datalab-api 0.2.4__tar.gz → 0.2.5__tar.gz

{datalab_api-0.2.4/src/datalab_api.egg-info → datalab_api-0.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: datalab-api
-Version: 0.2.4
+Version: 0.2.5
 Summary: A Python API for instances of the datalab data management platform (https://github.com/the-grey-group/datalab).
 Author-email: Matthew Evans <matthew@ml-evs.science>
 License: MIT
@@ -99,7 +99,7 @@ You can generate one for your account for a given *datalab* instance by visiting
 
 This API key can be set via the environment variable `DATALAB_API_KEY`.
 To suport the use case of needing to interact with multiple datalab instances, the client will also check prefixed environment variables that use the [`IDENTIFIER_PREFIX` of the chosen datalab instance](https://the-datalab.readthedocs.io/en/latest/config/#mandatory-settings), e.g., `GREY_DATALAB_API_KEY` or `PUBLIC_DATALAB_API_KEY`.
-Only keys that match will be read (e.g., other environment variables starting with `PUBLIC_` will be ignored, when connecting to the [public demo datalab](https://public.datalab.odbx.science)).
+Only keys that match will be read (e.g., other environment variables starting with `PUBLIC_` will be ignored, when connecting to the [public demo datalab](https://demo.datalab-org.io)).
 
 ### Python API
 
@@ -108,7 +108,7 @@ This package implements basic functionality for displaying and manipulating entr
 ```python
 from datalab_api import DatalabClient
 
-with DatalabClient("https://public.api.odbx.science") as client:
+with DatalabClient("https://demo-api.datalab-org.io") as client:
 
     # List all items of a given type
     items = client.get_items()
@@ -167,7 +167,7 @@ datalab > help get
 │ --help                       Show this message and exit.                                            │
 ╰─────────────────────────────────────────────────────────────────────────────────────────────────────╯
 
-datalab > get samples api.odbx.science --page-limit 2
+datalab > get samples demo-api.datalab-org.io --page-limit 2
                                                     /samples/
 ┏━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
 ┃ type ┃ ID              ┃ refcode     ┃ name                           ┃ nblocks ┃ collections ┃ creators      ┃

{datalab_api-0.2.4 → datalab_api-0.2.5}/README.md

@@ -53,7 +53,7 @@ You can generate one for your account for a given *datalab* instance by visiting
 
 This API key can be set via the environment variable `DATALAB_API_KEY`.
 To suport the use case of needing to interact with multiple datalab instances, the client will also check prefixed environment variables that use the [`IDENTIFIER_PREFIX` of the chosen datalab instance](https://the-datalab.readthedocs.io/en/latest/config/#mandatory-settings), e.g., `GREY_DATALAB_API_KEY` or `PUBLIC_DATALAB_API_KEY`.
-Only keys that match will be read (e.g., other environment variables starting with `PUBLIC_` will be ignored, when connecting to the [public demo datalab](https://public.datalab.odbx.science)).
+Only keys that match will be read (e.g., other environment variables starting with `PUBLIC_` will be ignored, when connecting to the [public demo datalab](https://demo.datalab-org.io)).
 
 ### Python API
 
@@ -62,7 +62,7 @@ This package implements basic functionality for displaying and manipulating entr
 ```python
 from datalab_api import DatalabClient
 
-with DatalabClient("https://public.api.odbx.science") as client:
+with DatalabClient("https://demo-api.datalab-org.io") as client:
 
     # List all items of a given type
     items = client.get_items()
@@ -121,7 +121,7 @@ datalab > help get
 │ --help                       Show this message and exit.                                            │
 ╰─────────────────────────────────────────────────────────────────────────────────────────────────────╯
 
-datalab > get samples api.odbx.science --page-limit 2
+datalab > get samples demo-api.datalab-org.io --page-limit 2
                                                     /samples/
 ┏━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
 ┃ type ┃ ID              ┃ refcode     ┃ name                           ┃ nblocks ┃ collections ┃ creators      ┃

{datalab_api-0.2.4 → datalab_api-0.2.5}/src/datalab_api/__init__.py

@@ -1,3 +1,5 @@
+from __future__ import annotations
+
 import warnings
 from collections.abc import Iterable
 from pathlib import Path
@@ -19,7 +21,7 @@ class DatalabClient(BaseDatalabClient):
     amenable for use as a context manager, e.g.,
 
