diff --git a/api/dao/containerstorage.py b/api/dao/containerstorage.py
index 673c9182c18428e2328236bd394cd01cab87835d..16ad589d4f147a8875424ca2debfecd496adb7a7 100644
--- a/api/dao/containerstorage.py
+++ b/api/dao/containerstorage.py
@@ -1,6 +1,5 @@
import bson.errors
import bson.objectid
-import json
import pymongo.errors
from .. import util
@@ -222,20 +221,6 @@ class ProjectStorage(ContainerStorage):
def __init__(self):
super(ProjectStorage,self).__init__('projects', use_object_id=True)
- def _from_mongo(self, cont):
- if cont:
- template = cont.get('template')
- if template:
- cont['template'] = json.loads(template)
- return super(ProjectStorage,self)._from_mongo(cont)
-
- def _to_mongo(self, payload):
- if payload:
- template = payload.get('template')
- if template:
- payload['template'] = json.dumps(template)
- return super(ProjectStorage,self)._to_mongo(payload)
-
def update_el(self, _id, payload, unset_payload=None, recursive=False, r_payload=None, replace_metadata=False):
result = super(ProjectStorage, self).update_el(_id, payload, unset_payload=unset_payload, recursive=recursive, r_payload=r_payload, replace_metadata=replace_metadata)
diff --git a/api/dao/hierarchy.py b/api/dao/hierarchy.py
index aeb54d8d20ad91ab4a54c08e9cf6ee0975821a40..469492ec3010110cfc6890f3725643973bcbdd7a 100644
--- a/api/dao/hierarchy.py
+++ b/api/dao/hierarchy.py
@@ -3,7 +3,6 @@ import copy
import datetime
import dateutil.parser
import difflib
-from jsonschema import Draft4Validator, ValidationError
import pymongo
import re
@@ -118,32 +117,77 @@ def is_session_compliant(session, template):
Given a project-level session template and a session,
returns True/False if the session is in compliance with the template
"""
+
+ def check_req(cont, req_k, req_v):
+ """
+ Return True if container satisfies specific requirement.
+ """
+ cont_v = cont.get(req_k)
+ if cont_v:
+ if isinstance(req_v, dict):
+ for k,v in req_v.iteritems():
+ if not check_req(cont_v, k, v):
+ return False
+ elif isinstance(cont_v, list):
+ found_in_list = False
+ for v in cont_v:
+ if bool(re.match(req_v, cont_v)):
+ found_in_list = True
+ break
+ if not found_in_list:
+ return False
+ else:
+ # Assume regex for now
+ if not bool(re.match(req_v, cont_v)):
+ return False
+ else:
+ return False
+ return True
+
+
+ def check_cont(cont, reqs):
+ """
+ Return True if container satisfies requirements.
+ Return False otherwise.
+ """
+
+ for req_k, req_v in reqs.iteritems():
+ if req_k == 'files':
+ file_reqs = req_v
+ min_count = file_reqs.pop('minimum')
+ count = 0
+ for f in cont.get('files', []):
+ if not check_cont(f, req_v):
+ # Didn't find a match, on to the next one
+ continue
+ else:
+ count += 1
+ if count >= min_count:
+ break
+ if count < min_count:
+ return False
+
+ else:
+ if not check_req(cont, req_k, req_v):
+ return False
+ return True
+
+
s_requirements = template.get('session')
a_requirements = template.get('acquisitions')
- f_requirements = template.get('files')
-
- acquisitions = []
- if a_requirements or f_requirements:
- if session.get('_id'):
- # Only grab acquisitions when not validating a newly created session
- acquisitions = list(config.db.acquisitions.find({'session': session['_id']}))
if s_requirements:
- validator = Draft4Validator(s_requirements.get('schema'))
- try:
- validator.validate(session)
- except ValidationError:
+ if not check_cont(session, s_requirements):
return False
if a_requirements:
+ acquisitions = list(config.db.acquisitions.find({'session': session['_id']}))
for req in a_requirements:
- validator = Draft4Validator(req.get('schema'))
- min_count = req.get('minimum')
+ min_count = req.pop('minimum')
count = 0
for a in acquisitions:
- try:
- validator.validate(a)
- except ValidationError:
