diff --git a/collections_.py b/collections_.py
new file mode 100644
index 0000000000000000000000000000000000000000..8bfb6c9eb105212892a33681faaa1af1c702768e
--- /dev/null
+++ b/collections_.py
@@ -0,0 +1,273 @@
+# @author: Gunnar Schaefer
+
+import re
+import json
+import webapp2
+import bson.json_util
+
+import nimsapiutil
+
+# curator (later: multiple curators and authorizers)
+# name
+# permissions
+# epochs point to collections
+
+# /collections
+# /collections/<cid>/sessions
+# /collections/<cid>/epochs?session=<sid>
+# /collections/<cid>/sessions/<sid>/epochs
+
+class Collections(nimsapiutil.NIMSRequestHandler):
+
+ """/collections """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Collection List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Collection',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
+ },
+ 'group': {
+ 'title': 'Group',
+ 'type': 'string',
+ },
+ 'name': {
+ 'title': 'Name',
+ 'type': 'string',
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'permissions': {
+ 'title': 'Permissions',
+ 'type': 'object',
+ },
+ }
+ }
+ }
+
+ def count(self):
+ """Return the number of Collections."""
+ self.response.write(json.dumps(self.app.db.collections.count()))
+
+ def post(self):
+ """Create a new Collection."""
+ self.response.write('collections post\n')
+
+ def get(self):
+ """Return the list of Collections."""
+ query = {'permissions.' + self.userid: {'$exists': 'true'}} if not self.user_is_superuser else None
+ projection = ['curator', 'name', 'permissions.'+self.userid]
+ collections = list(self.app.db.collections.find(query, projection))
+ #session_aggregates = self.app.db.sessions.aggregate([
+ # {'$match': {'collection': {'$in': [col['_id'] for col in collections]}}},
+ # {'$group': {'_id': '$collection', 'timestamp': {'$max': '$timestamp'}}},
+ # ])['result']
+ #timestamps = {sa['_id']: sa['timestamp'] for sa in session_aggregates}
+ #for col in collections:
+ # col['timestamp'] = timestamps[col['_id']]
+ self.response.write(json.dumps(collections, default=bson.json_util.default))
+
+ def put(self):
+ """Update many Collections."""
+ self.response.write('collections put\n')
+
+
+class Collection(nimsapiutil.NIMSRequestHandler):
+
+ """/collections/<cid> """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Collection',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
+ },
+ 'group': {
+ 'title': 'Group',
+ 'type': 'string',
+ },
+ 'name': {
+ 'title': 'Name',
+ 'type': 'string',
+ 'maxLength': 32,
+ },
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
+ 'permissions': {
+ 'title': 'Permissions',
+ 'type': 'object',
+ 'minProperties': 1,
+ },
+ 'files': {
+ 'title': 'Files',
+ 'type': 'array',
+ 'items': nimsapiutil.NIMSRequestHandler.file_schema,
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id', 'group', 'name'], #FIXME
+ }
+
+ def get(self, cid):
+ """Return one Collection, conditionally with details."""
+ collection = self.app.db.collections.find_one({'_id': bson.objectid.ObjectId(cid)})
+ if not collection:
+ self.abort(404)
+ collection['timestamp'] = self.app.db.sessions.aggregate([
+ {'$match': {'collection': bson.objectid.ObjectId(cid)}},
+ {'$group': {'_id': '$collection', 'timestamp': {'$max': '$timestamp'}}},
+ ])['result'][0]['timestamp']
+ if not self.user_is_superuser:
+ if self.userid not in collection['permissions']:
+ self.abort(403)
+ if collection['permissions'][self.userid] != 'admin' and collection['permissions'][self.userid] != 'pi':
+ collection['permissions'] = {self.userid: collection['permissions'][self.userid]}
+ self.response.write(json.dumps(collection, default=bson.json_util.default))
+
+ def put(self, cid):
+ """Update an existing Collection."""
+ self.response.write('collection %s put, %s\n' % (exp_id, self.request.params))
+
+ def delete(self, cid):
+ """Delete an Collection."""
+ self.response.write('collection %s delete, %s\n' % (exp_id, self.request.params))
+
+
+class Sessions(nimsapiutil.NIMSRequestHandler):
+
+ """/collections/<cid>/sessions """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Session List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Session',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'name': {
+ 'title': 'Session',
+ 'type': 'string',
+ },
+ 'subject': {
+ 'title': 'Subject',
+ 'type': 'string',
+ },
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
+ def count(self):
+ """Return the number of Sessions."""
