[SYNPY-1551] Tables refactor

docs/css/custom.css

@@ -7,3 +7,7 @@ div.doc-contents {
 .md-typeset table tbody {
     font-size: .7rem
 }
+
+.md-grid {
+    max-width: 1700px;
+}

docs/reference/oop/table_refactor.md

@@ -0,0 +1,34 @@
+Contained within this file are proposed changes for interacting with Tables via this
+client.
+
+
+
+::: synapseclient.models.Table
+    options:
+        inherited_members: true
+        members:
+        - get
+        - store
+        - delete
+        - query
+        - store_rows
+        - delete_rows
+        - snapshot
+        - delete_column
+        - add_column
+        - reorder_column
+        - set_columns
+        - get_permissions
+        - get_acl
+        - set_permissions
+
+::: synapseclient.models.table.SchemaStorageStrategy
+::: synapseclient.models.table.ColumnExpansionStrategy
+
+::: synapseclient.models.FacetType
+::: synapseclient.models.ColumnType
+::: synapseclient.models.table.JsonSubColumn
+
+::: synapseclient.models.Column
+    options:
+        members:

mkdocs.yml

@@ -75,8 +75,9 @@ nav:
       - Core: reference/core.md
       - REST Apis: reference/rest_apis.md
       - Experimental:
-          - Object-Orientated Models: reference/oop/models.md
-          - Async Object-Orientated Models: reference/oop/models_async.md
+        - Object-Orientated Models: reference/oop/models.md
+        - Async Object-Orientated Models: reference/oop/models_async.md
+        - Table refactor: reference/oop/table_refactor.md
   - Further Reading:
       - Home: explanations/home.md
       - Domain Models of Synapse: explanations/domain_models_of_synapse.md
@@ -120,6 +121,8 @@ theme:
     - toc.follow
     - navigation.tabs
     - navigation.tabs.sticky
+    - navigation.instant
+    - navigation.instant.progress
 
 extra_css:
   - css/custom.css

synapseclient/api/__init__.py

@@ -38,6 +38,7 @@
     put_file_multipart_add,
     put_file_multipart_complete,
 )
+from .table_services import get_columns
 
 __all__ = [
     # annotations
@@ -78,4 +79,6 @@
     "get_transfer_config",
     # entity_factory
     "get_from_entity_factory",
+    # columns
+    "get_columns",
 ]

synapseclient/api/table_services.py

@@ -0,0 +1,93 @@
+"""
+The purpose of this module is to provide any functions that are needed to interact with
+columns in the Synapse REST API.
+"""
+
+from typing import TYPE_CHECKING, List, Optional
+
+if TYPE_CHECKING:
+    from synapseclient import Synapse
+    from synapseclient.models import Column
+
+
+async def get_columns(
+    table_id: str,
+    *,
+    synapse_client: Optional["Synapse"] = None,
+) -> List["Column"]:
+    """Call to synapse and set the annotations for the given input.
+
+    Arguments:
+        table_id: The ID of the Table to get the columns for.
+        synapse_client: If not passed in and caching was not disabled by
+                `Synapse.allow_client_caching(False)` this will use the last created
+                instance from the Synapse class constructor.
+
+    Returns: The annotations set in Synapse.
+    """
+    from synapseclient import Synapse
+    from synapseclient.models import Column
+
+    result = await Synapse.get_client(synapse_client=synapse_client).rest_get_async(
+        f"/entity/{table_id}/column",
+    )
+
+    columns = []
+
+    for column in result.get("results", []):
+        columns.append(Column().fill_from_dict(synapse_column=column))
+
+    return columns
+
+
+# TODO: Finish this function, this was copied out of the Synapse class and will be used to implement this API: https://rest-docs.synapse.org/rest/org/sagebionetworks/repo/model/table/TableSchemaChangeRequest.html
+# async def table_updates(
+#     self,
+#     table_id: str,
+#     changes: List[dict] = [],
+#     create_snapshot: bool = False,
+#     comment: str = None,
+#     label: str = None,
+#     activity: str = None,
+#     wait: bool = True,
+# ) -> dict:
+#     """
+#     Creates view updates and snapshots
+
+#     Arguments:
+#         table:           The schema of the EntityView or its ID.
+#         changes:         Array of Table changes
+#         create_snapshot: Create snapshot
+#         comment:         Optional snapshot comment.
+#         label:           Optional snapshot label.
+#         activity:        Optional activity ID applied to snapshot version.
+#         wait:            True to wait for async table update to complete
+
+#     Returns:
+#         A Snapshot Response
+#     """
+#     snapshot_options = {
+#         "snapshotComment": comment,
+#         "snapshotLabel": label,
+#         "snapshotActivityId": activity,
+#     }
+#     new_snapshot = {
+#         key: value for key, value in snapshot_options.items() if value is not None
+#     }
+#     table_update_body = {
+#         "changes": changes,
+#         "createSnapshot": create_snapshot,
+#         "snapshotOptions": new_snapshot,
+#     }
+
+#     uri = "/entity/{}/table/transaction/async".format(id_of(table))
+
+#     if wait:
+#         result = self._waitForAsync(uri, table_update_body)
+
+#     else:
+#         result = self.restPOST(
+#             "{}/start".format(uri), body=json.dumps(table_update_body)
+#         )
+
+#     return result

