Merge pull request #483 from scitran/analysis-chaining

Allow analysis files from session to be used as input in other analyses

api/dao/containerutil.py

@@ -5,6 +5,7 @@ from ..auth import INTEGER_ROLES
 
 CONT_TYPES = ['acquisition', 'analysis', 'collection', 'group', 'project', 'session']
 
+
 def getPerm(name):
     return INTEGER_ROLES[name]
 
@@ -44,33 +45,35 @@ class ContainerReference(object):
     def __init__(self, type, id):
         if type not in CONT_TYPES:
             raise Exception('Container type must be one of {}'.format(CONT_TYPES))
+        if type == 'analysis':
+            self.__class__ = AnalysisReference
 
         if not isinstance(type, basestring):
             raise Exception('Container type must be of type str')
         if not isinstance(id, basestring):
             raise Exception('Container id must be of type str')
 
-        self.type = type
-        self.id   = id
+        self.type   = type
+        self.id     = id
 
     @classmethod
     def from_dictionary(cls, d):
         return cls(
             type = d['type'],
-            id   = d['id']
+            id = d['id']
         )
 
     @classmethod
     def from_filereference(cls, fr):
         return cls(
             type = fr.type,
-            id   = fr.id
+            id = fr.id
         )
 
     def get(self):
         result = config.db[self.type + 's'].find_one({'_id': bson.ObjectId(self.id)})
         if result is None:
-            raise Exception("No such " + self.type + " " + self.id + " in database")
+            raise Exception('No such {} {} in database'.format(self.type, self.id))
         return result
 
     def find_file(self, filename):
@@ -80,13 +83,34 @@ class ContainerReference(object):
                 return f
         return None
 
+    def file_uri(self, filename):
+        return '/' + self.type + 's/' + self.id + '/files/' + filename
+
     def check_access(self, userID, perm_name):
         perm = getPerm(perm_name)
         for p in self.get()['permissions']:
             if p['_id'] == userID and getPerm(p['access']) > perm:
                 return
 
-        raise Exception("User " + userID + " does not have " + perm_name + " access to " + self.type + " " + self.id)
+        raise Exception('User {} does not have {} access to {} {}'.format(userID, perm_name, self.type, self.id))
+
+class AnalysisReference(ContainerReference):
+    # pylint: disable=redefined-builtin
+    # TODO: refactor to resolve pylint warning
+
+    def get(self):
+        result = config.db.sessions.find_one({'analyses._id': self.id}, {'permissions':1, 'analyses': {'$elemMatch': {'_id': self.id}}})
+        if result is None or result.get('analyses') is None:
+            raise Exception('No such analysis {} in database'.format(self.id))
+        analysis = result['analyses'][0]
+        analysis['permissions'] = result['permissions']
+        analysis['session_id'] = result['_id']
+        return analysis
+
+    def file_uri(self, filename):
+        analysis = self.get()
+        return '/sessions/' + str(analysis['session_id']) + '/analyses/' + self.id + '/files/' + filename
+
 
 class FileReference(ContainerReference):
     # pylint: disable=redefined-builtin
@@ -100,10 +124,11 @@ class FileReference(ContainerReference):
     def from_dictionary(cls, d):
         return cls(
             type = d['type'],
-            id   = d['id'],
+            id = d['id'],
             name = d['name']
         )
 
+
 def create_filereference_from_dictionary(d):
     return FileReference.from_dictionary(d)
 

api/dao/liststorage.py

@@ -254,7 +254,7 @@ class AnalysesStorage(ListStorage):
             if next_job is None:
                 break
             job = Job.load(next_job)
-        if job.id_ != analysis['job']:
+        if job.id_ != str(analysis['job']):
             # Update analysis if job has changed
             # Remove old inputs and replace with new job inputs
             # (In practice these should never change)

api/handlers/listhandler.py

@@ -709,6 +709,7 @@ class AnalysesHandler(ListHandler):
             contref = create_containerreference_from_filereference(fileref)
             file_ = contref.find_file(fileref.name)
             if file_:
+                file_.pop('output', None) # If file was from an analysis
                 file_['input'] = True
                 files.append(file_)
         analysis['files'] = files

api/jobs/jobs.py

@@ -214,7 +214,7 @@ class Job(object):
 
             r['inputs'].append({
                 'type': 'scitran',
-                'uri': '/' + i.type + 's/' + i.id + '/files/' + i.name,
+                'uri': i.file_uri(i.name),
                 'location': '/flywheel/v0/input/' + input_name,
             })