+ self.response.write(json.dumps(self.app.db.sessions.count()))
+
+ def post(self):
+ """Create a new Session"""
+ self.response.write('sessions post\n')
+
+ def get(self, cid):
+ """Return the list of Session Epochs."""
+ collection = self.app.db.collections.find_one({'_id': bson.objectid.ObjectId(cid)})
+ if not collection:
+ self.abort(404)
+ if not self.user_is_superuser and self.userid not in collection['permissions']:
+ self.abort(403)
+ aggregated_epochs = self.app.db.epochs.aggregate([
+ {'$match': {'collections': bson.objectid.ObjectId(cid)}},
+ {'$group': {'_id': '$session'}},
+ ])['result']
+ query = {'_id': {'$in': [agg_epoch['_id'] for agg_epoch in aggregated_epochs]}}
+ projection = ['name', 'subject']
+ sessions = list(self.app.db.sessions.find(query, projection))
+ for sess in sessions:
+ sess['site'] = self.app.config['site_id']
+ self.response.write(json.dumps(sessions, default=bson.json_util.default))
+
+ def put(self):
+ """Update many Sessions."""
+ self.response.write('sessions put\n')
+
+
+class Epochs(nimsapiutil.NIMSRequestHandler):
+
+ """/collections/<cid>/epochs """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Epoch List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Epoch',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'name': {
+ 'title': 'Epoch',
+ 'type': 'string',
+ },
+ 'description': {
+ 'title': 'Description',
+ 'type': 'string',
+ },
+ 'datatype': {
+ 'title': 'Datatype',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
+ def count(self):
+ """Return the number of Epochs."""
+ self.response.write(json.dumps(self.app.db.epochs.count()))
+
+ def post(self):
+ """Create a new Epoch."""
+ self.response.write('epochs post\n')
+
+ def get(self, cid):
+ """Return the list of Session Epochs."""
+ collection = self.app.db.collections.find_one({'_id': bson.objectid.ObjectId(cid)})
+ if not collection:
+ self.abort(404)
+ if not self.user_is_superuser and self.userid not in collection['permissions']:
+ self.abort(403)
+ query = {'collections': bson.objectid.ObjectId(cid)}
+ sid = self.request.get('session')
+ if re.match(r'^[0-9a-f]{24}$', sid):
+ query['session'] = bson.objectid.ObjectId(sid)
+ elif sid != '':
+ self.abort(400)
+ projection = ['name', 'description', 'datatype']
+ epochs = list(self.app.db.epochs.find(query, projection))
+ self.response.write(json.dumps(epochs, default=bson.json_util.default))
+
+ def put(self):
+ """Update many Epochs."""
+ self.response.write('epochs put\n')
diff --git a/epochs.py b/epochs.py
deleted file mode 100644
index fb62300dda39543e851497b755c6690b14ade99b..0000000000000000000000000000000000000000
--- a/epochs.py
+++ /dev/null
@@ -1,133 +0,0 @@
-# @author: Gunnar Schaefer
-
-import json
-import webapp2
-import bson.json_util
-
-import nimsdata
-import nimsapiutil
-
-
-class Epochs(nimsapiutil.NIMSRequestHandler):
-
- """/nimsapi/epochs """
-
- json_schema = {
- '$schema': 'http://json-schema.org/draft-04/schema#',
- 'title': 'Epoch List',
- 'type': 'array',
- 'items': {
- 'title': 'Epoch',
- 'type': 'object',
- 'properties': {
- '_id': {
- 'title': 'Database ID',
- },
- 'timestamp': {
- 'title': 'Timestamp',
- },
- 'datatype': {
- 'title': 'Datatype',
- 'type': 'string',
- },
- 'series': {
- 'title': 'Series',
- 'type': 'integer',
- },
- 'acquisition': {
- 'title': 'Acquisition',
- 'type': 'integer',
- },
- 'description': {
- 'title': 'Description',
- 'type': 'string',
- },
- }
- }
- }
-
- def count(self):
- """Return the number of Epochs."""
- self.response.write(json.dumps(self.app.db.epochs.count()))
-
- def post(self):
- """Create a new Epoch."""
- self.response.write('epochs post\n')
-
- def get(self, sid):
- """Return the list of Session Epochs."""
