diff --git a/epochs.py b/epochs.py
index 14ef8273928d057c24548d4a92e8701f802e635d..fb62300dda39543e851497b755c6690b14ade99b 100644
--- a/epochs.py
+++ b/epochs.py
@@ -4,6 +4,7 @@ import json
import webapp2
import bson.json_util
+import nimsdata
import nimsapiutil
@@ -85,123 +86,12 @@ class Epoch(nimsapiutil.NIMSRequestHandler):
'_id': {
'title': 'Database ID',
},
- 'session': {
- 'title': 'Session ID',
- },
- 'timestamp': {
- 'title': 'Timestamp',
- },
- 'session_uid': {
- 'title': 'DICOM UID',
- 'type': 'string',
- },
- 'datatype': {
- 'title': 'Datatype',
- 'type': 'string',
- },
- 'series': {
- 'title': 'Series',
- 'type': 'integer',
- },
- 'acquisition': {
- 'title': 'Acquisition',
- 'type': 'integer',
- },
- 'description': {
- 'title': 'Description',
+ 'uid': {
+ 'title': 'UID',
'type': 'string',
- 'maxLength': 64,
},
- 'protocol': {
- 'title': 'Protocol',
- 'type': 'string',
- 'maxLength': 64,
- },
- 'rx_coil': {
- 'title': 'Coil',
- 'type': 'string',
- 'maxLength': 64,
- },
- 'device': {
- 'title': 'Device',
- 'type': 'string',
- 'maxLength': 64,
- },
- 'size': {
- 'title': 'Size',
- 'type': 'array',
- 'items': {
- 'type': 'integer',
- }
- },
- 'acquisition_matrix': {
- 'title': 'Acquisition Matrix',
- 'type': 'array',
- 'items': {
- 'type': 'number',
- }
- },
- 'fov': {
- 'title': 'Field of View',
- 'type': 'array',
- 'items': {
- 'type': 'number',
- }
- },
- 'mm_per_voxel': {
- 'title': 'mm per Voxel',
- 'type': 'array',
- 'items': {
- 'type': 'number',
- }
- },
- 'flip_angle': {
- 'title': 'Flip Angle',
- 'type': 'integer',
- },
- 'num_averages': {
- 'title': 'Averages',
- 'type': 'integer',
- },
- 'num_bands': {
- 'title': 'Bands',
- 'type': 'integer',
- },
- 'num_echos': {
- 'title': 'Echos',
- 'type': 'integer',
- },
- 'num_slices': {
- 'title': 'Slices',
- 'type': 'integer',
- },
- 'num_timepoints': {
- 'title': 'Time Points',
- 'type': 'integer',
- },
- 'pixel_bandwidth': {
- 'title': 'Pixel Bandwidth',
- 'type': 'number',
- },
- 'prescribed_duration': {
- 'title': 'Prescribed Duration',
- 'type': 'number',
- },
- 'duration': {
- 'title': 'Duration',
- 'type': 'number',
- },
- 'slice_encode_undersample': {
- 'title': 'Slice Encode Undersample',
- 'type': 'integer',
- },
- 'te': {
- 'title': 'Te',
- 'type': 'number',
- },
- 'tr': {
- 'title': 'Tr',
- 'type': 'number',
+ 'session': {
+ 'title': 'Session ID',
},
'files': {
'title': 'Files',
@@ -213,6 +103,12 @@ class Epoch(nimsapiutil.NIMSRequestHandler):
'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)})
diff --git a/experiments.py b/experiments.py
index c59785790ed8412b910a51779f2c3445b4903368..cb3a7fd1fca1f9e6fc05aad7325e3e55969ba116 100644
--- a/experiments.py
+++ b/experiments.py
@@ -22,17 +22,21 @@ class Experiments(nimsapiutil.NIMSRequestHandler):
'_id': {
'title': 'Database ID',
},
- 'firstname': {
- 'title': 'First Name',
- 'type': 'string',
+ 'timestamp': {
+ 'title': 'Timestamp',
},
- 'lastname': {
- 'title': 'Last Name',
+ 'group': {
