Update docs for classification

Author: nagem

api/config.py

@@ -1,6 +1,5 @@
 import os
 import copy
-import glob
 import json
 import logging
 import pymongo
@@ -132,80 +131,6 @@ def apply_env_variables(config):
 # validate the lists of json schemas
 schema_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), '../raml/schemas')
 
-expected_mongo_schemas = set([
-    'acquisition.json',
-    'analysis.json',
-    'collection.json',
-    'container.json',
-    'file.json',
-    'group.json',
-    'note.json',
-    'permission.json',
-    'project.json',
-    'session.json',
-    'subject.json',
-    'user.json',
-    'avatars.json',
-    'tag.json'
-])
-expected_input_schemas = set([
-    'acquisition.json',
-    'acquisition-update.json',
-    'analysis.json',
-    'analysis-job.json',
-    'analysis-update.json',
-    'avatars.json',
-    'classification_update.json',
-    'collection.json',
-    'collection-update.json',
-    'container.json',
-    'device.json',
-    'file.json',
-    'file-update.json',
-    'group-new.json',
-    'group-update.json',
-    'info_update.json',
-    'modality.json',
-    'note.json',
-    'packfile.json',
-    'permission.json',
-    'project.json',
-    'project-template.json',
-    'project-update.json',
-    'rule-new.json',
-    'rule-update.json',
-    'session.json',
-    'session-update.json',
-    'subject.json',
-    'user-new.json',
-    'user-update.json',
-    'download.json',
-    'tag.json',
-    'enginemetadata.json',
-    'labelupload.json',
-    'uidupload.json',
-    'uidmatchupload.json',
-    'search.json'
-])
-mongo_schemas = set()
-input_schemas = set()
-
-# check that the lists of schemas are correct
-for schema_filepath in glob.glob(schema_path + '/mongo/*.json'):
-    schema_file = os.path.basename(schema_filepath)
-    mongo_schemas.add(schema_file)
-    with open(schema_filepath, 'rU') as f:
-        pass
-
-assert mongo_schemas == expected_mongo_schemas, '{} is different from {}'.format(mongo_schemas, expected_mongo_schemas)
-
-for schema_filepath in glob.glob(schema_path + '/input/*.json'):
-    schema_file = os.path.basename(schema_filepath)
-    input_schemas.add(schema_file)
-    with open(schema_filepath, 'rU') as f:
-        pass
-
-assert input_schemas == expected_input_schemas, '{} is different from {}'.format(input_schemas, expected_input_schemas)
 
 def create_or_recreate_ttl_index(coll_name, index_name, ttl):
     if coll_name in db.collection_names():

api/handlers/listhandler.py

@@ -528,7 +528,7 @@ def modify_classification(self, cont_name, list_name, **kwargs):
 
         payload = self.request.json_body
 
-        validators.validate_data(payload, 'classification_update.json', 'input', 'POST')
+        validators.validate_data(payload, 'classification-update.json', 'input', 'POST')
 
         permchecker(noop)('PUT', _id=_id, query_params=kwargs, payload=payload)
         storage.modify_classification(_id, kwargs, payload)

api/handlers/modalityhandler.py

@@ -127,7 +127,7 @@ def check_and_format_classification(modality_name, classification_map):
     """
     try:
         modality = containerstorage.ContainerStorage('modalities', use_object_id=False).get_container(modality_name)
-    except APINotFoundException as e:
+    except APINotFoundException:
         keys = classification_map.keys()
         if len(keys) == 1 and keys[0].lower() == 'custom':
             # for unknown modalities allow only list of custom values

api/jobs/queue.py

@@ -234,6 +234,17 @@ def enqueue_job(job_map, origin, perm_check_uid=None):
                 whitelisted_keys = ['info', 'tags', 'classification', 'mimetype', 'type', 'modality', 'size']
                 obj_projection = { key: obj.get(key) for key in whitelisted_keys }
 
+                ###
+                # recreate `measurements` list on object
+                # Can be removed when `classification` key has been adopted everywhere
+
+                obj_projection['measurements'] = []
+                if obj_projection.get('classification'):
+                    for v in obj_projection['classification'].itervalues():
+                        obj_projection.extend(v)
+                #
+                ###
+
                 config_['inputs'][x] = {
                     'base': 'file',
                     'hierarchy': cr.__dict__,

