Upload API convenience fixes (#9) (#10)

* return the HTTP response when posting a model

* drop internal MaveDB attributes

* make virtual method explicit

* update authors

Author: afrubin

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Alan F Rubin
+Copyright (c) 2020-2022, MaveDB Developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

mavetools/client/client.py

@@ -71,6 +71,12 @@ def post_model_instance(self, model_instance):
 
         Returns
         -------
+        requests.model.Response
+            The HTTP response object from the request, which contains the URN
+            of the newly-created model in the `Response.text` field.
+
+        Raises
+        ------
         AuthTokenMissingException
             If the auth_token is missing
         """
@@ -100,3 +106,6 @@ def post_model_instance(self, model_instance):
 
         # No errors or exceptions at this point, log successful upload
         logging.info(f"Successfully uploaded {model_instance}!")
+
+        # return the HTTP response
+        return r

mavetools/models/dataset.py

@@ -37,29 +37,27 @@ class Dataset(TimeStamped, Urn):
     """
     Instantiates Dataset object and declares attributes
     """
-
+    # record keeping attributes
     publish_date: str = attr.ib(kw_only=True)
     created_by: str = attr.ib(kw_only=True)
     modified_by: str = attr.ib(kw_only=True)
-    # optional attributes
-    approved: Optional[str] = attr.ib(kw_only=True, default=None)
-    private: Optional[bool] = attr.ib(kw_only=True, default=None)
-    last_child_value: Optional[Any] = attr.ib(kw_only=True, default=None)
+
+    # required attributes
+    short_description: str = attr.ib(kw_only=True)
+    title: str = attr.ib(kw_only=True)
+    contributors: List[str] = attr.ib(kw_only=True)
+
     # optional attribute
-    extra_metadata: Optional[Dict[str, str]] = attr.ib(kw_only=True, default=None)
     abstract_text: str = attr.ib(kw_only=True)
     method_text: str = attr.ib(kw_only=True)
-    short_description: str = attr.ib(kw_only=True)
-    title: str = attr.ib(kw_only=True)
     keywords: List[Keyword] = attr.ib(kw_only=True)
     sra_ids: Optional[List[ExternalIdentifier]] = attr.ib(kw_only=True, default=None)
     doi_ids: Optional[List[ExternalIdentifier]] = attr.ib(kw_only=True, default=None)
     pubmed_ids: Optional[List[ExternalIdentifier]] = attr.ib(kw_only=True, default=None)
-    contributors: List[str] = attr.ib(kw_only=True)
+    extra_metadata: Optional[Dict[str, str]] = attr.ib(kw_only=True, default=None)
 
     def deserialize():
-        # why pass?
-        pass
+        raise NotImplementedError()
 
 
 @attr.s
@@ -68,8 +66,10 @@ class NewDataset:
     Instantiates NewDataset object and declares object attributes
     """
 
+    # required attributes
     title: str = attr.ib(kw_only=True)
     short_description: str = attr.ib(kw_only=True)
+
     # optional attributes
     abstract_text: Optional[str] = attr.ib(kw_only=True, default=None)
     method_text: Optional[str] = attr.ib(kw_only=True, default=None)

setup.py

@@ -21,7 +21,7 @@
 setup(
     name="mavetools",
     version="0.1.1",
-    author="Alan F Rubin",
+    author="MaveDB Developers",
     author_email="[email protected]",
     description=(
         "Useful functions for manipulating Multiplex Assay of Variant Effect datasets."