Clean up a few measurement references

Author: nagem

api/handlers/modalityhandler.py

@@ -1,7 +1,8 @@
 from ..web import base
 from .. import config
 from ..auth import require_login, require_admin
-from ..dao import containerstorage, APINotFoundException, APIValidationException
+from ..dao import containerstorage
+from ..web.errors import APINotFoundException, APIValidationException
 #from ..validators import validate_data
 
 log = config.log

api/jobs/queue.py

@@ -229,7 +229,7 @@ def enqueue_job(job_map, origin, perm_check_uid=None):
                 cr = create_containerreference_from_filereference(inputs[x])
 
                 # Whitelist file fields passed to gear to those that are scientific-relevant
-                whitelisted_keys = ['info', 'tags', 'measurements', 'mimetype', 'type', 'modality', 'size']
+                whitelisted_keys = ['info', 'tags', 'classification', 'mimetype', 'type', 'modality', 'size']
                 obj_projection = { key: obj[key] for key in whitelisted_keys }
 
                 config_['inputs'][x] = {

api/jobs/rules.py

@@ -1,5 +1,6 @@
 import fnmatch
 import re
+import itertools
 
 from .. import config
 from ..types import Origin
@@ -33,15 +34,15 @@
 #             'value': '*.dcm'
 #         },
 #         {
-#             'type': 'file.measurements', # Match any of the file's measurements
+#             'type': 'file.classification', # Match any of the file's classification
 #             'value': 'diffusion'
 #         },
 #         {
 #             'type': 'container.has-type', # Match the container having any file (including this one) with this type
 #             'value': 'bvec'
 #         },
 #         {
-#             'type': 'container.has-measurement', # Match the container having any file (including this one) with this measurement
+#             'type': 'container.has-classification', # Match the container having any file (including this one) with this classification
 #             'value': 'functional'
 #         }
 #     ]
@@ -86,10 +87,11 @@ def match(value):
     elif match_type == 'file.name':
         return match(file_['name'])
 
-    # Match any of the file's measurements
-    elif match_type == 'file.measurements':
+    # Match any of the file's classification
+    elif match_type == 'file.classification':
         if match_param:
-            return any(match(value) for value in file_.get('measurements', []))
+            classification_values = list(itertools.chain.from_iterable(file_.get('classification', {}).itervalues()))
+            return any(match(value) for value in classification_values)
         else:
             return False
 
@@ -102,11 +104,12 @@ def match(value):
 
         return False
 
-    # Match the container having any file (including this one) with this measurement
-    elif match_type == 'container.has-measurement':
+    # Match the container having any file (including this one) with this classification
+    elif match_type == 'container.has-classification':
         if match_param:
             for c_file in container['files']:
-                if any(match(value) for value in c_file.get('measurements', [])):
+                classification_values = list(itertools.chain.from_iterable(c_file.get('classification', {}).itervalues()))
+                if any(match(value) for value in classification_values):
                     return True
 
         return False

api/placer.py

@@ -512,7 +512,7 @@ def finalize(self):
 
             # OPPORTUNITY: packfile endpoint could be extended someday to take additional metadata.
             'modality': None,
-            'measurements': [],
+            'classification': {},
             'tags': [],
             'info': {},
 

api/upload.py

@@ -129,7 +129,7 @@ def process_upload(request, strategy, container_type=None, id_=None, origin=None
 
             'type': None,
             'modality': None,
-            'measurements': [],
+            'classification': {},
             'tags': [],
             'info': {}
         }

raml/schemas/definitions/rule.json

@@ -11,9 +11,9 @@
                         "enum": [
                             "file.type",
                             "file.name",
-                            "file.measurements",
+                            "file.classification",
                             "container.has-type",
-                            "container.has-measurement"
+                            "container.has-classification"
                         ]
                     },
                     "value": { "type": "string" },