raml/examples/input/analysis.json

@@ -8,7 +8,7 @@
         "hash": "v0-sha384-12188e00a26650b2baa3f0195337dcf504f4362bb2136eef0cdbefb57159356b1355a0402fca0ab5ab081f21c305e5c2",
         "name": "cortical_surface_right_hemisphere.obj",
         "tags": [],
-        "measurements": [],
+        "classification": {},
         "modified": "2016-10-18T15:26:35.701000+00:00",
         "instrument": null,
         "input": true,
@@ -25,7 +25,7 @@
         "hash": "v0-sha384-12188e00a26650b2baa3f0195337dcf504f4362bb2136eef0cdbefb57159356b1355a0402fca0ab5ab081f21c305e5c2",
         "name": "cortical_surface_right_hemisphere.obj",
         "tags": [],
-        "measurements": [],
+        "classification": {},
         "modified": "2016-10-18T17:45:17.776000+00:00",
         "instrument": null,
         "output": true,
@@ -44,4 +44,4 @@
 	"job": "54759eb3c090d83494e2d804",
 	"label": "Analysis label",
 	"user": "user_1"
-}
+}

raml/examples/input/classification-update.json

@@ -0,0 +1,6 @@
+{
+    "replace": {
+        "Contrast": ["B0", "Diffusion"],
+        "Intent": ["Structural"]
+    }
+}

raml/examples/input/file.json

@@ -2,7 +2,7 @@
   "name": "4784_1_1_localizer_dicom.zip",
   "type": "dicom",
   "mimetype": "application/zip",
-  "measurements": [],
+  "classification": {},
   "tags": [],
   "info": {}
 }

raml/examples/input/modality.json

@@ -0,0 +1,8 @@
+{
+    "_id": "MR",
+    "classifications": {
+        "Contrast": ["B0", "B1", "T1", "T2", "T2*", "PD", "MT", "ASL", "Perfusion", "Diffusion", "Spectroscopy", "Susceptibility", "Velocity", "Fingerprinting"],
+        "Intent": ["Structural", "Functional", "Localizer", "Shim", "Calibration"],
+        "Features": ["Quantitative", "Multi-Shell", "Multi-Echo", "Multi-Flip", "Multi-Band", "Steady-State", "3D", "Compressed-Sensing", "Eddy-Current-Corrected", "Fieldmap-Corrected", "Gradient-Unwarped", "Motion-Corrected", "Physio-Corrected"]
+    }
+}

raml/examples/input/project-template.json

@@ -15,11 +15,11 @@
                     "$schema": "http://json-schema.org/draft-04/schema#",
                     "type": "object",
                     "properties": {
-                        "measurement": {
+                        "classification": {
                             "type":     "string",
                             "pattern":  "^[aA]natomical$" }
                     },
-                    "required": ["measurement"]
+                    "required": ["classification"]
                 },
                 "minimum": 2
             },
@@ -28,11 +28,11 @@
                     "$schema": "http://json-schema.org/draft-04/schema#",
                     "type": "object",
                     "properties": {
-                        "measurement": {
+                        "classification": {
                             "type":     "string",
                             "pattern":  "^functional$" }
                     },
-                    "required": ["measurement"]
+                    "required": ["classification"]
                 },
                 "minimum": 1
             },
@@ -41,13 +41,13 @@
                     "$schema": "http://json-schema.org/draft-04/schema#",
                     "type": "object",
                     "properties": {
-                        "measurement": { "enum": ["Localizer"] },
+                        "classification": { "enum": ["Localizer"] },
                         "label":  {
                             "type": "string",
                             "pattern": "t1"
                         }
                     },
-                    "required": ["label", "measurement"]
+                    "required": ["label", "classification"]
                 },
                 "minimum": 1
             }

raml/examples/input/rule-new.json

@@ -6,7 +6,7 @@
   "all": [
     {
       "regex": true,
-      "type": "file.measurements",
+      "type": "file.classification",
       "value": "^(?!non-image).+$"
     },
     {

raml/examples/output/rule-list.json

@@ -4,7 +4,7 @@
     "all": [
       {
         "regex": true,
-        "type": "file.measurements",
+        "type": "file.classification",
         "value": "^(?!non-image).+$"
       },
       {
@@ -25,7 +25,7 @@
       },
       {
         "regex": true,
-        "type": "file.measurements",
+        "type": "file.classification",
         "value": "^(?!non-image).+$"
       }
     ],
@@ -42,7 +42,7 @@
       },
       {
         "regex": true,
-        "type": "file.measurements",
+        "type": "file.classification",
         "value": "(functional|anatomy_t1w|anatomy_t2w)"
       }
     ],

raml/schemas/definitions/modality.json

@@ -15,8 +15,8 @@
           "items": {
             "type": "string"
           }
-        },
-      },
+        }
+      }
     },
     "modality":{
         "type": "object",