
-    ]
+    "subject_id": "50785"
   },
   "cjv": 0.3881841572763748,
   "cnr": 3.139893975583801,

test/testGetPost.py

@@ -29,7 +29,7 @@ def getRequest(post_resp, url):
     return get_resp.json()
 
 
-###### MAIN ######
+# MAIN ######
 header = {'content-type': 'application/json', 'Accept-Charset': 'UTF-8'}
 authenticated_header = header.copy()
 authenticated_header['Authorization'] = os.environ.get('API_TOKEN', '<secret_token>')
@@ -62,8 +62,7 @@ def test_00_GETAllData(self):
                   input_count)
         self.assertTrue(input_count == get_resp['_meta']['total'])
 
-
-    ########## Testing Bold ############
+    # Testing Bold ############
     def test_01_ConnectionStatus(self):
         log = logging.getLogger("mriqcwebapi")
 
@@ -85,10 +84,7 @@ def test_01_ConnectionStatus(self):
                 log.debug('Response: %s', get_resp.json())
                 self.assertTrue(get_resp.raise_for_status() is None)
 
-
     def test_02_MissingFieldInput(self):
-        log = logging.getLogger("mriqcwebapi")
-
         for file_name in glob(boldMissingPattern):
             with open(file_name) as fp:
                 input_data = json.load(fp)
@@ -99,8 +95,7 @@ def test_02_MissingFieldInput(self):
                 # print post_resp.status_code
                 self.assertTrue(post_resp.status_code == codeForInvalid)
 
-
-    ########## Testing T1w ############
+    # Testing T1w ############
     def test_03_ConnectionStatus(self):
         log = logging.getLogger("mriqcwebapi")
 
@@ -122,10 +117,7 @@ def test_03_ConnectionStatus(self):
                 log.debug('Response: %s', get_resp.json())
                 self.assertTrue(get_resp.raise_for_status() is None)
 
-
     def test_04_MissingFieldInput(self):
-        log = logging.getLogger("mriqcwebapi")
-
         for file_name in glob(T1wMissingPattern):
             with open(file_name) as fp:
                 input_data = json.load(fp)
@@ -136,11 +128,8 @@ def test_04_MissingFieldInput(self):
                 # print post_resp.status_code
                 self.assertTrue(post_resp.status_code == codeForInvalid)
 
-
-    ########## Cross Testing: send data to wrong end point ############
+    # Cross Testing: send data to wrong end point ############
     def test_05_boldDataToT1wEndPoint(self):
-        log = logging.getLogger("mriqcwebapi")
-
         for file_name in glob(boldPattern):
             with open(file_name) as fp:
                 input_data = json.load(fp)
@@ -150,10 +139,7 @@ def test_05_boldDataToT1wEndPoint(self):
                     headers=authenticated_header)
                 self.assertTrue(post_resp.status_code == codeForInvalid)
 
-
     def test_06_T1wDataToBoldEndPoint(self):
-        log = logging.getLogger("mriqcwebapi")
-
         for file_name in glob(T1wPattern):
             with open(file_name) as fp:
                 input_data = json.load(fp)
@@ -163,7 +149,6 @@ def test_06_T1wDataToBoldEndPoint(self):
                     headers=authenticated_header)
                 self.assertTrue(post_resp.status_code == codeForInvalid)
 
-
     def test_07_T1wDataValid(self):
         for file_name in glob(T1wPattern):
             with open(file_name) as fp:
@@ -182,7 +167,6 @@ def test_07_T1wDataValid(self):
                     # check key-value pair match
                     self.assertTrue(input_data[key] == queried_data[key])
 
-
     def test_08_boldDataValid(self):
         for file_name in glob(boldPattern):
             with open(file_name) as fp:
@@ -203,7 +187,6 @@ def test_08_boldDataValid(self):
                 # check key-value pair match
                 self.assertTrue(input_data[key] == queried_data[key])
 
-
     def test_09_failedAuth(self):
         with open(glob(boldPattern)[0]) as fp:
             inputData = json.load(fp)
@@ -234,6 +217,7 @@ def test_10_ratingDataValid(self):
             if elem['_id'] == "bad":
                 self.assertTrue(elem['count'] == 1)
 
+
 if __name__ == '__main__':
     logging.basicConfig(stream=sys.stderr)
     logging.getLogger("mriqcwebapi").setLevel(logging.DEBUG)