+ if not check_cont(a, req):
+ # Didn't find a match, on to the next one
continue
else:
count += 1
@@ -151,25 +195,6 @@ def is_session_compliant(session, template):
break
if count < min_count:
return False
-
- if f_requirements:
- files_ = [f for a in acquisitions for f in a.get('files', [])]
- for req in f_requirements:
- validator = Draft4Validator(req.get('schema'))
- min_count = req.get('minimum')
- count = 0
- for f in files_:
- try:
- validator.validate(a)
- except ValidationError:
- continue
- else:
- count += 1
- if count >= min_count:
- break
- if count < min_count:
- return False
-
return True
def upsert_fileinfo(cont_name, _id, fileinfo):
@@ -412,7 +437,6 @@ def upsert_bottom_up_hierarchy(metadata, user=None, site=None):
def upsert_top_down_hierarchy(metadata, type_='label', user=None, site=None):
- log.debug('I know my type is {}'.format(type_))
group = metadata['group']
project = metadata['project']
session = metadata.get('session')
@@ -491,7 +515,6 @@ def _update_container_nulls(base_query, update, container_type):
q.update(base_query)
q['$or'] = [{k: {'$exists': False}}, {k: None}]
u = {'$set': {k: v}}
- log.debug('the query is {} and the update is {}'.format(q,u))
bulk.find(q).update_one(u)
bulk.execute()
return config.db[coll_name].find_one(base_query)
diff --git a/bin/database.py b/bin/database.py
index c710e3f8ff988fe4e41fefa6240eca0a48016608..9d122e351e93ef12718f8257cc854ef6a04db4fd 100755
--- a/bin/database.py
+++ b/bin/database.py
@@ -542,17 +542,20 @@ def upgrade_to_21():
Acquisition fields `instrument` and `measurement` removed
"""
-
-
-
- # def update_project_template(template):
- # for a in template.get('acquisitions', []):
- # properties = a['schema']['properties']
- # if 'measurement' in properties:
- # m_req = properties.pop('measurement')
- # a['files']['schema']
-
- # return template
+ def update_project_template(template):
+ new_template = {'acquisitions': []}
+ for a in template.get('acquisitions', []):
+ new_a = {'minimum': a['minimum']}
+ properties = a['schema']['properties']
+ if 'measurement' in properties:
+ m_req = properties.pop('measurement')
+ new_a['files']=[{'measurement': m_req['pattern'], 'minimum': 1}]
+ if 'label' in properties:
+ l_req = properties.pop('label')
+ new_a['label'] = l_req['pattern']
+ new_template['acquisitions'].append(new_a)
+
+ return new_template
def dm_v2_updates(cont_list, cont_name):
for container in cont_list:
@@ -561,7 +564,9 @@ def upgrade_to_21():
update = {'$rename': {'metadata': 'info'}}
if cont_name == 'projects' and container.get('template'):
- pass
+ new_template = update_project_template(json.loads(container.get('template')))
+ update['$set'] = {'template': new_template}
+
if cont_name == 'sessions':
update['$rename'].update({'subject.metadata': 'subject.info'})
@@ -597,7 +602,7 @@ def upgrade_to_21():
dm_v2_updates(config.db.collections.find(query), 'collections')
query['$or'].append({'template': { '$exists': True}})
- dm_v2_updates(config.db.projects.find(query), 'projects')
+ dm_v2_updates(config.db.projects.find({}), 'projects')
query['$or'].append({'subject': { '$exists': True}})
dm_v2_updates(config.db.sessions.find(query), 'sessions')
diff --git a/raml/schemas/definitions/project-template.json b/raml/schemas/definitions/project-template.json
index d70bfb700010e0aedc308b19479107aff0576a86..b45e8c316dd3ce210aeb8e777387a2a8b856a67c 100644
--- a/raml/schemas/definitions/project-template.json
+++ b/raml/schemas/definitions/project-template.json
@@ -9,29 +9,19 @@
{"required": ["maximum"]}
],
"properties": {
- "schema": {"$ref": "http://json-schema.org/draft-04/schema"},
"minimum": {"type": "integer", "minimum": 0},
"maximum": {"type": "integer", "minimum": 0}
- },
- "required": ["schema"]
