Merge pull request #150 from fgcz/main

bfabric-scripts 1.13.23

.gitattributes

@@ -0,0 +1 @@
+changelog.md merge=manual

.github/workflows/build_app_runner.yml

@@ -1,10 +1,6 @@
 name: Build App Runner
 on:
   workflow_dispatch:
-  release:
-    types: [published]
-  pull_request:
-    branches: [stable]
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
@@ -32,7 +28,6 @@ jobs:
     # - It's a release with valid tag
     if: >
       ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' || (github.event_name == 'release' && needs.check_release_tag.outputs.is_valid_tag == 'true') }}
-
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4

.github/workflows/publish_release.yml

@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
     permissions:
       id-token: write
-      contents: write # permission to create tags
+      contents: write # permission to create tags and releases
     steps:
       - uses: actions/checkout@v4
       # Step: Determine the package that is being built
@@ -86,6 +86,48 @@ jobs:
           TAG_NAME="${{ env.PACKAGE }}/${{ env.VERSION }}"
           git tag -a "$TAG_NAME" -m "Release ${{ env.PACKAGE }} version ${{ env.VERSION }}"
           git push origin "$TAG_NAME"
+      - name: Extract changelog and create release
+        run: |
+          set -x
+          CHANGELOG_PATH="${{ env.PACKAGE }}/docs/changelog.md"
+          TAG_NAME="${{ env.PACKAGE }}/${{ env.VERSION }}"
+
+          if [ -f "$CHANGELOG_PATH" ]; then
+            # Extract the changelog section for the current version
+            # This assumes the changelog follows the keep-a-changelog format
+            CHANGELOG_CONTENT=$(awk -v ver="${{ env.VERSION }}" '
+            BEGIN { found=0; }
+            $0 ~ "^## \\\\[" ver "\\\\]" { found=1; next }
+            found && $0 ~ "^## \\\\[" { exit }
+            found { print }
+            ' "$CHANGELOG_PATH")
+
+            if [ -n "$CHANGELOG_CONTENT" ]; then
+              # Create GitHub release
+              gh release create "$TAG_NAME" \
+                --title "Release ${{ env.PACKAGE }} ${{ env.VERSION }}" \
+                --notes "$CHANGELOG_CONTENT" \
+                --target ${{ github.sha }} \
+                --draft
+            else
+              # Create release with basic notes if no changelog section is found
+              gh release create "$TAG_NAME" \
+                --title "Release ${{ env.PACKAGE }} ${{ env.VERSION }}" \
+                --notes "Release of ${{ env.PACKAGE }} version ${{ env.VERSION }}" \
+                --target ${{ github.sha }} \
+                --draft
+            fi
+          else
+            echo "Warning: Changelog file not found at $CHANGELOG_PATH"
+            # Create release with basic notes
+            gh release create "$TAG_NAME" \
+              --title "Release ${{ env.PACKAGE }} ${{ env.VERSION }}" \
+              --notes "Release of ${{ env.PACKAGE }} version ${{ env.VERSION }}" \
+              --target ${{ github.sha }} \
+              --draft
+          fi
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Debug package info
         run: |
           echo "Built and published package: ${{ env.PACKAGE }}"

.github/workflows/run_unit_tests.yml

@@ -13,7 +13,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install nox
         run: pip install nox uv
       - name: Run checks
@@ -25,7 +25,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.9
+          python-version: 3.11
       - name: Install nox
         run: pip install nox uv
       - name: Check code with ruff

docs/changelog.md → bfabric/docs/changelog.md

@@ -8,11 +8,17 @@ Versioning currently follows `X.Y.Z` where
 - `Y` should be the current bfabric release
 - `Z` is increased for feature releases, that should not break the API
 
-## \[Unreleased\]
+## \[1.13.21\] - 2025-02-19
 
 ### Added
 
 - `Entity.load_yaml` and `Entity.dump_yaml`
+- `Bfabric.from_token` to create a `Bfabric` instance from a token
+- `bfabric.rest.token_data` to get token data from the REST API, low-level functionality
+
+### Changed
+
+- Internally, the user password is now in a `pydantic.SecretStr` until we construct the API call. This should prevent some logging related accidents.
 
 ## \[1.13.20\] - 2025-02-10
 

bfabric/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "bfabric"
 description = "Python client for the B-Fabric API"
-version = "1.13.20"
+version = "1.13.21"
 license = { text = "GPL-3.0" }
 authors = [
     { name = "Christian Panse", email = "[email protected]" },
@@ -29,6 +29,7 @@ dependencies = [
     "eval_type_backport; python_version < '3.10'",
     "python-dateutil >= 2.9.0",
     "cyclopts >= 2.9.9",
+    "requests >= 2.26.0",
     #"platformdirs >= 4.3",
 ]
 

bfabric/src/bfabric/bfabric.py

@@ -15,7 +15,6 @@
 
 import base64
 import importlib.metadata
-import sys
 from contextlib import contextmanager
 from datetime import datetime
 from enum import Enum
@@ -24,16 +23,18 @@
 from pprint import pprint
 from typing import Literal, Any, TYPE_CHECKING
 
