Merge pull request #152 from UMEssen/151-auth-with-a-static-token-not-working

151 auth with a static token not working

Author: JannisStraus

.github/workflows/mypy-flake-test.yml .github/workflows/pre-commit-test.yml.github/workflows/mypy-flake-test.yml renamed to .github/workflows/pre-commit-test.yml

@@ -28,10 +28,10 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -41,10 +41,11 @@ jobs:
           pip install uv
           uv sync --group dev --extra all
 
-      - name: Run pre-commit
+      - if: matrix.python-version == '3.10'
+        name: Run pre-commit
         run: |
           uv run pre-commit run -a
 
       - name: Run pytest
         run: |
-          uv run pytest -q
+          uv run pytest

.pre-commit-config.yaml

@@ -1,17 +1,16 @@
-# See https://gitlab.uk-essen.de/ship-ai/templates/pre-commit-hooks
-
+exclude: ^tests/
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.14.14
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.12
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: [--fix]
         exclude: examples
       - id: ruff-format
         exclude: examples
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v1.20.2
     hooks:
       - id: mypy
         language_version: python3.10
@@ -25,36 +24,31 @@ repos:
         exclude: node_modules
 
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.12.0
+    rev: v2.21.2
     hooks:
       - id: pyproject-fmt
         types: [toml]
 
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.20.0
+    rev: v0.22.1
     hooks:
       - id: markdownlint-cli2
         args: [--fix]
 
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.1
+    rev: v2.4.2
     hooks:
       - id: codespell
         types: [markdown]
 
-  - repo: local
-    hooks:
-      - id: export-requirements
-        name: Export requirements from uv
-        entry: uv pip compile
-        args: ["pyproject.toml", "--output-file", "requirements.txt"]
-        language: system
-        pass_filenames: false
-        always_run: true
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
-      - id: end-of-file-fixer
-      - id: check-merge-conflict
       - id: check-added-large-files
+      - id: check-json
+      - id: check-merge-conflict
+      - id: check-toml
+      - id: check-yaml
+      - id: detect-private-key
+      - id: end-of-file-fixer
+      - id: trailing-whitespace

README.md

@@ -1,10 +1,10 @@
 # FHIR-PYrate
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
-[![Supported Python version](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/release/python-31011/)
+[![Supported Python version](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org)
 [![Stable Version](https://img.shields.io/pypi/v/fhir-pyrate?label=stable)](https://pypi.org/project/fhir-pyrate/)
 [![Pre-release Version](https://img.shields.io/github/v/release/UMEssen/fhir-pyrate?label=pre-release&include_prereleases&sort=semver)](https://pypi.org/project/fhir-pyrate/#history)
-[![DOI](https://zenodo.org/badge/456893108.svg)](https://zenodo.org/badge/latestdoi/456893108)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7025226.svg)](https://doi.org/10.5281/zenodo.7025226)
 [![Affiliated with RTG WisPerMed](https://img.shields.io/badge/Affiliated-RTG%202535%20WisPerMed-blue)](https://wispermed.org/)
 
 <!-- PROJECT LOGO -->
@@ -46,7 +46,7 @@ Table of Contents:
 
 * [Install](https://github.com/UMEssen/FHIR-PYrate/#install)
   * [Either Pip](https://github.com/UMEssen/FHIR-PYrate/#either-pip)
-  * [Or Within Poetry](https://github.com/UMEssen/FHIR-PYrate/#or-within-poetry)
+  * [Or Within uv](https://github.com/UMEssen/FHIR-PYrate/#or-within-uv)
 * [Run Tests](https://github.com/UMEssen/FHIR-PYrate/#run-tests)
 * [Explanations &amp; Examples](https://github.com/UMEssen/FHIR-PYrate/#explanations--examples)
   * [Ahoy](https://github.com/UMEssen/FHIR-PYrate/#ahoy)
@@ -86,49 +86,32 @@ pip install "fhir-pyrate[downloader]" # only for downloader
 pip install "fhir-pyrate[all]" # for both
 ```
 
-### Or Within Poetry
+### Or Within uv
 
-We can also use poetry for this same purpose. Using PyPi we need to run the following commands.
+We can also use [uv](https://docs.astral.sh/uv/) for this same purpose. To add it from PyPi run:
 
