Merge branch 'dev' into email-name-parameter-726

crc/api.yml

@@ -83,6 +83,11 @@ paths:
         required : false
         schema :
           type : integer
+      - name : include_archived
+        in : query
+        required : false
+        schema :
+          type : boolean
     get:
       operationId: crc.api.document.get_document_directory
       summary: Returns a directory of all files for study in a nested structure

crc/api/document.py

@@ -5,12 +5,12 @@ from crc.services.lookup_service import LookupService
 from crc.services.user_file_service import UserFileService
 
 
-def get_document_directory(study_id, workflow_id=None):
+def get_document_directory(study_id, workflow_id=None, include_archived=False):
     """
     return a nested list of files arranged according to the category hierarchy
     defined in the doc dictionary
     """
-    file_models = UserFileService.get_files_for_study(study_id=study_id)
+    file_models = UserFileService.get_files_for_study(study_id=study_id, irb_doc_code=None, include_archived=include_archived)
     doc_dict = DocumentService.get_dictionary()
     files = (File.from_file_model(model, doc_dict) for model in file_models)
     directory = DocumentService.get_directory(doc_dict, files, workflow_id)

crc/api/file.py

@@ -67,7 +67,7 @@ def update_file_data(file_id):
     file = connexion.request.files['file']
     if file_model is None:
         raise ApiError('no_such_file', f'The file id you provided ({file_id}) does not exist')
-    file_model = UserFileService.update_file(file_model, file.stream.read(), file.content_type)
+    file_model = UserFileService().update_file(file_model, file.stream.read(), file.content_type)
     return FileSchema().dump(to_file_api(file_model))
 
 

crc/models/file.py

@@ -123,6 +123,8 @@ class File(object):
         self.last_modified = None
         self.size = None
         self.data_store = {}
+        self.user_uid = None
+        self.archived = None
 
     @classmethod
     def from_file_model(cls, file_model: FileModel, doc_dictionary):
@@ -140,6 +142,8 @@ class File(object):
         instance.document = document
         instance.last_modified = file_model.date_modified
         instance.size = None
+        instance.user_uid = file_model.user_uid
+        instance.archived = file_model.archived
         instance.data_store = {}
         for ds in file_model.data_stores:
             instance.data_store[ds.key] = ds.value
@@ -184,7 +188,7 @@ class FileSchema(Schema):
     class Meta:
         model = File
         fields = ["id", "name", "content_type", "workflow_id",
-                  "irb_doc_code", "last_modified", "type",
+                  "irb_doc_code", "last_modified", "type", "archived",
                   "size", "data_store", "document", "user_uid", "url"]
         unknown = INCLUDE
     url = Method("get_url")

crc/services/user_file_service.py

@@ -116,13 +116,16 @@ class UserFileService(object):
         return file_model
 
     @staticmethod
-    def get_files_for_study(study_id, irb_doc_code=None):
+    def get_files_for_study(study_id, irb_doc_code=None, include_archived=False):
         query = session.query(FileModel).\
                 join(WorkflowModel).\
                 filter(WorkflowModel.study_id == study_id)
+        if not include_archived:
+            # Current documents have an archived value of False
+            query = query.filter(FileModel.archived == False)
         if irb_doc_code is not None:
             query = query.filter(FileModel.irb_doc_code == irb_doc_code)
-        return query.all()
+        return query.order_by(desc(FileModel.date_modified)).all()
 
     @staticmethod
     def get_files(workflow_id=None, name=None, irb_doc_code=None):