+import sys
 from loguru import logger
 from rich.console import Console
 
 from bfabric.bfabric_config import read_config
-from bfabric.utils.cli_integration import DEFAULT_THEME, HostnameHighlighter
 from bfabric.config import BfabricAuth
 from bfabric.config import BfabricClientConfig
 from bfabric.engine.engine_suds import EngineSUDS
 from bfabric.engine.engine_zeep import EngineZeep
+from bfabric.rest.token_data import get_token_data
 from bfabric.results.result_container import ResultContainer
+from bfabric.utils.cli_integration import DEFAULT_THEME, HostnameHighlighter
 from bfabric.utils.paginator import compute_requested_pages, BFABRIC_QUERY_LIMIT
 
 if TYPE_CHECKING:
@@ -93,12 +94,33 @@ def from_config(
         :param config_path: Path to the config file, in case it is different from default
         :param auth: Authentication to use. If "config" is given, the authentication will be read from the config file.
             If it is set to None, no authentication will be used.
-        :param engine: Engine to use for the API. Default is SUDS.
+        :param engine: Engine to use for the API.
         """
         config, auth_config = get_system_auth(config_env=config_env, config_path=config_path)
         auth_used: BfabricAuth | None = auth_config if auth == "config" else auth
         return cls(config, auth_used, engine=engine)
 
+    @classmethod
+    def from_token(
+        cls,
+        token: str,
+        config_env: str | None = None,
+        config_path: str | None = None,
+        engine: BfabricAPIEngineType = BfabricAPIEngineType.SUDS,
+    ) -> Bfabric:
+        """Returns a new Bfabric instance, configured with the user configuration file and the provided token.
+        Any authentication in the configuration file will be ignored, but it will be used to determine the correct
+        B-Fabric instance.
+        :param token: the token to use for authentication
+        :param config_env: the config environment to use (if not specified, see `from_config`)
+        :param config_path: the path to the config file (if not specified, see `from_config`)
+        :param engine: the engine to use for the API.
+        """
+        config, _ = get_system_auth(config_env=config_env, config_path=config_path)
+        token_data = get_token_data(client_config=config, token=token)
+        auth = BfabricAuth(login=token_data.user, password=token_data.user_ws_password)
+        return cls(config, auth, engine=engine)
+
     @property
     def config(self) -> BfabricClientConfig:
         """Returns the config object."""

bfabric/src/bfabric/config/bfabric_auth.py

@@ -2,16 +2,11 @@
 
 from typing import Annotated
 
-from pydantic import BaseModel, Field
+from pydantic import BaseModel, Field, SecretStr
 
 
 class BfabricAuth(BaseModel):
     """Holds the authentication data for the B-Fabric client."""
 
     login: Annotated[str, Field(min_length=3)]
-    password: Annotated[str, Field(min_length=32, max_length=32)]
-
-    def __repr__(self) -> str:
-        return f"BfabricAuth(login={repr(self.login)}, password=...)"
-
-    __str__ = __repr__
+    password: Annotated[SecretStr, Field(min_length=32, max_length=32)]

bfabric/src/bfabric/engine/engine_suds.py

@@ -49,7 +49,7 @@ def read(
         full_query = dict(
             login=auth.login,
             page=page,
-            password=auth.password,
+            password=auth.password.get_secret_value(),
             query=query,
             idonly=return_id_only,
         )
@@ -65,7 +65,7 @@ def save(self, endpoint: str, obj: dict, auth: BfabricAuth, method: str = "save"
         :param method: the method to use for saving, generally "save", but in some cases e.g. "checkandinsert" is more
             appropriate to be used instead.
         """
-        query = {"login": auth.login, "password": auth.password, endpoint: obj}
+        query = {"login": auth.login, "password": auth.password.get_secret_value(), endpoint: obj}
         service = self._get_suds_service(endpoint)
         try:
             response = getattr(service, method)(query)
@@ -84,7 +84,7 @@ def delete(self, endpoint: str, id: int | list[int], auth: BfabricAuth) -> Resul
             # TODO maybe use error here (and make sure it's consistent)
             return ResultContainer([], total_pages_api=0)
 
-        query = {"login": auth.login, "password": auth.password, "id": id}
+        query = {"login": auth.login, "password": auth.password.get_secret_value(), "id": id}
         service = self._get_suds_service(endpoint)
         response = service.delete(query)
         return self._convert_results(response=response, endpoint=endpoint)

bfabric/src/bfabric/engine/engine_zeep.py

@@ -59,7 +59,7 @@ def read(
         full_query = dict(
             login=auth.login,
             page=page,
-            password=auth.password,
+            password=auth.password.get_secret_value(),
             query=query,
             idonly=return_id_only,
         )
@@ -84,7 +84,7 @@ def save(self, endpoint: str, obj: dict, auth: BfabricAuth, method: str = "save"
             excl_keys = ["name", "sampleid", "storageid", "workunitid", "relativepath"]
             _zeep_query_append_skipped(query, excl_keys, inplace=True, overwrite=False)
 
-        full_query = {"login": auth.login, "password": auth.password, endpoint: query}
+        full_query = {"login": auth.login, "password": auth.password.get_secret_value(), endpoint: query}
 
         client = self._get_client(endpoint)
 