+ 'title': 'Group',
'type': 'string',
},
- 'email_hash': {
+ 'name': {
+ 'title': 'Name',
'type': 'string',
},
+ 'permissions': {
+ 'title': 'Permissions',
+ 'type': 'object',
+ },
}
}
}
diff --git a/nimsapi.wsgi b/nimsapi.wsgi
index 92ea735cd4e2f1eb7fdae127fe5deea7314e84f1..8f7b59ae06b0e0c7d4c2be599ae552a72471ade1 100644
--- a/nimsapi.wsgi
+++ b/nimsapi.wsgi
@@ -16,18 +16,20 @@ import webapp2
import nimsapi
import nimsutil
-logfile = '/var/local/log/nimsapi.log'
+log_file = '/var/local/log/nimsapi.log'
+pubkey_file = '/var/local/nims/internims/internims.pub'
db_uri = 'mongodb://nims:cnimr750@cnifs.stanford.edu,cnibk.stanford.edu/nims?replicaSet=cni'
stage_path = '/scratch/upload'
-nimsutil.configure_log(logfile, False)
+nimsutil.configure_log(log_file, False)
db_client = pymongo.MongoReplicaSetClient(db_uri) if 'replicaSet' in db_uri else pymongo.MongoClient(db_uri)
try:
- pubkey = open('/var/local/nims/internims/NIMSpubkey.pub').read()
-except IOError as e:
+ pubkey = open(pubkey_file).read() # FIXME: don't read too much
+ # FIXME: verify that this is a valid public key
+except IOError:
pubkey = None
application = nimsapi.app
-application.config = dict(stage_path=stage_path, site_id='demo_nims_coronal2', pubkey=pubkey)
+application.config = dict(stage_path=stage_path, site_id='stanford-cni', pubkey=pubkey)
application.db = db_client.get_default_database()
diff --git a/nimsapiutil.py b/nimsapiutil.py
index bc8f2827e617ac3f1062eafab3a938eb3c018dc7..c44e6e26bf12535047c7d56e111c3b9c07d6d532 100644
--- a/nimsapiutil.py
+++ b/nimsapiutil.py
@@ -144,4 +144,4 @@ class NIMSRequestHandler(webapp2.RequestHandler):
self.response.write(r.content)
def schema(self, *args, **kwargs):
- self.response.write(json.dumps(self.json_schema, default=bson.json_util.default))
\ No newline at end of file
+ self.response.write(json.dumps(self.json_schema, default=bson.json_util.default))
diff --git a/sessions.py b/sessions.py
index d0c43ce497be85b932dffe2af7c40a3c25300e09..a86cc17a98477758c370301be0353aca11767c7d 100644
--- a/sessions.py
+++ b/sessions.py
@@ -4,6 +4,7 @@ import json
import webapp2
import bson.json_util
+import nimsdata
import nimsapiutil
@@ -70,35 +71,20 @@ class Session(nimsapiutil.NIMSRequestHandler):
'_id': {
'title': 'Database ID',
},
+ 'uid': {
+ 'title': 'UID',
+ 'type': 'string',
+ },
'experiment': {
'title': 'Experiment ID',
},
'timestamp': {
'title': 'Timestamp',
},
- 'uid': {
- 'title': 'DICOM UID',
- 'type': 'string',
- },
- 'firstname': {
- 'title': 'First Name',
- 'type': 'string',
- },
- 'lastname': {
- 'title': 'Last Name',
- 'type': 'string',
- },
- 'patient_id': {
- 'title': 'Patient ID',
- 'type': 'string',
- },
'subject': {
'title': 'Subject Code',
'type': 'string',
- },
- 'exam': {
- 'title': 'Exam Number',
- 'type': 'integer',
+ 'maxLength': 16,
},
'files': {
'title': 'Files',
@@ -110,6 +96,12 @@ class Session(nimsapiutil.NIMSRequestHandler):
'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)})