Merge branch 'main' into cli-dataset-cmds

bfabric_app_runner/docs/changelog.md

@@ -8,6 +8,10 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 
 - Implement `--force-storage` to pass a yaml to a forced storage instead of the real one.
 
+### Changed
+
+- Resolve workunit_ref to absolute path if it is a Path instance for CLI.
+
 ## \[0.0.15\] - 2025-02-06
 
 ### Added

bfabric_app_runner/src/bfabric_app_runner/app_runner/resolve_app.py

@@ -1,16 +1,16 @@
 from __future__ import annotations
 
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 import yaml
 from pydantic import ValidationError
 
+from bfabric.experimental.workunit_definition import WorkunitDefinition
 from bfabric_app_runner.specs.app.app_spec import AppSpec
 from bfabric_app_runner.specs.app.app_version import AppVersion
-from bfabric.experimental.workunit_definition import WorkunitDefinition
 
 if TYPE_CHECKING:
-    from pathlib import Path
     from bfabric import Bfabric
 
 
@@ -57,6 +57,8 @@ def load_workunit_information(
         steps to avoid unnecessary B-Fabric lookups. (If the workunit_ref was already a path, it will be returned as is,
         otherwise the file will be created in the work directory.)
     """
+    if isinstance(workunit_ref, Path):
+        workunit_ref = workunit_ref.resolve()
     workunit_definition_file = work_dir / "workunit_definition.yml"
     workunit_definition = WorkunitDefinition.from_ref(workunit_ref, client, cache_file=workunit_definition_file)
     app_parsed = _load_spec(

bfabric_scripts/doc/changelog.md

@@ -16,6 +16,12 @@ Versioning currently follows `X.Y.Z` where
 
 - Add missing default value for columns in `bfabric-cli api read`
 
+### Added
+
+- `bfabric-cli api update` command to update an existing entity
+- `bfabric-cli api create` command to create a new entity
+- `bfabric-cli api delete` command to delete an existing entity
+
 ## \[1.13.20\] - 2025-02-10
 
 ### Added

bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_create.py

@@ -0,0 +1,37 @@
+import cyclopts
+from cyclopts import Parameter
+from loguru import logger
+from pydantic import BaseModel, field_validator, Field, ValidationError
+from rich.pretty import pprint
+
+from bfabric import Bfabric
+from bfabric.utils.cli_integration import use_client
+
+app = cyclopts.App()
+
+
+@Parameter(name="*")
+class Params(BaseModel):
+    endpoint: str
+    """Endpoint to update, e.g. 'resource'."""
+    attributes: list[tuple[str, str]] | None = Field(min_length=1)
+    """List of attribute-value pairs to update the entity with."""
+
+    @field_validator("attributes")
+    def _must_not_contain_id(cls, value):
+        if value:
+            for attribute, _ in value:
+                if attribute == "id":
+                    raise ValueError("Attribute 'id' is not allowed in the attributes.")
+        return value
+
+
+@app.default
+@use_client
+@logger.catch(reraise=True)
+def create(params: Params, *, client: Bfabric) -> None:
+    """Creates a new entity in B-Fabric."""
+    attributes_dict = {attribute: value for attribute, value in params.attributes}
+    result = client.save(params.endpoint, attributes_dict)
+    logger.info(f"{params.endpoint} entity with ID {result[0]["id"]} created successfully.")
+    pprint(result)

bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_delete.py

@@ -0,0 +1,55 @@
+import cyclopts
+import rich
+from loguru import logger
+from pydantic import BaseModel
+from rich.panel import Panel
+from rich.pretty import Pretty
+from rich.prompt import Confirm
+
+from bfabric import Bfabric
+from bfabric.utils.cli_integration import use_client
+
+app = cyclopts.App()
+
+
+@cyclopts.Parameter(name="*")
+class Params(BaseModel):
+    endpoint: str
+    """The endpoint to delete from, e.g. 'resource'."""
+
+    id: list[int]
+    """The id or ids to delete."""
+
+    no_confirm: bool = False
+    """Whether to ask for confirmation before deleting."""
+
+
+def _perform_delete(client: Bfabric, endpoint: str, id: list[int]) -> None:
+    """Deletes the entity with the given id from the given endpoint."""
+    result = client.delete(endpoint=endpoint, id=id).to_list_dict()
+    logger.info(f"Entity with ID(s) {id} deleted successfully.")
+
+
+@app.default
+@logger.catch(reraise=True)
+@use_client
+def cli_api_delete(params: Params, *, client: Bfabric) -> None:
+    """Deletes entities from B-Fabric by id."""
+    if params.no_confirm:
+        _perform_delete(client=client, endpoint=params.endpoint, id=params.id)
+    else:
+        existing_entities = client.read(params.endpoint, {"id": params.id})
+
+        for id in params.id:
+            existing_entity = next((e for e in existing_entities if e["id"] == id), None)
+            if not existing_entity:
+                logger.warning(f"No entity found with ID {id}")
+                continue
+
+            rich.print(
+                Panel.fit(
+                    Pretty(existing_entity, expand_all=False), title=f"{params.endpoint.capitalize()} with ID {id}"
+                )
+            )
+            if Confirm.ask(f"Delete entity with ID {id}?"):
+                _perform_delete(client=client, endpoint=params.endpoint, id=[id])

bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_log.py

@@ -7,7 +7,7 @@
 from bfabric import Bfabric
 from bfabric.utils.cli_integration import use_client
 