+ }
}
},
"properties": {
"session": {
- "properties": {
- "schema": {"$ref": "http://json-schema.org/draft-04/schema"}
- },
- "required": ["schema"]
+ "type": "object"
},
"acquisitions": {
"type": "array",
"minItems": 1,
"items": {"$ref": "#/definitions/requirement"}
- },
- "files": {
- "type": "array",
- "minItems": 1,
- "items": {"$ref": "#/definitions/requirement"}
}
},
"additionalProperties": false
diff --git a/test/integration_tests/postman/integration_tests.postman_collection b/test/integration_tests/postman/integration_tests.postman_collection
index a6f651ee53d6c8231bedf2c581b0bca73d855fbf..43a654db98e23dd9d889f209cc52978a13a63880 100644
--- a/test/integration_tests/postman/integration_tests.postman_collection
+++ b/test/integration_tests/postman/integration_tests.postman_collection
@@ -38,8 +38,7 @@
"body": {
"mode": "raw",
"raw": "{\"_id\":\"jane.doe@gmail.com\",\"firstname\":\"Jane\",\"lastname\":\"Doe\",\"email\":\"jane.doe@gmail.com\"}"
- },
- "description": "List users\n\n"
+ }
},
"response": []
},
@@ -76,8 +75,7 @@
"body": {
"mode": "raw",
"raw": "{\"_id\":\"jane.doe@gmail.com\", \"lastname\":\"Doe\",\"email\":\"jane.doe@gmail.com\"}"
- },
- "description": "\n\n"
+ }
},
"response": []
},
@@ -121,8 +119,7 @@
"enabled": true
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -155,8 +152,7 @@
"body": {
"mode": "raw",
"raw": "{\n\"_id\":\"test-group\"\n}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -207,8 +203,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -253,8 +248,7 @@
"body": {
"mode": "raw",
"raw": "{\"_id\":\"jane.doe@gmail.com\",\"firstname\":\"Jane\",\"lastname\":\"Doe\",\"email\":\"jane.doe@gmail.com\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -296,8 +290,7 @@
"body": {
"mode": "raw",
"raw": "{\"_id\":\"jane.doe@gmail.com\",\"firstname\":\"Jane\",\"lastname\":\"Doe\",\"email\":\"jane.doe@gmail.com\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -327,8 +320,7 @@
"body": {
"mode": "raw",
"raw": "{\n\t\"category\": \"converter\",\n\t\"input\": { },\n\t\"name\": \"test_gear\",\n\t\"manifest\": {\n\t\t\"name\": \"test_gear\",\n\t\t\"inputs\": {\n\t\t\t\"any text file <= 100 KB\": {\n\t\t\t\t\"base\": \"file\",\n\t\t\t\t\"name\": {\n\t\t\t\t\t\"pattern\": \"^.*.txt$\"\n\t\t\t\t},\n\t\t\t\t\"size\": {\n\t\t\t\t\t\"maximum\": 100000\n\t\t\t\t}\n\t\t\t}\n\t\t},\n\t\t\"description\": \"A gear to test the API\",\n\t\t\"license\": \"Other\",\n\t\t\"author\": \"\",\n\t\t\"url\": \"https://unknown.example\",\n\t\t\"label\": \"An exported gear\",\n\t\t\"source\": \"https://unknown.example\",\n\t\t\"config\": {\n\t\t\t\"two-digit multiple of ten\": {\n\t\t\t\t\"exclusiveMaximum\": true,\n\t\t\t\t\"type\": \"number\",\n\t\t\t\t\"multipleOf\": 10,\n\t\t\t\t\"maximum\": 100\n\t\t\t}\n\t\t}\n\t}\n}"
- },
- "description": "Create or update a gear.\n\"Name\" field of gear must match \"GearName\" uri parameter\nIf no existing gear is found, one will be created\nOtherwise, the specified gear will be updated\n\n\nParameters:\n\nGearName: Name of the gear to interact with\n\n"
+ }
},
"response": []
},
@@ -389,8 +381,7 @@
"body": {
"mode": "raw",
"raw": "{\n \"gear\": \"test-case-gear\",\n \"inputs\": {\n \"dicom\": {\n \"type\": \"acquisition\",\n \"id\": \"{{test-acquisition-1-id}}\",\n \"name\" : \"1_1_dicom.zip\"\n }\n },\n \"config\": {\n\t\t\"two-digit multiple of ten\": 20\n\t},\n \"destination\": {\n \"type\": \"acquisition\",\n \"id\": \"{{test-acquisition-1-id}}\"\n },\n \"tags\": [\n \"ad-hoc\"\n ]\n}\n"
- },
- "description": ""
+ }
},
"response": []
},
@@ -425,8 +416,7 @@
"body": {
"mode": "raw",
"raw": "{\n \"label\":\"test-collection-1\"\n}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -457,8 +447,7 @@
"body": {
"mode": "raw",