- session = self.app.db.sessions.find_one({'_id': bson.objectid.ObjectId(sid)})
- if not session:
- self.abort(404)
- experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(session['experiment'])})
- if not experiment:
- self.abort(500)
- if not self.user_is_superuser and self.userid not in experiment['permissions']:
- self.abort(403)
- query = {'session': bson.objectid.ObjectId(sid)}
- projection = ['timestamp', 'series', 'acquisition', 'description', 'datatype']
- epochs = list(self.app.db.epochs.find(query, projection))
- self.response.write(json.dumps(epochs, default=bson.json_util.default))
-
- def put(self):
- """Update many Epochs."""
- self.response.write('epochs put\n')
-
-
-class Epoch(nimsapiutil.NIMSRequestHandler):
-
- """/nimsapi/epochs/<eid> """
-
- json_schema = {
- '$schema': 'http://json-schema.org/draft-04/schema#',
- 'title': 'Epoch',
- 'type': 'object',
- 'properties': {
- '_id': {
- 'title': 'Database ID',
- },
- 'uid': {
- 'title': 'UID',
- 'type': 'string',
- },
- 'session': {
- 'title': 'Session ID',
- },
- 'files': {
- 'title': 'Files',
- 'type': 'array',
- 'items': nimsapiutil.NIMSRequestHandler.file_schema,
- 'uniqueItems': True,
- },
- },
- 'required': ['_id'],
- }
-
- def schema(self, *args, **kwargs):
- import copy
- json_schema = copy.deepcopy(self.json_schema)
- json_schema['properties'].update(nimsdata.nimsdicom.NIMSDicom.epoch_properties)
- self.response.write(json.dumps(json_schema, default=bson.json_util.default))
-
- def get(self, eid):
- """Return one Epoch, conditionally with details."""
- epoch = self.app.db.epochs.find_one({'_id': bson.objectid.ObjectId(eid)})
- if not epoch:
- self.abort(404)
- session = self.app.db.sessions.find_one({'_id': epoch['session']})
- if not session:
- self.abort(500)
- experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(session['experiment'])})
- if not experiment:
- self.abort(500)
- if not self.user_is_superuser and self.userid not in experiment['permissions']:
- self.abort(403)
- self.response.write(json.dumps(epoch, default=bson.json_util.default))
-
- def put(self, eid):
- """Update an existing Epoch."""
- self.response.write('epoch %s put, %s\n' % (epoch_id, self.request.params))
-
- def delete(self, eid):
- """Delete an Epoch."""
- self.response.write('epoch %s delete, %s\n' % (epoch_id, self.request.params))
diff --git a/experiments.py b/experiments.py
index cb3a7fd1fca1f9e6fc05aad7325e3e55969ba116..1a88fb1d5a18f67e24c007eac825bb0963568804 100644
--- a/experiments.py
+++ b/experiments.py
@@ -4,6 +4,7 @@ import json
import webapp2
import bson.json_util
+#import nimsdata
import nimsapiutil
@@ -22,8 +23,9 @@ class Experiments(nimsapiutil.NIMSRequestHandler):
'_id': {
'title': 'Database ID',
},
- 'timestamp': {
- 'title': 'Timestamp',
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
},
'group': {
'title': 'Group',
@@ -33,6 +35,9 @@ class Experiments(nimsapiutil.NIMSRequestHandler):
'title': 'Name',
'type': 'string',
},
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
'permissions': {
'title': 'Permissions',
'type': 'object',
@@ -54,13 +59,14 @@ class Experiments(nimsapiutil.NIMSRequestHandler):
query = {'permissions.' + self.userid: {'$exists': 'true'}} if not self.user_is_superuser else None
projection = ['group', 'name', 'permissions.'+self.userid]
experiments = list(self.app.db.experiments.find(query, projection))
- session_aggregates = self.app.db.sessions.aggregate([
+ aggregated_sessions = self.app.db.sessions.aggregate([
{'$match': {'experiment': {'$in': [exp['_id'] for exp in experiments]}}},
{'$group': {'_id': '$experiment', 'timestamp': {'$max': '$timestamp'}}},
])['result']
- timestamps = {sa['_id']: sa['timestamp'] for sa in session_aggregates}
+ timestamps = {agg_sess['_id']: agg_sess['timestamp'] for agg_sess in aggregated_sessions}
for exp in experiments:
exp['timestamp'] = timestamps[exp['_id']]
+ exp['site'] = self.app.config['site_id']
self.response.write(json.dumps(experiments, default=bson.json_util.default))
def put(self):
@@ -80,8 +86,9 @@ class Experiment(nimsapiutil.NIMSRequestHandler):
'_id': {
'title': 'Database ID',
},
- 'timestamp': {
- 'title': 'Timestamp',
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
},
'group': {
'title': 'Group',
@@ -92,6 +99,9 @@ class Experiment(nimsapiutil.NIMSRequestHandler):
'type': 'string',
'maxLength': 32,
},
+ 'timestamp': {
+ 'title': 'Timestamp',
+ },
'permissions': {
'title': 'Permissions',
'type': 'object',
@@ -104,7 +114,7 @@ class Experiment(nimsapiutil.NIMSRequestHandler):
'uniqueItems': True,
},
},
- 'required': ['_id', 'group', 'name'],
+ 'required': ['_id', 'group', 'name'], #FIXME
}
def get(self, xid):
@@ -130,3 +140,246 @@ class Experiment(nimsapiutil.NIMSRequestHandler):
def delete(self, xid):
"""Delete an Experiment."""
