dcicutils 8.5.0.1b2__tar.gz → 8.5.0.1b4__tar.gz

{dcicutils-8.5.0.1b2 → dcicutils-8.5.0.1b4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.5.0.1b2
+Version: 8.5.0.1b4
 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-8.5.0.1b2 → dcicutils-8.5.0.1b4}/dcicutils/portal_utils.py

@@ -23,15 +23,14 @@ class Portal:
     2. From a key dictionary, containing "key" and "secret" property values.
     3. From a key tuple, containing (in order) a key and secret values.
     4. From a keys file assumed to reside in ~/.{app}-keys.json where the given "app" value is either "smaht", "cgap",
-       or "fourfront"; and where this file is assumed to contain a dictionary with a key equal to the given "env"
-       value (e.g. smaht-localhost) and with a dictionary value containing "key" and "secret" property values; if
-       an "app" value is not specified but the given "env" value begins with one of the app values then that value
-       will be used, i.e. e.g. if env is "smaht-localhost" and app is unspecified than it is assumed to be "smaht".
+       or "fourfront"; where is assumed to contain a dictionary with a key for the given "env" value, e.g. smaht-local;
+       and with a dictionary value containing "key" and "secret" property values, and an optional "server" property;
+       if an "app" value is not specified but the given "env" value begins with one of the app values then that value
+       will be used, i.e. e.g. if "env" is "smaht-local" and app is unspecified than it is assumed to be "smaht".
     5. From a keys file as described above (#4) but rather than be identified by the given "env" value it
-       is looked up by the given "server" name and the "server" key dictionary value in the key file.
+       is looked up via the given "server" name and the "server" key dictionary value in the key file.
     6. From a given "vapp" value (which is assumed to be a TestApp or VirtualApp).
-    7. From another Portal object.
-    8. From a a pyramid Router object.
+    7. From another Portal object; or from a a pyramid Router object.
     """
     def __init__(self,
                  arg: Optional[Union[VirtualApp, TestApp, Router, Portal, dict, tuple, str]] = None,
@@ -62,6 +61,7 @@ class Portal:
             self._server = portal._server
             self._key = portal._key
             self._key_pair = portal._key_pair
+            self._key_id = portal._key_id
             self._key_file = portal._key_file
             return
         self._vapp = None
@@ -70,6 +70,7 @@ class Portal:
         self._server = server
         self._key = None
         self._key_pair = None
+        self._key_id = None
         self._key_file = None
         if isinstance(portal, (VirtualApp, TestApp)):
             self._vapp = portal
@@ -95,6 +96,10 @@ class Portal:
                 self._key = key_manager.get_keydict_for_server(self._server)
             self._key_pair = key_manager.keydict_to_keypair(self._key) if self._key else None
             self._key_file = key_manager.keys_file
+        if self._key and (key_id := self._key.get("key")):
+            self._key_id = key_id
+        elif self._key_pair and (key_id := self._key_pair[1]):
+            self._key_id = key_id
 
     @property
     def env(self):
@@ -116,6 +121,10 @@ class Portal:
     def key_pair(self):
         return self._key_pair
 
+    @property
+    def key_id(self):
+        return self._key_id
+
     @property
     def key_file(self):
         return self._key_file
@@ -206,13 +215,19 @@ class Portal:
             super_type_map_flattened[super_type_name] = breadth_first(super_type_map, super_type_name)
         return super_type_map_flattened
 
+    def ping(self) -> bool:
+        try:
+            return self.get("/health").status_code == 200
+        except Exception:
+            return False
+
     def _uri(self, uri: str) -> str:
         if not isinstance(uri, str) or not uri:
             return "/"
         if uri.lower().startswith("http://") or uri.lower().startswith("https://"):
             return uri
         uri = re.sub(r"/+", "/", uri)
-        return (self._server + ("/" if uri.startswith("/") else "") + uri) if self._server else uri
+        return (self._server + ("/" if not uri.startswith("/") else "") + uri) if self._server else uri
 
     def _kwargs(self, **kwargs) -> dict:
         result_kwargs = {"headers":