     ```python
-    with DatalabClient("https://public.api.odbx.science") as client:
+    with DatalabClient("https://demo-api.datalab-org.io") as client:
         client.get_items()
     ```
 
@@ -46,7 +48,7 @@ class DatalabClient(BaseDatalabClient):
             )
         return user_resp.json()
 
-    def get_items(self, item_type: Optional[str] = "samples") -> list[dict[str, Any]]:
+    def get_items(self, item_type: str | None = "samples") -> list[dict[str, Any]]:
         """List items of the given type available to the authenticated user.
 
         Parameters:
@@ -71,7 +73,7 @@ class DatalabClient(BaseDatalabClient):
         return items[item_type]
 
     def search_items(
-        self, query: str, item_types: Union[Iterable[str], str] = ("samples", "cells")
+        self, query: str, item_types: Iterable[str] | str = ("samples", "cells")
     ) -> list[dict[str, Any]]:
         """Search for items of the given types that match the query.
 
@@ -102,15 +104,15 @@ class DatalabClient(BaseDatalabClient):
 
     def create_item(
         self,
-        item_id: str,
-        item_type: str,
-        item_data: Optional[dict[str, Any]] = None,
-        collection_id: Optional[str] = None,
+        item_id: str | None = None,
+        item_type: str = "samples",
+        item_data: dict[str, Any] | None = None,
+        collection_id: str | None = None,
     ) -> dict[str, Any]:
         """Create an item with a given ID and item data.
 
         Parameters:
-            item_id: The ID of the item to create.
+            item_id: The ID of the item to create, if set to `None`, the server will generate one.
             item_type: The type of item to create, e.g., 'samples', 'cells'.
             item_data: The data for the item.
             collection_id: The ID of the collection to add the item to (optional).
@@ -133,7 +135,7 @@ class DatalabClient(BaseDatalabClient):
         create_item_url = f"{self.datalab_api_url}/new-sample/"
         create_item_resp = self.session.post(
             create_item_url,
-            json=new_item,
+            json={"new_sample_data": new_item, "generate_id_automatically": item_id is None},
             follow_redirects=True,
         )
         try:
@@ -182,8 +184,8 @@ class DatalabClient(BaseDatalabClient):
 
     def get_item(
         self,
-        item_id: Optional[str] = None,
-        refcode: Optional[str] = None,
+        item_id: str | None = None,
+        refcode: str | None = None,
         load_blocks: bool = False,
     ) -> dict[str, Any]:
         """Get an item with a given ID or refcode.
@@ -287,7 +289,7 @@ class DatalabClient(BaseDatalabClient):
             raise RuntimeError(f"Failed to get block at {block_url}: {block['status']!r}.")
         return block["new_block_data"]
 
-    def upload_file(self, item_id: str, file_path: Union[Path, str]) -> dict[str, Any]:
+    def upload_file(self, item_id: str, file_path: Path | str) -> dict[str, Any]:
         """Upload a file to an item with a given ID.
 
         Parameters:
@@ -327,8 +329,8 @@ class DatalabClient(BaseDatalabClient):
         self,
         item_id: str,
         block_type: str,
-        file_ids: Optional[Union[str, list[str]]] = None,
-        file_paths: Optional[Union[Path, list[Path]]] = None,
+        file_ids: str | list[str] | None = None,
+        file_paths: Path | list[Path] | None = None,
     ) -> dict[str, Any]:
         """Creates a data block for an item with the given block type and file ID.
 
@@ -385,7 +387,7 @@ class DatalabClient(BaseDatalabClient):
         return block_data
 
     def _update_data_block(
-        self, block_type: str, block_data: dict, file_ids: Optional[Union[str, list[str]]] = None
+        self, block_type: str, block_data: dict, file_ids: str | list[str] | None = None
     ) -> dict[str, Any]:
         """Attaches files to blocks: should only be used via wrapper methods."""
         if file_ids and isinstance(file_ids, str):
@@ -436,7 +438,7 @@ class DatalabClient(BaseDatalabClient):
         return collection["data"]
 
     def create_collection(
-        self, collection_id: str, collection_data: Optional[dict] = None
+        self, collection_id: str, collection_data: dict | None = None
     ) -> dict[str, Any]:
         """Create a collection with a given ID and collection data.
 