"raw": "{\n \"contents\":{\n \t\"operation\":\"add\",\n \t\"nodes\":[\n \t\t{\n \t\t\t\"level\":\"session\",\n \t\t\t\"_id\":\"{{test-session-1-id}}\"\n \t\t}\n \t]\n }\n}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -498,8 +487,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -530,8 +518,7 @@
"body": {
"mode": "raw",
"raw": "{\n \"label\":\"test-collection-2\"\n}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -571,8 +558,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -612,8 +598,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -645,8 +630,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -678,8 +662,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -711,8 +694,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -744,8 +726,7 @@
"body": {
"mode": "raw",
"raw": "{\n \"text\":\"test note\"\n}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -785,8 +766,7 @@
"body": {
"mode": "raw",
"raw": "{\n \"analysis\": {\n \"label\": \"Test Analysis 1\"\n },\n \"job\" : {\n \"gear\": \"test-case-gear\",\n \"inputs\": {\n \"dicom\": {\n \"type\": \"acquisition\",\n \"id\": \"{{test-acquisition-1-id}}\",\n \"name\" : \"test-1.dcm\"\n }\n },\n \"tags\": [\"example\"]\n }\n}\n"
- },
- "description": ""
+ }
},
"response": []
},
@@ -835,8 +815,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -874,8 +853,7 @@
"body": {
"mode": "raw",
"raw": ""
- },
- "description": ""
+ }
},
"response": []
},
@@ -924,8 +902,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -971,8 +948,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -1021,8 +997,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -1069,8 +1044,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -1119,8 +1093,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -1166,8 +1139,7 @@
"value": ""
}
]
- },
- "description": ""
+ }
},
"response": []
},
@@ -1199,8 +1171,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -1232,8 +1203,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -1265,8 +1235,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -1298,8 +1267,7 @@
"body": {
"mode": "raw",
"raw": "{\"text\":\"test note\"}"
- },
- "description": ""
+ }
},
"response": []
},
@@ -1334,8 +1302,7 @@
"body": {
"mode": "raw",
"raw": " {\n \"group\": \"test-group\",\n \"label\": \"Project with template\",\n \"public\": false\n }"
- },
- "description": "Create the project for testing session templates"
+ }
},
"response": []
},
@@ -1370,8 +1337,7 @@
"body": {
"mode": "raw",
"raw": " {\n \"subject\": {\n \"code\": \"ex8945\"\n },\n \"label\": \"Compliant Session\",\n \"project\": \"{{ST-project-id}}\",\n \"public\": false\n }"
- },
- "description": "Create a session that will be compliant with the project-level session template"
+ }
},
"response": []
},
@@ -1406,8 +1372,7 @@
"body": {
"mode": "raw",
"raw": " {\n \"subject\": {\n \"code\": \"ex9849\"\n },\n \"label\": \"Non-compliant Session\",\n \"project\": \"{{ST-project-id}}\",\n \"public\": false\n }"
- },
- "description": "Create a session that will NOT be compliant with the project-level session template"
+ }
},
"response": []
},
@@ -1441,9 +1406,8 @@
],
"body": {
"mode": "raw",
- "raw": "{\n \"label\": \"c-acquisition-1-t1\",\n \"session\":\"{{ST-compliant-session-id}}\",\n \"public\": false,\n \"measurement\": \"localizer\"\n}"
- },
- "description": "Create an acquisition for the compliant session"
+ "raw": "{\n \"label\": \"c-acquisition-1-t1\",\n \"session\":\"{{ST-compliant-session-id}}\",\n \"public\": false\n}"
+ }
},
"response": []
},
@@ -1477,9 +1441,8 @@
],
"body": {
"mode": "raw",
- "raw": "{\n \"label\": \"c-acquisition-2\",\n \"session\":\"{{ST-compliant-session-id}}\",\n \"public\": false,\n \"measurement\": \"localizer\"\n}"
- },