 ```bash
-poetry add fhir-pyrate
-poetry install
+uv add fhir-pyrate
 ```
 
-Whereas to add it from GitHub, we have different options, because until recently
-[poetry used to exclusively install from the master branch](https://github.com/python-poetry/poetry/issues/3366).
-
-Poetry 1.2.0a2+:
-
-```bash
-poetry add git+https://github.com/UMEssen/FHIR-PYrate.git
-poetry install
-```
-
-For the previous versions you need to add the following line to your `pyproject.toml` file:
-
-```bash
-fhir-pyrate = {git = "https://github.com/UMEssen/FHIR-PYrate.git", branch = "main"}
-```
-
-and then run
+Whereas to add it from GitHub (always the newest version):
 
 ```bash
-poetry lock
+uv add git+https://github.com/UMEssen/FHIR-PYrate.git
 ```
 
-Also in poetry, the above only installs the packages for **Pirate**. If you also want to use the **Miner** or the **DicomDownloader**, then you need to install them as extra dependencies with
+Also in uv, the above only installs the packages for **Pirate**. If you also want to use the **Miner** or the **DicomDownloader**, then you need to install them as extra dependencies with
 
 ```bash
-poetry add "fhir-pyrate[miner]" # only for miner
-poetry add "fhir-pyrate[downloader]" # only for downloader
-poetry add "fhir-pyrate[all]" # for both
+uv add "fhir-pyrate[miner]" # only for miner
+uv add "fhir-pyrate[downloader]" # only for downloader
+uv add "fhir-pyrate[all]" # for both
 ```
 
-or by adding the following to your `pyproject.toml` file:
+The extras can be combined with the GitHub source as well:
 
 ```bash
-fhir-pyrate = {git = "https://github.com/UMEssen/FHIR-PYrate.git", branch = "main", extras = ["all"]}
+uv add "fhir-pyrate[all] @ git+https://github.com/UMEssen/FHIR-PYrate.git"
 ```
 
 ## Run Tests
@@ -138,7 +121,7 @@ unit tests. First set the `FHIR_USER` and `FHIR_PASSWORD` environment variables
 username and password for the FHIR server and then run the tests.
 
 ```bash
-poetry run python -m unittest discover tests
+uv run pytest
 ```
 
 If you implement a new feature, please add a small test for it in
@@ -269,7 +252,7 @@ generated. You can drop the ID duplicates once you have built a DataFrame with y
 
 #### [`trade_rows_for_bundles`](https://github.com/UMEssen/FHIR-PYrate/blob/main/fhir_pyrate/pirate.py)
 
-In case we already have an Excel sheet or CSV file with `fhir_patient_id`s or any other
+In case we already have an Excel sheet or CSV file with `fhir_patient_id`s (or any other
 identifier), and we want to request resources based on those
 identifiers we can use the function `trade_rows_for_bundles`:
 
@@ -292,7 +275,7 @@ DataFrame in `df_constraints`. This dictionary should contain pairs of (`fhir_id
 `identifier_column`) where `fhir_identifier` is the API search parameter and `identifier_column`
 is the column where the values that we want to search for are stored.
 Additionally, a system can be used to better identify the constraints of the DataFrame.
-For example, let us assume that we have a column of the DataFrame (called `loinc_code` that
+For example, let us assume that we have a column of the DataFrame called `loinc_code` that
 contains a bunch of different LOINC codes. Our `df_constraints` could look as follows:
 
 ```python
@@ -522,8 +505,8 @@ your institute, please do not hesitate and contact us, or write a pull request!
 The **DicomDownloader** downloads a complete Study (StudyInstanceUID) or a specific series (
 StudyInstanceUID + SeriesInstanceUID).
 
-The relevant data can be downloaded either es DICOM (`.dcm`) or NIfTI (`.nii.gz`).
-In the NIfTI case there will be an  additional `.dcm` file to store some metadata.
+The relevant data can be downloaded either as DICOM (`.dcm`) or NIfTI (`.nii.gz`).
+In the NIfTI case there will be an additional `.dcm` file to store some metadata.
 