{datalab_api-0.2.4 → datalab_api-0.2.5}/src/datalab_api/_base.py

@@ -113,8 +113,8 @@ class BaseDatalabClient(metaclass=AutoPrettyPrint):
         Parameters:
             datalab_api_url: The URL of the Datalab API.
                 TODO: If the URL of a datalab *UI* is provided, a request will be made to attempt
-                to resolve the underlying API URL (e.g., `https://public.datalab.odbx.science`
-                will 'redirect' to `https://public.api.odbx.science`).
+                to resolve the underlying API URL (e.g., `https://demo-api.datalab-org.io`
+                will 'redirect' to `https://demo-api.datalab-org.io`).
             log_level: The logging level to use for the client. Defaults to "WARNING".
 
 

{datalab_api-0.2.4 → datalab_api-0.2.5}/src/datalab_api/helpers.py

@@ -31,13 +31,11 @@ def import_cheminventory(filename: Path, client: DatalabClient):
     inventory_df["item_id"] = inventory_df["Barcode"]
     # Fill missing barcodes
     inventory_df["item_id"] = inventory_df["item_id"].fillna(
-        inventory_df["item_id"].apply(lambda _: _generate_random_startingmaterial_id())
+        inventory_df["item_id"].apply(lambda _: next(_generate_random_startingmaterial_id()))
     )
     inventory_df["Molecular Weight"] = inventory_df["Molecular Weight"].replace(" ", float("nan"))
 
-    inventory_df = inventory_df.dropna()
-
-    counts = {"success": 0, "duplicate": 0}
+    counts = {"success": 0, "duplicate": 0, "failed": 0}
 
     for item in inventory_df.to_dict(orient="records"):
         try:
@@ -47,5 +45,9 @@ def import_cheminventory(filename: Path, client: DatalabClient):
             counts["success"] += 1
         except DuplicateItemError:
             counts["duplicate"] += 1
+        except Exception as exc:
+            counts["failed"] += 1
+            print(f"Failed to import item: {item}. Error: {exc}")
+            continue
 
     print(f"Done: {counts=}")

{datalab_api-0.2.4 → datalab_api-0.2.5/src/datalab_api.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: datalab-api
-Version: 0.2.4
+Version: 0.2.5
 Summary: A Python API for instances of the datalab data management platform (https://github.com/the-grey-group/datalab).
 Author-email: Matthew Evans <matthew@ml-evs.science>
 License: MIT
@@ -99,7 +99,7 @@ You can generate one for your account for a given *datalab* instance by visiting
 
 This API key can be set via the environment variable `DATALAB_API_KEY`.
 To suport the use case of needing to interact with multiple datalab instances, the client will also check prefixed environment variables that use the [`IDENTIFIER_PREFIX` of the chosen datalab instance](https://the-datalab.readthedocs.io/en/latest/config/#mandatory-settings), e.g., `GREY_DATALAB_API_KEY` or `PUBLIC_DATALAB_API_KEY`.
-Only keys that match will be read (e.g., other environment variables starting with `PUBLIC_` will be ignored, when connecting to the [public demo datalab](https://public.datalab.odbx.science)).
+Only keys that match will be read (e.g., other environment variables starting with `PUBLIC_` will be ignored, when connecting to the [public demo datalab](https://demo.datalab-org.io)).
 
 ### Python API
 
@@ -108,7 +108,7 @@ This package implements basic functionality for displaying and manipulating entr
 ```python
 from datalab_api import DatalabClient
 
-with DatalabClient("https://public.api.odbx.science") as client:
+with DatalabClient("https://demo-api.datalab-org.io") as client:
 
     # List all items of a given type
     items = client.get_items()
@@ -167,7 +167,7 @@ datalab > help get
 │ --help                       Show this message and exit.                                            │
 ╰─────────────────────────────────────────────────────────────────────────────────────────────────────╯
 
-datalab > get samples api.odbx.science --page-limit 2
+datalab > get samples demo-api.datalab-org.io --page-limit 2
                                                     /samples/
 ┏━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━┓
 ┃ type ┃ ID              ┃ refcode     ┃ name                           ┃ nblocks ┃ collections ┃ creators      ┃