diff --git a/api/config.py b/api/config.py
index b4af832c4cd3e52d5cbec34fcfed50a6fdec54b3..f2acf5e9c765789afc6c75fa237232a7ffdbf0a7 100644
--- a/api/config.py
+++ b/api/config.py
@@ -104,6 +104,7 @@ schema_path = __config['persistent']['schema_path']
expected_mongo_schemas = set([
'acquisition.json',
+ 'analysis.json',
'collection.json',
'container.json',
'file.json',
@@ -119,6 +120,7 @@ expected_mongo_schemas = set([
])
expected_input_schemas = set([
'acquisition.json',
+ 'analysis.json',
'collection.json',
'container.json',
'file.json',
diff --git a/api/handlers/listhandler.py b/api/handlers/listhandler.py
index d1de460d0ae281b856e1919b9592b361e9d21408..cff21c7bc4d8fca905f068ab2f55130108b705b6 100644
--- a/api/handlers/listhandler.py
+++ b/api/handlers/listhandler.py
@@ -65,7 +65,9 @@ def initialize_list_configurations():
'analyses': {
'storage': liststorage.AnalysesStorage,
'permchecker': listauth.default_sublist,
- 'use_object_id': True
+ 'use_object_id': True,
+ 'storage_schema_file': 'analysis.json',
+ 'input_schema_file': 'analysis.json'
}
}
list_container_configurations = {
@@ -202,17 +204,11 @@ class ListHandler(base.RequestHandler):
else:
self.abort(404, 'Element {} not found in container {}'.format(_id, storage.cont_name))
- mongo_validator = None
- input_validator = None
- keycheck = None
-
- if conf.get('storage_schema_file'):
- mongo_schema_uri = validators.schema_uri('mongo', conf.get('storage_schema_file'))
- mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
- keycheck = validators.key_check(mongo_schema_uri)
- if conf.get('input_schema_file'):
- input_schema_uri = validators.schema_uri('input', conf.get('input_schema_file'))
- input_validator = validators.from_schema_path(input_schema_uri)
+ mongo_schema_uri = validators.schema_uri('mongo', conf.get('storage_schema_file'))
+ mongo_validator = validators.decorator_from_schema_path(mongo_schema_uri)
+ keycheck = validators.key_check(mongo_schema_uri)
+ input_schema_uri = validators.schema_uri('input', conf.get('input_schema_file'))
+ input_validator = validators.from_schema_path(input_schema_uri)
return permchecker, storage, mongo_validator, input_validator, keycheck
@@ -674,12 +670,14 @@ class AnalysesHandler(ListHandler):
"""
_id = kwargs.pop('cid')
- permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, _, payload_validator, _ = self._initialize_request(cont_name, list_name, _id)
permchecker(noop)('POST', _id=_id)
if self.is_true('job'):
if cont_name == 'sessions':
- return self._create_job_and_analysis(cont_name, _id, storage)
+ payload = self.request.json_body
+ payload_validator(payload.get('analysis',{}), 'POST')
+ return self._create_job_and_analysis(cont_name, _id, storage, payload)
else:
self.abort(400, 'Analysis created via a job must be at the session level')
@@ -692,8 +690,7 @@ class AnalysesHandler(ListHandler):
else:
self.abort(500, 'Element not added in list analyses of container {} {}'.format(cont_name, _id))
- def _create_job_and_analysis(self, cont_name, cid, storage):
- payload = self.request.json_body
+ def _create_job_and_analysis(self, cont_name, cid, storage, payload):
analysis = payload.get('analysis')
job = payload.get('job')
if job is None or analysis is None:
@@ -918,9 +915,14 @@ class AnalysesHandler(ListHandler):
def add_note(self, cont_name, list_name, **kwargs):
_id = kwargs.pop('cid')
analysis_id = kwargs.get('_id')
- permchecker, storage, _, input_validator, _ = self._initialize_request(cont_name, list_name, _id)
+ permchecker, storage, _, _, _ = self._initialize_request(cont_name, list_name, _id)
payload = self.request.json_body
+
+ notes_schema_file = list_handler_configurations[cont_name]['notes']['storage_schema_file']
+ input_schema_uri = validators.schema_uri('input', notes_schema_file)
+ input_validator = validators.from_schema_path(input_schema_uri)
input_validator(payload, 'POST')
+
payload['_id'] = str(bson.objectid.ObjectId())
payload['user'] = payload.get('user', self.uid)
payload['created'] = datetime.datetime.utcnow()
diff --git a/api/placer.py b/api/placer.py
index 6dc1b21c3124690a338f0b49b220f406b976c806..37c28d0523fbd6d3a49ab9c8e539169535f827fb 100644
--- a/api/placer.py
+++ b/api/placer.py
@@ -506,7 +506,7 @@ class AnalysisPlacer(Placer):
def check(self):
self.requireMetadata()
- #validators.validate_data(self.metadata, 'analysis.json', 'input', 'POST', optional=True)
+ validators.validate_data(self.metadata, 'analysis.json', 'input', 'POST', optional=True)
def process_file_field(self, field, info):
self.save_file(field)
@@ -533,7 +533,6 @@ class AnalysisJobPlacer(Placer):
def check(self):
if self.id_ is None:
raise Exception('Must specify a target analysis')
- #validators.validate_data(self.metadata, 'analysis.json', 'input', 'POST', optional=True)
def process_file_field(self, field, info):
if self.metadata is not None:
diff --git a/api/schemas/input/analysis.json b/api/schemas/input/analysis.json
new file mode 100644
index 0000000000000000000000000000000000000000..3b598eac1a75989e9e25dca678f66e34e19dc390
--- /dev/null
+++ b/api/schemas/input/analysis.json
@@ -0,0 +1,26 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "title": "Analysis",
+ "type": "object",
+ "properties": {
+ "inputs": {
+ "type": ["array", "null"],
+ "items": {
+ "$ref": "file.json"
+ }
+ },
+ "outputs": {
+ "type": ["array", "null"],
+ "items": {
+ "$ref": "file.json"
+ }
+ },
+ "notes": {"type": "array", "items": {"$ref": "note.json"}},
+ "description" : {"type": "string"},
+ "job": {"type": "string"},
+ "label": {"type": "string", "minLength": 1, "maxLength": 256},
+ "user": {"type": "string"}
+ },
+ "required": ["label"],
+ "additionalProperties": false
+}
diff --git a/api/schemas/mongo/analysis.json b/api/schemas/mongo/analysis.json
new file mode 100644
index 0000000000000000000000000000000000000000..ab39251273ad32681166b936e5d1a68fae7b4134
--- /dev/null
+++ b/api/schemas/mongo/analysis.json
@@ -0,0 +1,24 @@
+{
+ "$schema": "http://json-schema.org/draft-04/schema#",
+ "title": "Analysis",
+ "type": "object",
+ "properties": {
+ "_id": {"type": "string"},
+ "created": {},
+ "modified": {},
+ "notes": {"type": "array", "items": {"$ref": "note.json"}},
+ "files": {
+ "type": ["array", "null"],
+ "items": {
+ "$ref": "file.json",
+ "additionalProperties": {
+ "output": {"type": "boolean"},
+ "input": {"type": "boolean"}
+ }
+ }
+ },
+ "job": {"type": "string"},
+ "label": {"type": "string", "minLength": 1, "maxLength": 256},
+ "user": {"type": "string"}
+ }
+}