Merge pull request #18 from scitran/timezone_support

Provide timestamps with timezone in ISO format

acquisitions.py

@@ -58,7 +58,7 @@ class Acquisitions(containers.ContainerList):
         if not self.app.db.sessions.find_one({'_id': _id}):
             self.abort(404, 'no such Session')
         query = {'session': _id}
-        projection = {'label': 1, 'description': 1, 'types': 1, 'notes': 1}
+        projection = {'label': 1, 'description': 1, 'types': 1, 'notes': 1, 'timestamp': 1, 'timezone': 1}
         acquisitions = self._get(query, projection, self.request.get('admin').lower() in ('1', 'true'))
         if self.debug:
             for acquisition in acquisitions:

collections_.py

@@ -198,7 +198,7 @@ class Collections(containers.ContainerList):
     def get(self):
         """Return the list of Collections."""
         query = {'curator_id': self.request.get('curator')} if self.request.get('curator') else {}
-        projection = {'curator_id': 1, 'name': 1, 'notes': 1}
+        projection = {'curator_id': 1, 'name': 1, 'notes': 1, 'timestamp': 1, 'timezone': 1}
         collections = self._get(query, projection, self.request.get('admin').lower() in ('1', 'true'))
         for coll in collections:
             coll['_id'] = str(coll['_id'])
@@ -296,7 +296,7 @@ class CollectionSessions(sessions.Sessions):
                 {'$group': {'_id': '$session'}},
                 ])
         query = {'_id': {'$in': [ar['_id'] for ar in agg_res]}}
-        projection = {'label': 1, 'subject.code': 1, 'notes': 1}
+        projection = {'label': 1, 'subject.code': 1, 'notes': 1, 'timestamp': 1, 'timezone': 1}
         projection['permissions'] = {'$elemMatch': {'_id': self.uid, 'site': self.source_site}}
         sessions = list(self.dbc.find(query, projection))
         for sess in sessions:
@@ -333,7 +333,7 @@ class CollectionAcquisitions(acquisitions.Acquisitions):
             query['session'] = bson.ObjectId(sid)
         elif sid != '':
             self.abort(400, sid + ' is not a valid ObjectId')
-        projection = {'label': 1, 'description': 1, 'types': 1, 'notes': 1}
+        projection = {'label': 1, 'description': 1, 'types': 1, 'notes': 1, 'timestamp': 1, 'timezone': 1}
         projection['permissions'] = {'$elemMatch': {'_id': self.uid, 'site': self.source_site}}
         acquisitions = list(self.dbc.find(query, projection))
         for acq in acquisitions:

containers.py

@@ -5,8 +5,8 @@ log = logging.getLogger('scitran.api')
 
 import os
 import json
+import pytz
 import hashlib
-import datetime
 import jsonschema
 import bson.json_util
 
@@ -16,7 +16,6 @@ import base
 import util
 import users
 
-import tempdir as tempfile
 
 FILE_SCHEMA = {
     '$schema': 'http://json-schema.org/draft-04/schema#',
@@ -112,6 +111,13 @@ FILE_DOWNLOAD_SCHEMA = {
 }
 
 
+def fixup_timestamps(container):
+    if 'timestamp' in container:
+        container_timezone = pytz.timezone(container.get('timezone', None) or 'UTC')
+        container['timestamp'] = container_timezone.localize(container['timestamp']).isoformat()
+        container['timezone'] = container_timezone.zone
+
+
 class ContainerList(base.RequestHandler):
 
     def _get(self, query, projection, admin_only=False):
@@ -127,6 +133,7 @@ class ContainerList(base.RequestHandler):
         containers = list(self.dbc.find(query, projection))
         for container in containers:
             container['_id'] = str(container['_id'])
+            fixup_timestamps(container)
         return containers
 
 
@@ -154,6 +161,7 @@ class Container(base.RequestHandler):
             for file_info in container['files']:
                 file_info['path'] = str(_id)[-3:] + '/' + str(_id) + '/' + file_info['name'] + file_info['ext']
         container['_id'] = str(container['_id'])
+        fixup_timestamps(container)
         return container, user_perm
 
     def put(self, _id):

projects.py

@@ -113,7 +113,7 @@ class Projects(containers.ContainerList):
     def get(self):
         """Return the User's list of Projects."""
         query = {'group_id': self.request.get('group')} if self.request.get('group') else {}
-        projection = {'group_id': 1, 'name': 1, 'notes': 1}
+        projection = {'group_id': 1, 'name': 1, 'notes': 1, 'timestamp': 1, 'timezone': 1}
         projects = self._get(query, projection, self.request.get('admin').lower() in ('1', 'true'))
         if self.debug:
             for proj in projects:

sessions.py

@@ -64,7 +64,7 @@ class Sessions(containers.ContainerList):
             query = {'project': _id}
         else:
             query = {}
-        projection = {'label': 1, 'subject.code': 1, 'notes': 1, 'project': 1}
+        projection = {'label': 1, 'subject.code': 1, 'notes': 1, 'project': 1, 'timestamp': 1, 'timezone': 1}
         sessions = self._get(query, projection, self.request.get('admin').lower() in ('1', 'true'))
         for sess in sessions:
             sess['project'] = str(sess['project'])

util.py

@@ -146,11 +146,12 @@ def _update_db(db, dataset):
             fields=[],
             )
     if dataset.nims_timestamp:
-        db.projects.update({'_id': project['_id']}, {'$max': dict(timestamp=dataset.nims_timestamp)})
+        db.projects.update({'_id': project['_id']}, {'$max': dict(timestamp=dataset.nims_timestamp), '$set': dict(timezone=dataset.nims_timezone)})
         db.sessions.update({'_id': session['_id']}, {'$min': dict(timestamp=dataset.nims_timestamp), '$set': dict(timezone=dataset.nims_timezone)})
     # create a job, if necessary
     return acquisition['_id']
 
+
 # TODO: create job should be use-able from bootstrap.py with only database information
 def create_job(dbc, dataset):
     db = dbc.database