dcicutils 8.4.0.1b9__tar.gz → 8.4.0.1b11__tar.gz

{dcicutils-8.4.0.1b9 → dcicutils-8.4.0.1b11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.4.0.1b9
+Version: 8.4.0.1b11
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.4.0.1b9 → dcicutils-8.4.0.1b11}/dcicutils/structured_data.py

@@ -37,6 +37,7 @@ ARRAY_NAME_SUFFIX_CHAR = "#"
 ARRAY_NAME_SUFFIX_REGEX = re.compile(rf"{ARRAY_NAME_SUFFIX_CHAR}\d+")
 DOTTED_NAME_DELIMITER_CHAR = "."
 FILE_SCHEMA_NAME = "File"
+FILE_SCHEMA_NAME_PROPERTY = "filename"
 
 # Forward type references for type hints.
 Portal = Type["Portal"]
@@ -104,6 +105,17 @@ class StructuredDataSet:
     def resolved_refs(self) -> List[str]:
         return self._resolved_refs
 
+    @property
+    def upload_files(self) -> List[str]:
+        result = []
+        if self._portal:
+            for type_name in self.data:
+                if self._portal.is_file_schema(type_name):
+                    for item in self.data[type_name]:
+                        if (file_name := item.get(FILE_SCHEMA_NAME_PROPERTY)):
+                            result.append({"type": type_name, "file": file_name})
+        return result
+
     def _load_file(self, file: str) -> None:
         # Returns a dictionary where each property is the name (i.e. the type) of the data,
         # and the value is array of dictionaries for the data itself. Handle these kinds of files:
@@ -531,11 +543,11 @@ class Schema:
 class PortalBase:
 
     def __init__(self,
-                 arg: Optional[Union[VirtualApp, TestApp, Router, Portal, dict, tuple, str]] = None,
+                 arg: Optional[Union[VirtualApp, TestApp, Router, PortalBase, dict, tuple, str]] = None,
                  env: Optional[str] = None, app: OrchestratedApp = APP_SMAHT, server: Optional[str] = None,
                  key: Optional[Union[dict, tuple]] = None,
-                 portal: Optional[Union[VirtualApp, TestApp, Router, Portal, str]] = None) -> PortalBase:
-        if ((isinstance(arg, (VirtualApp, TestApp, Router, Portal)) or
+                 portal: Optional[Union[VirtualApp, TestApp, Router, PortalBase, str]] = None) -> PortalBase:
+        if ((isinstance(arg, (VirtualApp, TestApp, Router, PortalBase)) or
              isinstance(arg, str) and arg.endswith(".ini")) and not portal):
             portal = arg
         elif isinstance(arg, str) and not env:
@@ -545,8 +557,11 @@ class PortalBase:
         self._vapp = None
         self._key = None
         self._key_pair = None
+        self._key_file = None
+        self._env = env
+        self._app = app
         self._server = None
-        if isinstance(portal, Portal):
+        if isinstance(portal, PortalBase):
             self._vapp = portal._vapp
             self._key = portal._key
             self._key_pair = portal._key_pair
@@ -573,6 +588,35 @@ class PortalBase:
                 self._key = key_manager.get_keydict_for_server(server)
                 self._server = server
             self._key_pair = key_manager.keydict_to_keypair(self._key) if self._key else None
+            self._key_file = key_manager.keys_file
+
+    @property
+    def env(self):
+        return self._env
+
+    @property
+    def app(self):
+        return self._app
+
+    @property
+    def key(self):
+        return self._key
+
+    @property
+    def key_pair(self):
+        return self._key_pair
+
+    @property
+    def key_file(self):
+        return self._key_file
+
+    @property
+    def server(self):
+        return self._server
+
+    @property
+    def vapp(self):
+        return self._vapp
 
     def get_metadata(self, object_id: str) -> Optional[dict]:
         return get_metadata(obj_id=object_id, vapp=self._vapp, key=self._key)
@@ -636,7 +680,7 @@ class PortalBase:
     def _response(self, response) -> Optional[RequestResponse]:
         if response and isinstance(getattr(response.__class__, "json"), property):
             class RequestResponseWrapper:  # For consistency change json property to method.
-                def __init__(self, respnose, **kwargs):
+                def __init__(self, response, **kwargs):
                     super().__init__(**kwargs)
                     self._response = response
                 def __getattr__(self, attr):  # noqa
@@ -649,15 +693,15 @@ class PortalBase:
     @staticmethod
     def create_for_testing(ini_file: Optional[str] = None) -> PortalBase:
         if isinstance(ini_file, str):
-            return Portal(Portal._create_testapp(ini_file))
+            return PortalBase(PortalBase._create_testapp(ini_file))
         minimal_ini_for_unit_testing = "[app:app]\nuse = egg:encoded\nsqlalchemy.url = postgresql://dummy\n"
         with temporary_file(content=minimal_ini_for_unit_testing, suffix=".ini") as ini_file:
-            return Portal(Portal._create_testapp(ini_file))
+            return PortalBase(PortalBase._create_testapp(ini_file))
 
     @staticmethod
-    def create_for_testing_local(ini_file: Optional[str] = None) -> Portal:
+    def create_for_testing_local(ini_file: Optional[str] = None) -> PortalBase:
         if isinstance(ini_file, str) and ini_file:
-            return Portal(Portal._create_testapp(ini_file))
+            return PortalBase(PortalBase._create_testapp(ini_file))
         minimal_ini_for_testing_local = "\n".join([
             "[app:app]\nuse = egg:encoded\nfile_upload_bucket = dummy",
             "sqlalchemy.url = postgresql://postgres@localhost:5441/postgres?host=/tmp/snovault/pgdata",
@@ -678,7 +722,7 @@ class PortalBase:
             "multiauth.policy.auth0.base = encoded.authentication.Auth0AuthenticationPolicy"
         ])
         with temporary_file(content=minimal_ini_for_testing_local, suffix=".ini") as minimal_ini_file:
-            return Portal(Portal._create_testapp(minimal_ini_file))
+            return PortalBase(PortalBase._create_testapp(minimal_ini_file))
 
     @staticmethod
     def _create_testapp(value: Union[str, Router, TestApp] = "development.ini") -> TestApp:

{dcicutils-8.4.0.1b9 → dcicutils-8.4.0.1b11}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.4.0.1b9"  # TODO: To become 8.4.1
+version = "8.4.0.1b11"  # TODO: To become 8.4.1
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"