divbase-cli 0.1.0a3__tar.gz → 0.1.0a9__tar.gz

{divbase_cli-0.1.0a3 → divbase_cli-0.1.0a9}/.gitignore

@@ -22,6 +22,9 @@ __pycache__/
 tests/fixtures/temp*
 tests/fixtures/merged*
 divbase_metadata_template*.tsv
+# query results files
+result_of_job_*.vcf.gz
+result_of_job_*.log
 
 # query job config files
 bcftools_divbase_job_config.json
@@ -40,6 +43,10 @@ scripts/benchmarking/results
 htmlcov/
 docker/coverage-data/
 
+# log files written by docker compose, if env var set to do so (by default no)
+docker/logs/*
+!docker/logs/.gitkeep
+
 #MacOS artifacts
 .DS_Store
 

{divbase_cli-0.1.0a3 → divbase_cli-0.1.0a9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: divbase-cli
-Version: 0.1.0a3
+Version: 0.1.0a9
 Summary: Command Line Interface for Divbase
 Project-URL: Homepage, https://divbase.scilifelab-2-prod.sys.kth.se
 Project-URL: Documentation, https://scilifelabdatacentre.github.io/divbase
@@ -18,9 +18,9 @@ Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Classifier: Programming Language :: Python :: 3.14
 Requires-Python: >=3.12
-Requires-Dist: divbase-lib==0.1.0a3
+Requires-Dist: divbase-lib==0.1.0a9
 Requires-Dist: keyring>=25.7.0
-Requires-Dist: typer==0.24.1
+Requires-Dist: typer==0.26.7
 Description-Content-Type: text/markdown
 
 # divbase-cli

{divbase_cli-0.1.0a3 → divbase_cli-0.1.0a9}/pyproject.toml

@@ -8,9 +8,9 @@ authors = [
 ]
 requires-python = ">=3.12"
 dependencies = [
-    "typer==0.24.1",
+    "typer==0.26.7",
     "keyring>=25.7.0",
-    "divbase-lib==0.1.0a3",
+    "divbase-lib==0.1.0a9",
 ]
 dynamic = ["version"]
 

divbase_cli-0.1.0a9/src/divbase_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0a9"

