datalab-api 0.2.10__tar.gz → 0.2.12__tar.gz

{datalab_api-0.2.10/src/datalab_api.egg-info → datalab_api-0.2.12}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: datalab-api
-Version: 0.2.10
+Version: 0.2.12
 Summary: A Python API for instances of the datalab data management platform (https://github.com/datalab-org/datalab).
 Author-email: Matthew Evans <matthew@ml-evs.science>
-License: MIT
+License-Expression: MIT
 Project-URL: homepage, https://github.com/datalab-org/datalab-api
 Project-URL: repository, https://github.com/datalab-org/datalab-api
 Project-URL: documentation, https://datalab-python-api.readthedocs.io

{datalab_api-0.2.10 → datalab_api-0.2.12}/pyproject.toml

@@ -7,7 +7,7 @@ name = "datalab-api"
 readme = "README.md"
 description = "A Python API for instances of the datalab data management platform (https://github.com/datalab-org/datalab)."
 keywords = []
-license = { text = "MIT" }
+license = "MIT"
 authors = [{ name = "Matthew Evans", email = "matthew@ml-evs.science" }]
 dynamic = ["version"]
 classifiers = [

{datalab_api-0.2.10 → datalab_api-0.2.12}/src/datalab_api/__init__.py

@@ -83,9 +83,17 @@ class DatalabClient(BaseDatalabClient):
             A list of items of the given type.
 
         """
+        endpoint_type_map = {
+            "cells": "samples",
+            "samples": "samples",
+            "starting_materials": "starting-materials",
+            "equipment": "equipment",
+        }
+
         if item_type is None:
             item_type = "samples"
-        items_url = f"{self.datalab_api_url}/{item_type}"
+
+        items_url = f"{self.datalab_api_url}/{endpoint_type_map.get(item_type, item_type.replace('_', '-'))}"
         items_resp = self.session.get(items_url, follow_redirects=True)
         if items_resp.status_code != 200:
             raise RuntimeError(
@@ -94,7 +102,15 @@ class DatalabClient(BaseDatalabClient):
         items = items_resp.json()
         if items["status"] != "success":
             raise RuntimeError(f"Failed to list items at {items_url}: {items['status']!r}.")
-        return items[item_type]
+
+        if item_type in items:
+            # Old approach
+            return items[item_type]
+        if "items" in items:
+            return items["items"]
+
+        else:
+            return items
 
     def search_items(
         self, query: str, item_types: Iterable[str] | str = ("samples", "cells")
@@ -153,10 +169,10 @@ class DatalabClient(BaseDatalabClient):
 
         if collection_id is not None:
             try:
-                collection_immutable_id = self.get_collection(collection_id)["immutable_id"]
+                collection_immutable_id = self.get_collection(collection_id)[0]["immutable_id"]
             except RuntimeError:
                 self.create_collection(collection_id)
-                collection_immutable_id = self.get_collection(collection_id)["immutable_id"]
+                collection_immutable_id = self.get_collection(collection_id)[0]["immutable_id"]
             new_item["collections"] = new_item.get("collections", [])
             new_item["collections"].append({"immutable_id": collection_immutable_id})
 
@@ -173,6 +189,10 @@ class DatalabClient(BaseDatalabClient):
                     f"Item {item_id=} already exists at {create_item_url}: {created_item['status']!r}."
                 )
             if created_item["status"] != "success":
+                if "DuplicateKeyError" in created_item["message"]:
+                    raise DuplicateItemError(
+                        f"Item {item_id=} already exists at {create_item_url}: {created_item['status']!r}."
+                    )
                 raise RuntimeError(f"Failed to create item at {create_item_url}: {created_item}.")
             return created_item["sample_list_entry"]
 
@@ -468,14 +488,15 @@ class DatalabClient(BaseDatalabClient):
 
         return resp.json()["new_block_data"]
 
-    def get_collection(self, collection_id: str) -> dict[str, Any]:
+    def get_collection(self, collection_id: str) -> tuple[dict[str, Any], list[dict[str, Any]]]:
         """Get a collection with a given ID.
 
         Parameters:
             collection_id: The ID of the collection to search for.
 
         Returns:
-            A dictionary of collection data for the collection with the given ID.
+            A dictionary of collection data for the collection with the given ID,
+            and a list of the member items.
 
         """
         collection_url = f"{self.datalab_api_url}/collections/{collection_id}"
@@ -489,7 +510,7 @@ class DatalabClient(BaseDatalabClient):
             raise RuntimeError(
                 f"Failed to get collection at {collection_url}: {collection['status']!r}."
             )
-        return collection["data"]
+        return collection["data"], collection["child_items"]
 
     def create_collection(
         self, collection_id: str, collection_data: dict | None = None

{datalab_api-0.2.10 → datalab_api-0.2.12/src/datalab_api.egg-info}/PKG-INFO

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: datalab-api
-Version: 0.2.10
+Version: 0.2.12
 Summary: A Python API for instances of the datalab data management platform (https://github.com/datalab-org/datalab).
 Author-email: Matthew Evans <matthew@ml-evs.science>
-License: MIT
+License-Expression: MIT
 Project-URL: homepage, https://github.com/datalab-org/datalab-api
 Project-URL: repository, https://github.com/datalab-org/datalab-api
 Project-URL: documentation, https://datalab-python-api.readthedocs.io

{datalab_api-0.2.10 → datalab_api-0.2.12}/tests/test_client.py

@@ -55,3 +55,27 @@ def test_sample_list(fake_samples_json, fake_info_json, fake_sample_json, fake_b
         sample = client.get_item("KUVEKJ", display=True)
         assert fake_item_api.called
         assert sample["item_id"] == "KUVEKJ"
+
+
+@respx.mock
+def test_collection_get(fake_info_json, fake_block_info_json, fake_collection_json):
+    fake_api = respx.get("https://api.datalab.industries/").mock(
+        return_value=Response(200, content="<!doctype html></html>")
+    )
+    fake_info_api = respx.get("https://api.datalab.industries/info").mock(
+        return_value=Response(200, json=fake_info_json)
+    )
+    fake_block_info_api = respx.get("https://api.datalab.industries/info/blocks").mock(
+        return_value=Response(200, json=fake_block_info_json)
+    )
+
+    fake_collection_api = respx.get(
+        "https://api.datalab.industries/collections/test_collection"
+    ).mock(return_value=Response(200, json=fake_collection_json))
+
+    with DatalabClient("https://api.datalab.industries") as client:
+        collection, children = client.get_collection("test_collection")
+        assert fake_api.called
+        assert fake_info_api.called
+        assert fake_block_info_api.called
+        assert fake_collection_api.called