feat(apiclient): add CRUD methods for instantiated entities

Author: gegnew

.flake8

@@ -1,4 +1,4 @@
 [flake8]
-ignore = E226,E302,E41,W503
+ignore = E226,E302,E41,W503,E704
 max-line-length = 88
 exclude = tests/*

.github/workflows/push.yml

@@ -25,7 +25,7 @@ jobs:
         uses: TrueBrain/actions-flake8@master
         with:
           max_line_length: 88
-          extend-ignore: E203
+          extend-ignore: E203, E704
   test:
     runs-on: ubuntu-latest
     strategy:

cellengine/utils/api_client/APIClient.py

@@ -1,15 +1,19 @@
 from __future__ import annotations
-import os
+from collections import defaultdict
+from functools import lru_cache
+from getpass import getpass
 import json
+import os
+from typing import Any, Dict, List, Optional, TypeVar, Union, overload
+
 import pandas
-from getpass import getpass
-from typing import Any, Dict, List, Union, Optional
-from functools import lru_cache
 from requests_toolbelt.multipart.encoder import MultipartEncoder
 
-from cellengine.utils.api_client.BaseAPIClient import BaseAPIClient
+from cellengine.utils import converter
 from cellengine.utils.api_client.APIError import APIError
+from cellengine.utils.api_client.BaseAPIClient import BaseAPIClient
 from cellengine.utils.singleton import Singleton
+
 from ...resources.attachment import Attachment
 from ...resources.compensation import Compensation
 from ...resources.experiment import Experiment
@@ -20,6 +24,28 @@
 from ...resources.scaleset import ScaleSet
 
 
+CE = TypeVar(
+    "CE",
+    bound=Union[
+        Attachment, Compensation, Experiment, FcsFile, Gate, Plot, Population, ScaleSet
+    ],
+)
+
+
+def create_many(client: APIClient, entities: List[CE], **kwargs) -> List[Gate]:
+    body = [client.unstructure_and_clean(e) for e in entities]
+    (classes, paths, payload) = list(zip(*body))
+    _class = set(classes)
+    if len(_class) != 1 or Gate not in _class:
+        raise TypeError(f"Type or types {_class} cannot be created in bulk.")
+    return client.post_and_structure(
+        List[_class.pop()],  # type: ignore
+        set(paths).pop(),
+        list(payload),
+        kwargs=kwargs,
+    )
+
+
 class APIClient(BaseAPIClient, metaclass=Singleton):
     _API_NAME = "CellEngine Python Toolkit"
 
@@ -119,6 +145,69 @@ def update_entity(self, experiment_id, _id, entity_type, body) -> dict:
             json=body,
         )
 
+    def _get_path(self, entity: CE) -> str:
+        fullpath = f"{self.base_url}/{entity.path}"
+        return fullpath
+
+    def post_and_structure(self, _class, path, body, **kwargs):
+        res = self._post(f"{self.base_url}/{path}", json=body, params=kwargs)
+        return converter.structure(res, _class)
+
+    def unstructure_and_clean(self, entity):
+        (cls, path, body) = (
+            entity.__class__,
+            entity.path,
+            converter.unstructure(entity),
+        )
+        if body["_id"] == "None" or body["_id"] is None:
+            del body["_id"]  # https://github.com/primitybio/cellengine/issues/5800
+        return (cls, path, body)
+
+    # fmt: off
+    # temporary fix for https://github.com/psf/black/issues/1797
+    @overload
+    def create(self, entity: Attachment, **kwargs) -> Attachment: ...
+    @overload
+    def create(self, entity: Compensation, **kwargs) -> Compensation: ...
+    @overload
+    def create(self, entity: Experiment, **kwargs) -> Experiment: ...
+    @overload
+    def create(self, entity: FcsFile, **kwargs) -> FcsFile: ...
+    @overload
+    def create(self, entity: Gate, **kwargs) -> Gate: ...
+    @overload
+    def create(self, entity: Population, **kwargs) -> Population: ...
+    @overload
+    def create(self, entity: ScaleSet, **kwargs) -> ScaleSet: ...
+    # fmt: on
+
+    def create(
+        self, entity, **kwargs
+    ) -> Union[
+        Attachment,
+        Compensation,
+        Experiment,
+        FcsFile,
+        Gate,
+        Population,
+        ScaleSet,
+    ]:
+        """Create a local entity on CellEngine."""
+        if isinstance(entity, list):
+            return create_many(self, entity, **kwargs)
+        body = self.unstructure_and_clean(entity)
+        return self.post_and_structure(*body)
+
+    def update(self, entity, params: Dict = None):
+        path = self._get_path(entity)
+        data = converter.unstructure(entity)
+        res = self._patch(path, json=data, params=params)
+        return converter.structure(res, entity.__class__)
+
+    def delete(self, entity, params: Dict = None) -> None:
+        path = self._get_path(entity)
+        self._delete(path, params=params)
+
     def delete_entity(self, experiment_id, entity_type, _id):
         url = f"{self.base_url}/experiments/{experiment_id}/{entity_type}/{_id}"
         self._delete(url)