self.response.write('experiment %s delete, %s\n' % (exp_id, self.request.params))
+
+
+class Sessions(nimsapiutil.NIMSRequestHandler):
+
+ """/sessions """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Session List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Session',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'name': {
+ 'title': 'Session',
+ 'type': 'string',
+ },
+ 'subject': {
+ 'title': 'Subject',
+ 'type': 'string',
+ },
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
+ def count(self):
+ """Return the number of Sessions."""
+ self.response.write(json.dumps(self.app.db.sessions.count()))
+
+ def post(self):
+ """Create a new Session"""
+ self.response.write('sessions post\n')
+
+ def get(self, xid):
+ """Return the list of Experiment Sessions."""
+ experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(xid)})
+ if not experiment:
+ self.abort(404)
+ if not self.user_is_superuser and self.userid not in experiment['permissions']:
+ self.abort(403)
+ query = {'experiment': bson.objectid.ObjectId(xid)}
+ projection = ['name', 'subject']
+ sessions = list(self.app.db.sessions.find(query, projection))
+ self.response.write(json.dumps(sessions, default=bson.json_util.default))
+
+ def put(self):
+ """Update many Sessions."""
+ self.response.write('sessions put\n')
+
+
+class Session(nimsapiutil.NIMSRequestHandler):
+
+ """/sessions/<sid> """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Session',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'uid': {
+ 'title': 'UID',
+ 'type': 'string',
+ },
+ 'experiment': {
+ 'title': 'Experiment ID',
+ },
+ 'site': {
+ 'title': 'Site',
+ 'type': 'string',
+ },
+ 'files': {
+ 'title': 'Files',
+ 'type': 'array',
+ 'items': nimsapiutil.NIMSRequestHandler.file_schema,
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id', 'experiment', 'uid', 'patient_id', 'subject'], #FIXME
+ }
+
+ def schema(self, *args, **kwargs):
+ import copy
+ json_schema = copy.deepcopy(self.json_schema)
+ json_schema['properties'].update(nimsdata.NIMSData.session_properties)
+ self.response.write(json.dumps(json_schema, default=bson.json_util.default))
+
+ def get(self, sid):
+ """Return one Session, conditionally with details."""
+ session = self.app.db.sessions.find_one({'_id': bson.objectid.ObjectId(sid)})
+ if not session:
+ self.abort(404)
+ experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(session['experiment'])})
+ if not experiment:
+ self.abort(500)
+ if not self.user_is_superuser and self.userid not in experiment['permissions']:
+ self.abort(403)
+ self.response.write(json.dumps(session, default=bson.json_util.default))
+
+ def put(self, sid):
+ """Update an existing Session."""
+ self.response.write('session %s put, %s\n' % (sid, self.request.params))
+
+ def delete(self, sid):
+ """Delete an Session."""
+ self.response.write('session %s delete, %s\n' % (sid, self.request.params))
+
+ def move(self, sid):
+ """
+ Move a Session to another Experiment.
+
+ Usage:
+ /nimsapi/sessions/123/move?dest=456
+ """
+ self.response.write('session %s move, %s\n' % (sid, self.request.params))
+
+
+class Epochs(nimsapiutil.NIMSRequestHandler):
+
+ """/nimsapi/epochs """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Epoch List',
+ 'type': 'array',
+ 'items': {
+ 'title': 'Epoch',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'name': {
+ 'title': 'Epoch',
+ 'type': 'string',
+ },
+ 'description': {
+ 'title': 'Description',
+ 'type': 'string',
+ },
+ 'datatype': {
+ 'title': 'Datatype',
+ 'type': 'string',
+ },
+ }
+ }
+ }
+
+ def count(self):
+ """Return the number of Epochs."""