-cmd = cyclopts.App(help="write log messages of external jobs")
+cmd = cyclopts.App(help="DEPRECATED")
 
 log_target = cyclopts.Group(
     "Log Target",

bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_read.py

@@ -101,9 +101,9 @@ def render_output(results: list[dict[str, Any]], params: Params, client: Bfabric
 
 @app.default
 @use_client
-@logger.catch()
+@logger.catch(reraise=True)
 def read(params: Annotated[Params, cyclopts.Parameter(name="*")], *, client: Bfabric) -> None | int:
-    """Reads one type of entity from B-Fabric."""
+    """Reads entities from B-Fabric."""
     console_user = Console(stderr=True)
     console_user.print(params)
 

bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_save.py

@@ -5,7 +5,7 @@
 from bfabric import Bfabric
 from bfabric.utils.cli_integration import use_client
 
-app = cyclopts.App()
+app = cyclopts.App(help="DEPRECATED")
 
 
 @app.default

bfabric_scripts/src/bfabric_scripts/cli/api/cli_api_update.py

@@ -0,0 +1,71 @@
+import cyclopts
+import rich
+import rich.prompt
+from cyclopts import Parameter
+from loguru import logger
+from pydantic import BaseModel
+from rich.panel import Panel
+from rich.pretty import Pretty, pprint
+
+from bfabric import Bfabric
+from bfabric.utils.cli_integration import use_client
+
+app = cyclopts.App()
+
+
+@Parameter(name="*")
+class Params(BaseModel):
+    endpoint: str
+    """Endpoint to update, e.g. 'resource'."""
+    entity_id: int
+    """ID of the entity to update."""
+    attributes: list[tuple[str, str]] | None = None
+    """List of attribute-value pairs to update the entity with."""
+    no_confirm: bool = False
+    """If set, the update will be performed without asking for confirmation."""
+
+
+@app.default
+@use_client
+@logger.catch(reraise=True)
+def update(params: Params, *, client: Bfabric) -> None:
+    """Updates an existing entity in B-Fabric."""
+    attributes_dict = _sanitize_attributes(params.attributes, params.entity_id)
+    if not attributes_dict:
+        return
+
+    if not params.no_confirm:
+        if not _confirm_action(attributes_dict, client, params.endpoint, params.entity_id):
+            return
+
+    result = client.save(params.endpoint, {"id": params.entity_id, **attributes_dict})
+    logger.info(f"Entity with ID {params.entity_id} updated successfully.")
+    pprint(result)
+
+
+def _confirm_action(attributes_dict: dict[str, str], client: Bfabric, endpoint: str, entity_id: int) -> bool:
+    logger.info(f"Updating {endpoint} entity with ID {entity_id} with attributes {attributes_dict}")
+    result_read = client.read(endpoint, {"id": entity_id}, max_results=1)
+    if not result_read:
+        raise ValueError(f"No entity found with ID {entity_id}")
+    rich.print(Panel.fit(Pretty(result_read[0], expand_all=False), title="Existing entity"))
+    rich.print(Panel.fit(Pretty(attributes_dict, expand_all=False), title="Updates"))
+    if not rich.prompt.Confirm.ask("Do you want to proceed with the update?"):
+        logger.info("Update cancelled by user.")
+        return False
+    return True
+
+
+def _sanitize_attributes(attributes: list[tuple[str, str]] | None, entity_id: int) -> dict[str, str] | None:
+    if not attributes:
+        logger.warning("No attributes provided, doing nothing.")
+        return None
+
+    attributes_dict = {attribute: value for attribute, value in attributes}
+    if "id" in attributes_dict:
+        if int(attributes_dict["id"]) == entity_id:
+            logger.warning("Attribute 'id' is not allowed in the attributes, removing it.")
+            del attributes_dict["id"]
+        else:
+            raise ValueError("Attribute 'id' must match the entity_id")
+    return attributes_dict

bfabric_scripts/src/bfabric_scripts/cli/cli_api.py

@@ -1,10 +1,19 @@
 import cyclopts
 
+from bfabric_scripts.cli.api.cli_api_create import app as _cmd_create
+from bfabric_scripts.cli.api.cli_api_delete import app as _cmd_delete
 from bfabric_scripts.cli.api.cli_api_log import cmd as _cmd_log
 from bfabric_scripts.cli.api.cli_api_read import app as _cmd_read
 from bfabric_scripts.cli.api.cli_api_save import app as _cmd_save
+from bfabric_scripts.cli.api.cli_api_update import app as _cmd_update
 
 app = cyclopts.App()
-app.command(_cmd_log, name="log")
+app.command(_cmd_create, name="create")
+app.command(_cmd_delete, name="delete")
 app.command(_cmd_read, name="read")
+app.command(_cmd_update, name="update")
+
+# TODO delete or move
+app.command(_cmd_log, name="log")
+# TODO delete
 app.command(_cmd_save, name="save")