{dcicutils-8.5.0.1b2 → dcicutils-8.5.0.1b4}/dcicutils/structured_data.py

@@ -42,8 +42,8 @@ StructuredDataSet = Type["StructuredDataSet"]
 class StructuredDataSet:
 
     def __init__(self, file: Optional[str] = None, portal: Optional[Union[VirtualApp, TestApp, Portal]] = None,
-                 schemas: Optional[List[dict]] = None, data: Optional[List[dict]] = None,
-                 order: Optional[List[str]] = None, prune: bool = True) -> None:
+                 schemas: Optional[List[dict]] = None, autoadd: Optional[dict] = None,
+                 data: Optional[List[dict]] = None, order: Optional[List[str]] = None, prune: bool = True) -> None:
         self.data = {} if not data else data  # If portal is None then no schemas nor refs.
         self._portal = Portal(portal, data=self.data, schemas=schemas) if portal else None
         self._order = order
@@ -52,13 +52,14 @@ class StructuredDataSet:
         self._errors = {}
         self._resolved_refs = set()
         self._validated = False
+        self._autoadd_properties = autoadd if isinstance(autoadd, dict) and autoadd else None
         self._load_file(file) if file else None
 
     @staticmethod
     def load(file: str, portal: Optional[Union[VirtualApp, TestApp, Portal]] = None,
-             schemas: Optional[List[dict]] = None,
+             schemas: Optional[List[dict]] = None, autoadd: Optional[dict] = None,
              order: Optional[List[str]] = None, prune: bool = True) -> StructuredDataSet:
-        return StructuredDataSet(file=file, portal=portal, schemas=schemas, order=order, prune=prune)
+        return StructuredDataSet(file=file, portal=portal, schemas=schemas, autoadd=autoadd, order=order, prune=prune)
 
     def validate(self, force: bool = False) -> None:
         if self._validated and not force:
@@ -163,6 +164,8 @@ class StructuredDataSet:
             structured_row = structured_row_template.create_row()
             for column_name, value in row.items():
                 structured_row_template.set_value(structured_row, column_name, value, reader.file, reader.row_number)
+                if self._autoadd_properties:
+                    self._add_properties(structured_row, self._autoadd_properties, schema)
             self._add(type_name, structured_row)
         self._note_warning(reader.warnings, "reader")
         if schema:
@@ -177,6 +180,11 @@ class StructuredDataSet:
         else:
             self.data[type_name] = [data] if isinstance(data, dict) else data
 
+    def _add_properties(self, structured_row: dict, properties: dict, schema: Optional[dict] = None) -> None:
+        for name in properties:
+            if name not in structured_row and (not schema or schema.data.get("properties", {}).get(name)):
+                structured_row[name] = properties[name]
+
     def _note_warning(self, item: Optional[Union[dict, List[dict]]], group: str) -> None:
         self._note_issue(self._warnings, item, group)
 
@@ -317,7 +325,8 @@ class Schema:
 
     @staticmethod
     def load_by_name(name: str, portal: Portal) -> Optional[dict]:
-        return Schema(portal.get_schema(Schema.type_name(name)), portal) if portal else None
+        schema_json = portal.get_schema(Schema.type_name(name)) if portal else None
+        return Schema(schema_json, portal) if schema_json else None
 
     def validate(self, data: dict) -> List[str]:
         errors = []
@@ -565,7 +574,9 @@ class Portal(PortalBase):
 
     @lru_cache(maxsize=256)
     def get_schema(self, schema_name: str) -> Optional[dict]:
-        if (schemas := self.get_schemas()) and (schema := schemas.get(schema_name := Schema.type_name(schema_name))):
+        if not (schemas := self.get_schemas()):
+            return None
+        if schema := schemas.get(schema_name := Schema.type_name(schema_name)):
             return schema
         if schema_name == schema_name.upper() and (schema := schemas.get(schema_name.lower().title())):
             return schema
@@ -573,8 +584,9 @@ class Portal(PortalBase):
             return schema
 
     @lru_cache(maxsize=1)
-    def get_schemas(self) -> dict:
-        schemas = super().get_schemas()
+    def get_schemas(self) -> Optional[dict]:
+        if not (schemas := super().get_schemas()) or (schemas.get("status") == "error"):
+            return None
         if self._schemas:
             schemas = copy.deepcopy(schemas)
             for user_specified_schema in self._schemas:

{dcicutils-8.5.0.1b2 → dcicutils-8.5.0.1b4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.5.0.1b2"  # TODO: To become 8.6.0
+version = "8.5.0.1b4"  # TODO: To become 8.6.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"