+ self.response.write(json.dumps(self.app.db.epochs.count()))
+
+ def post(self):
+ """Create a new Epoch."""
+ self.response.write('epochs post\n')
+
+ def get(self, sid):
+ """Return the list of Session Epochs."""
+ session = self.app.db.sessions.find_one({'_id': bson.objectid.ObjectId(sid)})
+ if not session:
+ self.abort(404)
+ experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(session['experiment'])})
+ if not experiment:
+ self.abort(500)
+ if not self.user_is_superuser and self.userid not in experiment['permissions']:
+ self.abort(403)
+ query = {'session': bson.objectid.ObjectId(sid)}
+ projection = ['name', 'description', 'datatype']
+ epochs = list(self.app.db.epochs.find(query, projection))
+ self.response.write(json.dumps(epochs, default=bson.json_util.default))
+
+ def put(self):
+ """Update many Epochs."""
+ self.response.write('epochs put\n')
+
+
+class Epoch(nimsapiutil.NIMSRequestHandler):
+
+ """/nimsapi/epochs/<eid> """
+
+ json_schema = {
+ '$schema': 'http://json-schema.org/draft-04/schema#',
+ 'title': 'Epoch',
+ 'type': 'object',
+ 'properties': {
+ '_id': {
+ 'title': 'Database ID',
+ },
+ 'uid': {
+ 'title': 'UID',
+ 'type': 'string',
+ },
+ 'session': {
+ 'title': 'Session ID',
+ },
+ 'files': {
+ 'title': 'Files',
+ 'type': 'array',
+ 'items': nimsapiutil.NIMSRequestHandler.file_schema,
+ 'uniqueItems': True,
+ },
+ },
+ 'required': ['_id'], #FIXME
+ }
+
+ def schema(self, *args, **kwargs):
+ import copy
+ json_schema = copy.deepcopy(self.json_schema)
+ json_schema['properties'].update(nimsdata.nimsdicom.NIMSDicom.epoch_properties)
+ self.response.write(json.dumps(json_schema, default=bson.json_util.default))
+
+ def get(self, eid):
+ """Return one Epoch, conditionally with details."""
+ epoch = self.app.db.epochs.find_one({'_id': bson.objectid.ObjectId(eid)})
+ if not epoch:
+ self.abort(404)
+ session = self.app.db.sessions.find_one({'_id': epoch['session']})
+ if not session:
+ self.abort(500)
+ experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(session['experiment'])})
+ if not experiment:
+ self.abort(500)
+ if not self.user_is_superuser and self.userid not in experiment['permissions']:
+ self.abort(403)
+ self.response.write(json.dumps(epoch, default=bson.json_util.default))
+
+ def put(self, eid):
+ """Update an existing Epoch."""
+ self.response.write('epoch %s put, %s\n' % (epoch_id, self.request.params))
+
+ def delete(self, eid):
+ """Delete an Epoch."""