- "description": "Create an acquisition for the compliant session"
+ "raw": "{\n \"label\": \"c-acquisition-2-t1\",\n \"session\":\"{{ST-compliant-session-id}}\",\n \"public\": false\n}"
+ }
},
"response": []
},
@@ -1513,9 +1476,8 @@
],
"body": {
"mode": "raw",
- "raw": "{\n \"label\": \"nc-acquisition-1\",\n \"session\":\"{{ST-noncompliant-session-id}}\",\n \"public\": false,\n \"measurement\": \"localizer\"\n}"
- },
- "description": "Create an acquisition for the noncompliant session"
+ "raw": "{\n \"label\": \"nc-acquisition-1-t1\",\n \"session\":\"{{ST-noncompliant-session-id}}\",\n \"public\": false\n}"
+ }
},
"response": []
},
@@ -1545,13 +1507,17 @@
"key": "Authorization",
"value": "scitran-user {{test_user_api_key}}",
"description": ""
+ },
+ {
+ "key": "Content-Type",
+ "value": "application/json",
+ "description": ""
}
],
"body": {
"mode": "raw",
- "raw": "{\n \"session\": {\n \"schema\": {\n \"$schema\": \"http://json-schema.org/draft-04/schema#\",\n \"properties\": {\n \"subject\": {\n \"type\": \"object\",\n \"properties\": {\n \"code\": {\n \"type\": \"string\",\n \"pattern\": \"^ex\" \n }\n },\n \"required\": [\"code\"]\n }\n },\n \"required\": [\"subject\"]\n }\n },\n \"acquisitions\": [\n {\n \"schema\": {\n \"$schema\": \"http://json-schema.org/draft-04/schema#\",\n \"type\": \"object\",\n \"properties\": {\n \"measurement\": {\n \"type\": \"string\",\n \"pattern\": \"^(?i)localizer$\" \n }\n },\n \"required\": [\"measurement\"]\n },\n \"minimum\": 2\n },\n {\n \"schema\": {\n \"$schema\": \"http://json-schema.org/draft-04/schema#\",\n \"type\": \"object\",\n \"properties\": {\n \"measurement\": {\n \"type\": \"string\",\n \"pattern\": \"^(?i)localizer$\" \n },\n \"label\": {\n \"type\": \"string\",\n \"pattern\": \"t1\"\n }\n },\n \"required\": [\"label\", \"measurement\"]\n },\n \"minimum\": 1\n }\n ]\n}"
- },
- "description": "Should modify project and it's sessions. Both sessions should have a \"project-has-template\" flag as \"true\" and the session setup to be compliant should have \"compliant\" flag set to True."
+ "raw": "{\n \"session\": {\n \"subject\": {\n \"code\" : \"^ex\"\n }\n },\n \"acquisitions\": [\n {\n \"label\": \"t1\",\n \"minimum\": 2\n }\n ]\n}"
+ }
},
"response": []
},
@@ -1588,8 +1554,7 @@
"body": {
"mode": "raw",
"raw": ""
- },
- "description": ""
+ }
},
"response": []
},
@@ -1626,8 +1591,7 @@
"body": {
"mode": "raw",
"raw": ""
- },
- "description": ""
+ }
},
"response": []
},
@@ -1657,13 +1621,17 @@
"key": "Authorization",
"value": "scitran-user {{test_user_api_key}}",
"description": ""
+ },
+ {
+ "key": "Content-Type",
+ "value": "application/json",
+ "description": ""
}
],
"body": {
"mode": "raw",
- "raw": "{\n \"label\": \"nc-acquisition-2-t1\",\n \"session\":\"{{ST-noncompliant-session-id}}\",\n \"public\": false,\n \"measurement\": \"localizer\"\n}"
- },
- "description": "This should make the session compliant"
+ "raw": "{\n \"label\": \"nc-acquisition-2-t1\",\n \"session\":\"{{ST-noncompliant-session-id}}\",\n \"public\": false\n}"
+ }
},
"response": []
},
@@ -1700,8 +1668,7 @@
"body": {
"mode": "raw",
"raw": ""
- },
- "description": ""
+ }
},
"response": []
},
@@ -1728,13 +1695,17 @@
"key": "Authorization",
"value": "scitran-user {{test_user_api_key}}",
"description": ""
+ },
+ {
+ "key": "Content-Type",
+ "value": "application/json",
+ "description": ""
}
],
"body": {
"mode": "raw",
"raw": " {\n \"subject\": {\n \"code\": \"bad-subject-code\"\n }\n }"
- },
- "description": "Create a session that will NOT be compliant with the project-level session template"
+ }
},
"response": []
},
@@ -1771,10 +1742,9 @@
"body": {
"mode": "raw",
"raw": ""
- },
- "description": ""
+ }
},
"response": []
}
]
-}
\ No newline at end of file
+}