divbase_cli-0.1.0a9/src/divbase_cli/cli_commands/auth_cli.py

@@ -0,0 +1,184 @@
+"""
+CLI subcommand for managing user auth with DivBase server.
+"""
+
+import logging
+import time
+from datetime import datetime
+
+import typer
+from pydantic import SecretStr
+from rich import print
+
+from divbase_cli.cli_config import cli_settings
+from divbase_cli.cli_exceptions import DivBaseAPIConnectionError, DivBaseAPIError
+from divbase_cli.config_resolver import resolve_url_for_non_project_specific_commands
+from divbase_cli.services.announcements import get_and_display_announcements
+from divbase_cli.user_auth import (
+    PERSONAL_ACCESS_TOKEN_EXPIRED_MESSAGE,
+    PATData,
+    check_existing_session,
+    delete_stored_pat,
+    load_stored_user_pat,
+    login_to_divbase,
+    logout_of_divbase,
+    make_authenticated_request,
+)
+from divbase_cli.user_config import load_user_config
+from divbase_lib.divbase_constants import PAT_TOKEN_PREFIX
+
+logger = logging.getLogger(__name__)
+
+divbase_home_url = cli_settings.DIVBASE_API_URL.replace("/api", "")
+
+auth_app = typer.Typer(
+    no_args_is_help=True,
+    help=f"Login/logout of DivBase server. To register, visit {divbase_home_url}.",
+)
+
+
+@auth_app.command("login")
+def login(
+    email: str,
+    divbase_url: str = typer.Option(cli_settings.DIVBASE_API_URL, help="DivBase server URL to connect to."),
+    force: bool = typer.Option(False, "--force", "-f", help="Force login again even if already logged in"),
+):
+    """
+    Log in to the DivBase server.
+
+    You'll be prompted for your password after running the command.
+    """
+    password: str = typer.prompt("please enter your password", hide_input=True, confirmation_prompt=False)
+    secret_password = SecretStr(password)
+    del password  # avoid user passwords showing up in error messages etc...
+
+    config = load_user_config()
+
+    if not force:
+        session_expires_at = check_existing_session(divbase_url=divbase_url, config=config)
+        if session_expires_at:
+            print(f"Already logged in to {divbase_url} with email: {config.logged_in_email}.")
+            print(f"Session expires: {datetime.fromtimestamp(session_expires_at)}")
+
+            if not typer.confirm("Do you want to login again? This will replace your current session."):
+                print("Login cancelled.")
+                return
+
+    login_to_divbase(email=email, password=secret_password, divbase_url=divbase_url)
+
+    try:
+        get_and_display_announcements(divbase_base_url=divbase_url)
+    except (DivBaseAPIError, DivBaseAPIConnectionError):
+        # lets not fail the login process if announcements are not working.
+        logger.info("Failed to get announcements after login. Error was: ", exc_info=True)
+
+    print(f"Logged in successfully as: {email}")
+
+
+@auth_app.command("logout")
+def logout():
+    """
+    Log out of the DivBase server.
+
+    Removes your locally stored credentials and invalidates the server-side refresh token.
+    """
+    logout_of_divbase()
+    print("Logged out successfully.")
+
+
+@auth_app.command("add-pat")
+def add_pat(
+    name: str = typer.Argument(..., help="Name of the personal access token (PAT). E.g. 'work-laptop-pat'"),
+    expires_unix_timestamp: int | None = typer.Option(
+        None,
+        "--expires",
+        "-e",
+        help="When the personal access token (PAT) expires (if it does), as a unix timestamp.",
+        min=1,
+    ),
+    overwrite_existing: bool = typer.Option(
+        False, "--overwrite-existing", "-o", help="Overwrite the existing stored PAT if one already exists."
+    ),
+):
+    """
+    Add a personal access token (PAT) to your device for authentication with DivBase.
+
+    PATs are used for authenticating with the DivBase API instead of using your password, and are recommended for use in scripts and pipelines.
+    See https://scilifelabdatacentre.github.io/divbase/user-guides/using-divbase-programmatically/ for more details on how to create a personal access token.
+    You can only store one personal access token at a time.
+    """
+    existing = load_stored_user_pat()
+    if existing and not overwrite_existing:
+        print(
+            f"A personal access token named '{existing.name}' is already stored on your device \n"
+            f"It is due to expire on: {existing.pat_expiry_formatted()} \n"
+            "Append the flag --overwrite-existing (-o) to this command if you want to replace it. \n"
+            "You can only store one PAT at a time."
+        )
+        raise typer.Exit(code=1)
+
+    if expires_unix_timestamp and expires_unix_timestamp < time.time():
+        print("The expiry time you entered is in the past. Please enter a valid expiry time for the PAT.")
+        raise typer.Exit(code=1)
+
+    pat = SecretStr(
+        typer.prompt("please paste your personal access token now", hide_input=True, confirmation_prompt=False)
+    )
+    if not pat.get_secret_value().startswith(PAT_TOKEN_PREFIX):
+        print(
+            "It looks like the token you entered is not a valid personal access token. "
+            f"Please make sure you copied the entire token, including the '{PAT_TOKEN_PREFIX}' prefix."
+        )
+        raise typer.Exit(code=1)
+
+    pat_data = PATData(name=name, pat=pat, pat_expires_at=expires_unix_timestamp)
+    pat_data.dump_pat_data()
+    print(f"Personal access token '{name}' stored successfully.")
+
+
+@auth_app.command("rm-pat")
+def rm_pat():
+    """
+    Remove the stored personal access token from your device.
+
+    If no such token exists the command will still succeed.
+    """
+    delete_stored_pat()
+    print("If a personal access token was stored, it has now been removed.")
+
+
+@auth_app.command("pat-info")
+def pat_info():
+    """
+    Display information about the personal access token stored on this device, if any.
+
+    The token will not be displayed for security reasons, but the name and expiry time will be shown.
+    """
+    pat_data = load_stored_user_pat()
+    if not pat_data:
+        print("No personal access token stored on this device.")
+        return
+
+    print(f"Name: {pat_data.name}")
+    print(f"Expires: {pat_data.pat_expiry_formatted()}")
+
+    if pat_data.is_pat_expired():
+        print("[red bold]Warning [/red bold]")
+        print(PERSONAL_ACCESS_TOKEN_EXPIRED_MESSAGE)
+
+
+@auth_app.command("whoami")
+def whoami():
+    """
+    Return information about the currently logged-in user.
+    """
+    divbase_url = resolve_url_for_non_project_specific_commands()
+
+    request = make_authenticated_request(
+        method="GET",
+        divbase_base_url=divbase_url,
+        api_route="v1/auth/whoami",
+    )
+
+    current_user = request.json()
+    print(f"Currently logged in as: {current_user['email']} (Name: {current_user['name']})")