+ self.response.write('epoch %s delete, %s\n' % (epoch_id, self.request.params))
diff --git a/nimsapi.py b/nimsapi.py
index e205035404d21b03dc58313cd7e3ad2c26d4be39..8d9dfbeb1d2bf8edcac3762021d9f5f761aeff95 100755
--- a/nimsapi.py
+++ b/nimsapi.py
@@ -20,10 +20,9 @@ import Crypto.PublicKey.RSA
import nimsutil
-import epochs
-import sessions
import experiments
import nimsapiutil
+import collections_
log = logging.getLogger('nimsapi')
@@ -39,38 +38,45 @@ class NIMSAPI(nimsapiutil.NIMSRequestHandler):
def get(self):
"""Return API documentation"""
resources = """
- Resource | Description
- :-------------------------------------------------|:-----------------------
- /nimsapi/download | download
- /nimsapi/dump | dump
- /nimsapi/upload | upload
- /nimsapi/remotes | list of remote instances
- [(/nimsapi/users)] | list of users
- [(/nimsapi/users/count)] | count of users
- [(/nimsapi/users/listschema)] | schema for user list
- [(/nimsapi/users/schema)] | schema for single user
- /nimsapi/users/*<uid>* | details for one user, *<uid>*
- [(/nimsapi/groups)] | list of groups
- [(/nimsapi/groups/count)] | count of groups
- [(/nimsapi/groups/listschema)] | schema for group list
- [(/nimsapi/groups/schema)] | schema for single group
- /nimsapi/groups/*<gid>* | details for one group, *<gid>*
- [(/nimsapi/experiments)] | list of experiments
- [(/nimsapi/experiments/count)] | count of experiments
- [(/nimsapi/experiments/listschema)] | schema for experiment list
- [(/nimsapi/experiments/schema)] | schema for single experiment
- /nimsapi/experiments/*<xid>* | details for one experiment, *<xid>*
- /nimsapi/experiments/*<xid>*/sessions | list sessions for one experiment, *<xid>*
- [(/nimsapi/sessions/count)] | count of sessions
- [(/nimsapi/sessions/listschema)] | schema for sessions list
- [(/nimsapi/sessions/schema)] | schema for single session
- /nimsapi/sessions/*<sid>* | details for one session, *<sid>*
- /nimsapi/sessions/*<sid>*/move | move one session, *<sid>*, to a different experiment
- /nimsapi/sessions/*<sid>*/epochs | list epochs for one session, *<sid>*
- [(/nimsapi/epochs/count)] | count of epochs
- [(/nimsapi/epochs/listschema)] | schema for epoch list
- [(/nimsapi/epochs/schema)] | schema for single epoch
- /nimsapi/epochs/*<eid>* | details for one epoch, *<eid>*"""
+ Resource | Description
+ :---------------------------------------------------|:-----------------------
+ nimsapi/download | download
+ nimsapi/upload | upload
+ nimsapi/remotes | list of remote instances
+ [(nimsapi/users)] | list of users
+ [(nimsapi/users/count)] | count of users
+ [(nimsapi/users/listschema)] | schema for user list
+ [(nimsapi/users/schema)] | schema for single user
+ nimsapi/users/*<uid>* | details for user *<uid>*
+ [(nimsapi/groups)] | list of groups
+ [(nimsapi/groups/count)] | count of groups
+ [(nimsapi/groups/listschema)] | schema for group list
+ [(nimsapi/groups/schema)] | schema for single group
+ nimsapi/groups/*<gid>* | details for group *<gid>*
+ [(nimsapi/experiments)] | list of experiments
+ [(nimsapi/experiments/count)] | count of experiments
+ [(nimsapi/experiments/listschema)] | schema for experiment list
+ [(nimsapi/experiments/schema)] | schema for single experiment
+ nimsapi/experiments/*<xid>* | details for experiment *<xid>*
+ nimsapi/experiments/*<xid>*/sessions | list sessions for experiment *<xid>*
+ [(nimsapi/sessions/count)] | count of sessions
+ [(nimsapi/sessions/listschema)] | schema for sessions list
+ [(nimsapi/sessions/schema)] | schema for single session
+ nimsapi/sessions/*<sid>* | details for session *<sid>*
+ nimsapi/sessions/*<sid>*/move | move session *<sid>* to a different experiment
+ nimsapi/sessions/*<sid>*/epochs | list epochs for session *<sid>*
+ [(nimsapi/epochs/count)] | count of epochs
+ [(nimsapi/epochs/listschema)] | schema for epoch list
+ [(nimsapi/epochs/schema)] | schema for single epoch
+ nimsapi/epochs/*<eid>* | details for epoch *<eid>*
+ [(nimsapi/collections)] | list of collections
+ [(nimsapi/collections/count)] | count of collections
+ [(nimsapi/collections/listschema)] | schema for collections list
+ [(nimsapi/collections/schema)] | schema for single collection
+ nimsapi/collections/*<cid>* | details for collection *<cid>*
+ nimsapi/collections/*<cid>*/sessions | list sessions for collection *<cid>*