@@ -108,7 +108,7 @@ def delete(self, endpoint: str, id: int | list[int], auth: BfabricAuth) -> Resul
             # TODO maybe use error here (and make sure it's consistent)
             return ResultContainer([], total_pages_api=0)
 
-        query = {"login": auth.login, "password": auth.password, "id": id}
+        query = {"login": auth.login, "password": auth.password.get_secret_value(), "id": id}
 
         client = self._get_client(endpoint)
         response = client.service.delete(query)

bfabric/src/bfabric/entities/dataset.py

@@ -31,6 +31,11 @@ def to_polars(self) -> DataFrame:
             data.append(dict(zip(column_names, row_values)))
         return DataFrame(data)
 
+    @property
+    def types(self) -> dict[str, str]:
+        """Returns a dictionary mapping column names to their data types."""
+        return {x["name"]: x["type"] for x in self.data_dict["attribute"]}
+
     def write_csv(self, path: Path, separator: str = ",") -> None:
         """Writes the dataset to a csv file at `path`, using the specified column `separator`."""
         self.to_polars().write_csv(path, separator=separator)

bfabric/src/bfabric/examples/compare_zeep_suds_query.py

@@ -52,7 +52,7 @@ def full_query(auth: BfabricAuth, query: dict, includedeletableupdateable: bool
     thisQuery = deepcopy(query)
     thisQuery["includedeletableupdateable"] = includedeletableupdateable
 
-    return {"login": auth.login, "password": auth.password, "query": thisQuery}
+    return {"login": auth.login, "password": auth.password.get_secret_value(), "query": thisQuery}
 
 
 def calc_both(

bfabric/src/bfabric/examples/zeep_debug.py

@@ -22,7 +22,7 @@ def full_query(auth: BfabricAuth, query: dict, includedeletableupdateable: bool
     thisQuery = deepcopy(query)
     thisQuery["includedeletableupdateable"] = includedeletableupdateable
 
-    return {"login": auth.login, "password": auth.password, "query": thisQuery}
+    return {"login": auth.login, "password": auth.password.get_secret_value(), "query": thisQuery}
 
 
 def read_zeep(wsdl, fullQuery, raw=True):

bfabric/src/bfabric/experimental/upload_dataset.py

@@ -15,8 +15,6 @@ def polars_to_bfabric_type(dtype: pl.DataType) -> str | None:
         return "Integer"
     elif str(dtype).startswith("String"):
         return "String"
-    elif str(dtype).startswith("Float"):
-        return "Float"
     else:
         return "String"
 

bfabric/src/bfabric/rest/token_data.py

@@ -0,0 +1,43 @@
+from __future__ import annotations
+
+from datetime import datetime
+from typing import TYPE_CHECKING
+
+import requests
+from pydantic import BaseModel, Field, SecretStr, ConfigDict
+
+if TYPE_CHECKING:
+    from bfabric import BfabricClientConfig
+
+
+class TokenData(BaseModel):
+    """Parsed token data from the B-Fabric token validation endpoint."""
+
+    model_config = ConfigDict(
+        populate_by_name=True, str_strip_whitespace=True, json_encoders={datetime: lambda v: v.isoformat()}
+    )
+
+    job_id: int = Field(alias="jobId")
+    application_id: int = Field(alias="applicationId")
+
+    entity_class: str = Field(alias="entityClassName")
+    entity_id: int = Field(alias="entityId")
+
+    user: str = Field(alias="user")
+    user_ws_password: SecretStr = Field(alias="userWsPassword")
+
+    token_expires: datetime = Field(alias="expiryDateTime")
+    environment: str
+
+
+def get_token_data(client_config: BfabricClientConfig, token: str) -> TokenData:
+    """Returns the token data for the provided token.
+
+    If the request fails, an exception is raised.
+    """
+    url = f"{client_config.base_url}/rest/token/validate"
+    response = requests.get(url, params={"token": token})
+    if not response.ok:
+        response.raise_for_status()
+    parsed = response.json()
+    return TokenData.model_validate(parsed)

bfabric_app_runner/docs/changelog.md

@@ -7,6 +7,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
 ### Added
 
 - Implement `--force-storage` to pass a yaml to a forced storage instead of the real one.
+- A Makefile will be created in the app folder for easier interaction with the app-runner (it uses uv and PyPI).
+
+### Changed
+
+- CopyResourceSpec.update_existing now defaults to `if_exists`.
+- Resolve workunit_ref to absolute path if it is a Path instance for CLI.
 
 ## \[0.0.15\] - 2025-02-06
 

bfabric_app_runner/pyproject.toml

@@ -18,6 +18,13 @@ dependencies = [
     "mako",
 ]
 
+[tool.hatch.build.targets.sdist]
+include = [
+    "src/bfabric_app_runner/**/*.py",
+    "src/bfabric_app_runner/py.typed",
+    "src/bfabric_app_runner/resources/*.mk"
+]
+
 [project.scripts]
 "bfabric-app-runner"="bfabric_app_runner.cli.__main__:app"