synapseclient/core/exceptions.py

@@ -2,13 +2,16 @@
 as handling error cases for HTTP requests."""
 
 import logging
+import re
 from typing import Union
 
 import httpx
 import requests
 
 from synapseclient.core import utils
 
+BEARER_TOKEN_PATTERN = re.compile(r"\'Bearer \S+\'")
+
 
 class SynapseError(Exception):
     """Generic exception thrown by the client."""
@@ -175,6 +178,7 @@ def _raise_for_status(response, verbose=False):
                 # Append the request sent
                 message += f"\n\n{REQUEST_PREFIX}\n{response.request.url} {response.request.method}"
                 message += f"\n{HEADERS_PREFIX}{response.request.headers}"
+                message = re.sub(BEARER_TOKEN_PATTERN, "'Bearer <redacted>'", message)
                 message += f"\n{BODY_PREFIX}{response.request.body}"
             except:  # noqa
                 message += f"\n{UNABLE_TO_APPEND_REQUEST}"
@@ -273,6 +277,7 @@ def _raise_for_status_httpx(
                 # Append the request sent
                 message += f"\n\n{REQUEST_PREFIX}\n{response.request.url} {response.request.method}"
                 message += f"\n{HEADERS_PREFIX}{response.request.headers}"
+                message = re.sub(BEARER_TOKEN_PATTERN, "'Bearer <redacted>'", message)
                 message += f"\n{BODY_PREFIX}{response.request.content}"
             except Exception:  # noqa
                 logger.exception(UNABLE_TO_APPEND_REQUEST)

synapseclient/core/utils.py

@@ -34,7 +34,7 @@
 from synapseclient.core.logging_setup import DEFAULT_LOGGER_NAME
 
 if TYPE_CHECKING:
-    from synapseclient.models import File, Folder, Project
+    from synapseclient.models import File, Folder, Project, Table
 
 R = TypeVar("R")
 
@@ -1376,10 +1376,10 @@ def delete_none_keys(incoming_object: typing.Dict) -> None:
 
 
 def merge_dataclass_entities(
-    source: typing.Union["Project", "Folder", "File"],
-    destination: typing.Union["Project", "Folder", "File"],
+    source: typing.Union["Project", "Folder", "File", "Table"],
+    destination: typing.Union["Project", "Folder", "File", "Table"],
     fields_to_ignore: typing.List[str] = None,
-) -> typing.Union["Project", "Folder", "File"]:
+) -> typing.Union["Project", "Folder", "File", "Table"]:
     """
     Utility function to merge two dataclass entities together. This is used when we are
     upserting an entity from the Synapse service with the requested changes.

synapseclient/models/__init__.py

@@ -8,9 +8,7 @@
 from synapseclient.models.table import (
     Column,
     ColumnType,
-    CsvResultFormat,
     FacetType,
-    Row,
     RowsetResultFormat,
     Table,
 )
@@ -33,7 +31,6 @@
     "FacetType",
     "CsvResultFormat",
     "RowsetResultFormat",
-    "Row",
     "Team",
     "TeamMember",
     "UserProfile",

synapseclient/models/activity.py

@@ -319,8 +319,8 @@ async def store_async(
                 ),
             )
         self.fill_from_dict(synapse_activity=saved_activity)
-        Synapse.get_client(synapse_client=synapse_client).logger.debug(
-            f"Stored activity {self.id}"
+        Synapse.get_client(synapse_client=synapse_client).logger.info(
+            f"[{parent.id}]: Stored activity"
         )
 
         return self

synapseclient/models/annotations.py

@@ -88,7 +88,7 @@ async def store_async(
         self.annotations = Annotations.from_dict(result)
         self.etag = result["etag"]
         Synapse.get_client(synapse_client=synapse_client).logger.debug(
-            f"Annotations stored for {self.id}"
+            f"[{self.id}]: Stored annotations"
         )
         return self