+ nimsapi/collections/*<cid>*/epochs?session=*<sid>* | list of epochs for collection *<cid>*, optionally restricted to session *<sid>*
+ """
resources = re.sub(r'\[\((.*)\)\]', r'[\1](\1)', resources).replace('<', '<').replace('>', '>').strip()
self.response.headers['Content-Type'] = 'text/html; charset=utf-8'
self.response.write('<html>\n')
@@ -123,9 +129,6 @@ class NIMSAPI(nimsapiutil.NIMSRequestHandler):
paths += _idpaths
symlinks += _idsymlinks
- def dump(self):
- self.response.write(json.dumps(list(self.app.db.sessions.find()), default=bson.json_util.default))
-
class Users(nimsapiutil.NIMSRequestHandler):
@@ -392,7 +395,7 @@ class ArgumentParser(argparse.ArgumentParser):
super(ArgumentParser, self).__init__()
self.add_argument('uri', help='NIMS DB URI')
self.add_argument('stage_path', help='path to staging area')
- self.add_argument('--privkey', help='path to private SSL key file')
+ self.add_argument('-k', '--privkey', help='path to private SSL key file')
self.add_argument('-u', '--uid', help='site UID')
self.add_argument('-f', '--logfile', help='path to log file')
self.add_argument('-l', '--loglevel', default='info', help='path to log file')
@@ -402,7 +405,6 @@ routes = [
webapp2.Route(r'/nimsapi', NIMSAPI),
webapp2_extras.routes.PathPrefixRoute(r'/nimsapi', [
webapp2.Route(r'/download', NIMSAPI, handler_method='download', methods=['GET']),
- webapp2.Route(r'/dump', NIMSAPI, handler_method='dump', methods=['GET']),
webapp2.Route(r'/upload', NIMSAPI, handler_method='upload', methods=['PUT']),
webapp2.Route(r'/remotes', Remotes),
webapp2.Route(r'/users', Users),
@@ -420,17 +422,24 @@ routes = [
webapp2.Route(r'/experiments/listschema', experiments.Experiments, handler_method='schema', methods=['GET']),
webapp2.Route(r'/experiments/schema', experiments.Experiment, handler_method='schema', methods=['GET']),
webapp2.Route(r'/experiments/<xid:[0-9a-f]{24}>', experiments.Experiment),
- webapp2.Route(r'/experiments/<xid:[0-9a-f]{24}>/sessions', sessions.Sessions),
- webapp2.Route(r'/sessions/count', sessions.Sessions, handler_method='count', methods=['GET']),
- webapp2.Route(r'/sessions/listschema', sessions.Sessions, handler_method='schema', methods=['GET']),
- webapp2.Route(r'/sessions/schema', sessions.Session, handler_method='schema', methods=['GET']),
- webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>', sessions.Session),
- webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>/move', sessions.Session, handler_method='move'),
- webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>/epochs', epochs.Epochs),
- webapp2.Route(r'/epochs/count', epochs.Epochs, handler_method='count', methods=['GET']),
- webapp2.Route(r'/epochs/listschema', epochs.Epochs, handler_method='schema', methods=['GET']),
- webapp2.Route(r'/epochs/schema', epochs.Epoch, handler_method='schema', methods=['GET']),
- webapp2.Route(r'/epochs/<eid:[0-9a-f]{24}>', epochs.Epoch),
+ webapp2.Route(r'/experiments/<xid:[0-9a-f]{24}>/sessions', experiments.Sessions),
+ webapp2.Route(r'/sessions/count', experiments.Sessions, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/sessions/listschema', experiments.Sessions, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/sessions/schema', experiments.Session, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>', experiments.Session),
+ webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>/move', experiments.Session, handler_method='move'),
+ webapp2.Route(r'/sessions/<sid:[0-9a-f]{24}>/epochs', experiments.Epochs),
+ webapp2.Route(r'/epochs/count', experiments.Epochs, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/epochs/listschema', experiments.Epochs, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/epochs/schema', experiments.Epoch, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/epochs/<eid:[0-9a-f]{24}>', experiments.Epoch),
+ webapp2.Route(r'/collections', collections_.Collections),
+ webapp2.Route(r'/collections/count', collections_.Collections, handler_method='count', methods=['GET']),
+ webapp2.Route(r'/collections/listschema', collections_.Collections, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/collections/schema', collections_.Collection, handler_method='schema', methods=['GET']),
+ webapp2.Route(r'/collections/<cid:[0-9a-f]{24}>', collections_.Collection),