 Using the function `download_data_from_dataframe` it is possible to download studies and series
 directly from the data of a given dataframe. The column that contain the study/series

fhir_pyrate/ahoy.py

@@ -3,7 +3,6 @@
 import os
 from datetime import timedelta
 from types import TracebackType
-from typing import Optional, Type, Union
 
 import requests
 from requests.auth import HTTPBasicAuth
@@ -27,8 +26,10 @@ class Ahoy:
     password will use the given username as username and ask to input a password;
     env will use the environment variables FHIR_USER and FHIR_PASSWORD;
     keyring will use a keyring [NOT IMPLEMENTED YET]
-    :param token: The token that can be used for authentication, if this variable is used then
-    the other variables do not need to be specified
+    :param token: A pre-existing token to use for authentication. If this is given, no login is
+    performed and the token is used as-is, so the username/password/auth_method variables do not
+    need to be specified. An auth_url and/or refresh_url are then only needed if the token should
+    be refreshed once it expires.
     :param max_login_attempts: The maximum number of logins that can be performed
     :param token_refresh_delta: Either a timedelta object that tells us how often the token
     should be refreshed, or a number of minutes; this does not need to be specified for JWT tokens
@@ -40,31 +41,33 @@ class Ahoy:
 
     def __init__(
         self,
-        auth_url: Optional[str] = None,
-        auth_type: Optional[str] = "token",
-        refresh_url: Optional[str] = None,
-        username: Optional[str] = None,
-        auth_method: Optional[str] = "password",
-        token: Optional[str] = None,
+        auth_url: str | None = None,
+        auth_type: str | None = "token",
+        refresh_url: str | None = None,
+        username: str | None = None,
+        auth_method: str | None = "password",
+        token: str | None = None,
         max_login_attempts: int = 5,
-        token_refresh_delta: Optional[Union[int, timedelta]] = None,
-        session: Optional[requests.Session] = None,
+        token_refresh_delta: int | timedelta | None = None,
+        session: requests.Session | None = None,
     ) -> None:
         self.auth_type = auth_type
         self.auth_method = auth_method
         self.auth_url = auth_url
         self.refresh_url = refresh_url
         self.username = username
         self._user_env_name = "FHIR_USER"
-        self._pass_env_name = "FHIR_PASSWORD"
+        self._pass_env_name = "FHIR_PASSWORD"  # noqa: S105
         self.token = token
         if session is None:
             self.session = requests.Session()
         else:
             self.session = session
         self.max_login_attempts = max_login_attempts
         self.token_refresh_delta = token_refresh_delta
-        if self.auth_type is not None and self.auth_method is not None:
+        if self.token is not None or (
+            self.auth_type is not None and self.auth_method is not None
+        ):
             self._authenticate()
 
     def __enter__(self) -> "Ahoy":
@@ -75,14 +78,14 @@ def close(self) -> None:
 
     def __exit__(
         self,
-        exctype: Optional[Type[BaseException]],
-        excinst: Optional[BaseException],
-        exctb: Optional[TracebackType],
+        exctype: type[BaseException] | None,
+        excinst: BaseException | None,
+        exctb: TracebackType | None,
     ) -> None:
         self.close()
 
     def change_environment_variable_name(
-        self, user_env: Optional[str] = None, pass_env: Optional[str] = None
+        self, user_env: str | None = None, pass_env: str | None = None
     ) -> None:
         """
         Change the name of the variables used to retrieve username and password.
@@ -100,6 +103,22 @@ def _authenticate(self) -> None:
         """
         Authenticate the user in the current session with a token or with BasicAuth.
         """
+        assert self.auth_type is not None
+        if self.token is not None:
+            if self.auth_type.lower() != "token":
+                raise ValueError(
+                    "A pre-existing token can only be used with the 'token' "
+                    f"authentication type, but {self.auth_type} was given."
+                )
+            self.session.auth = TokenAuth(
+                auth_url=self.auth_url,
+                refresh_url=self.refresh_url,
+                session=self.session,
+                max_login_attempts=self.max_login_attempts,
+                token_refresh_delta=self.token_refresh_delta,
+                token=self.token,
+            )
+            return
         assert self.auth_method is not None
         if self.auth_method.lower() == "password":
             assert self.username is not None, (
@@ -121,7 +140,6 @@ def _authenticate(self) -> None:
             raise ValueError(
                 f"Used authentication method {self.auth_method} is not defined."
             )
-        assert self.auth_type is not None
         if self.auth_type.lower() == "token":
             assert self.auth_url is not None, (
                 "The token authentication method cannot be used "