+ webapp2.Route(r'/collections/<cid:[0-9a-f]{24}>/sessions', collections_.Sessions),
+ webapp2.Route(r'/collections/<cid:[0-9a-f]{24}>/epochs', collections_.Epochs),
]),
]
diff --git a/nimsapiutil.py b/nimsapiutil.py
index a07d5a549dce91dd3bb95021e0b515b7af63e141..17025f02db1209c02d224dacab00042b50e465a4 100644
--- a/nimsapiutil.py
+++ b/nimsapiutil.py
@@ -27,17 +27,9 @@ class NIMSRequestHandler(webapp2.RequestHandler):
'title': 'File',
'type': 'object',
'properties': {
- 'datakind': {
- 'title': 'Data Kind',
- 'type': 'string',
- },
- 'datatype': {
- 'title': 'Data Type',
- 'type': 'string',
- },
- 'filetype': {
- 'title': 'File Type',
- 'type': 'string',
+ 'type': {
+ 'title': 'Type',
+ 'type': 'array',
},
'filename': {
'title': 'File Name',
diff --git a/sessions.py b/sessions.py
deleted file mode 100644
index a86cc17a98477758c370301be0353aca11767c7d..0000000000000000000000000000000000000000
--- a/sessions.py
+++ /dev/null
@@ -1,132 +0,0 @@
-# @author: Gunnar Schaefer
-
-import json
-import webapp2
-import bson.json_util
-
-import nimsdata
-import nimsapiutil
-
-
-class Sessions(nimsapiutil.NIMSRequestHandler):
-
- """/sessions """
-
- json_schema = {
- '$schema': 'http://json-schema.org/draft-04/schema#',
- 'title': 'Session List',
- 'type': 'array',
- 'items': {
- 'title': 'Session',
- 'type': 'object',
- 'properties': {
- '_id': {
- 'title': 'Database ID',
- },
- 'timestamp': {
- 'title': 'Timestamp',
- },
- 'subject': {
- 'title': 'Subject Code',
- 'type': 'string',
- },
- }
- }
- }
-
- def count(self):
- """Return the number of Sessions."""
- self.response.write(json.dumps(self.app.db.sessions.count()))
-
- def post(self):
- """Create a new Session"""
- self.response.write('sessions post\n')
-
- def get(self, xid):
- """Return the list of Experiment Sessions."""
- experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(xid)})
- if not experiment:
- self.abort(404)
- if not self.user_is_superuser and self.userid not in experiment['permissions']:
- self.abort(403)
- query = {'experiment': bson.objectid.ObjectId(xid)}
- projection = ['timestamp', 'subject']
- sessions = list(self.app.db.sessions.find(query, projection))
- self.response.write(json.dumps(sessions, default=bson.json_util.default))
-
- def put(self):
- """Update many Sessions."""
- self.response.write('sessions put\n')
-
-
-class Session(nimsapiutil.NIMSRequestHandler):
-
- """/sessions/<sid> """
-
- json_schema = {
- '$schema': 'http://json-schema.org/draft-04/schema#',
- 'title': 'Session',
- 'type': 'object',
- 'properties': {
- '_id': {
- 'title': 'Database ID',
- },
- 'uid': {
- 'title': 'UID',
- 'type': 'string',
- },
- 'experiment': {
- 'title': 'Experiment ID',
- },
- 'timestamp': {
- 'title': 'Timestamp',
- },
- 'subject': {
- 'title': 'Subject Code',
- 'type': 'string',
- 'maxLength': 16,
- },
- 'files': {
- 'title': 'Files',
- 'type': 'array',
- 'items': nimsapiutil.NIMSRequestHandler.file_schema,
- 'uniqueItems': True,
- },
- },
- 'required': ['_id', 'experiment', 'uid', 'patient_id', 'subject'],
- }
-
- def schema(self, *args, **kwargs):
- import copy
- json_schema = copy.deepcopy(self.json_schema)
- json_schema['properties'].update(nimsdata.NIMSData.session_properties)
- self.response.write(json.dumps(json_schema, default=bson.json_util.default))
-
- def get(self, sid):
- """Return one Session, conditionally with details."""
- session = self.app.db.sessions.find_one({'_id': bson.objectid.ObjectId(sid)})
- if not session:
- self.abort(404)
- experiment = self.app.db.experiments.find_one({'_id': bson.objectid.ObjectId(session['experiment'])})
- if not experiment:
- self.abort(500)
- if not self.user_is_superuser and self.userid not in experiment['permissions']:
- self.abort(403)
- self.response.write(json.dumps(session, default=bson.json_util.default))
-
- def put(self, sid):
- """Update an existing Session."""
- self.response.write('session %s put, %s\n' % (sid, self.request.params))
-
- def delete(self, sid):
- """Delete an Session."""
- self.response.write('session %s delete, %s\n' % (sid, self.request.params))
-
- def move(self, sid):
- """
- Move a Session to another Experiment.
-
- Usage:
- /nimsapi/sessions/123/move?dest=456
- """
- self.response.write('session %s move, %s\n' % (sid, self.request.params))