divbase-cli 0.1.0a1__tar.gz

divbase_cli-0.1.0a1/.gitignore

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+# repo secrets 
+.env 
+.env*
+
+# python stuff 
+.venv
+.ruff_cache/
+__pycache__/
+*.py[cod]
+*$py.class
+
+.vscode/
+
+# project specific files
+/sample_metadata.tsv
+/sample_metadata_*.tsv
+*.vcf
+*.vcf.gz
+*.vcf.gz.csi
+*.vcf.gz.tbi
+!tests/fixtures/*.vcf.gz
+tests/fixtures/temp*
+tests/fixtures/merged*
+divbase_metadata_template*.tsv
+
+# query job config files
+bcftools_divbase_job_config.json
+
+# benchmarking files
+vcf_dimensions.tsv
+mock*.tsv
+task_records*.json
+split_scaffold_files.txt
+scripts/benchmarking/*.yaml
+scripts/benchmarking/results
+
+#MacOS artifacts
+.DS_Store
+
+# mkdocs build cache
+.cache/
+# mkdocs auto generated files
+docs/cli/_auto_generated/*.md
+
+# pypi 
+dist/

divbase_cli-0.1.0a1/PKG-INFO

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+Metadata-Version: 2.4
+Name: divbase-cli
+Version: 0.1.0a1
+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
+Project-URL: Repository, https://github.com/ScilifelabDataCentre/divbase
+Project-URL: Issues, https://github.com/ScilifelabDataCentre/divbase/issues
+Author-email: SciLifeLab Data Centre <datacentre@scilifelab.se>
+License-Expression: MIT
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+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==0.1.0a1
+Requires-Dist: keyring>=25.7.0
+Requires-Dist: typer==0.24.1
+Description-Content-Type: text/markdown
+
+# divbase-cli
+
+Command Line Interface for Divbase. 
+
+## Installation
+
+```bash
+pipx install divbase-cli
+```
+
+## Usage
+
+```bash
+divbase --help # can also run divbase-cli --help
+```
+
+## Development
+
+This package is developed in the [DivBase repository](https://github.com/ScilifelabDataCentre/divbase) by Scilifelab Data Centre.

divbase_cli-0.1.0a1/README.md

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+# divbase-cli
+
+Command Line Interface for Divbase. 
+
+## Installation
+
+```bash
+pipx install divbase-cli
+```
+
+## Usage
+
+```bash
+divbase --help # can also run divbase-cli --help
+```
+
+## Development
+
+This package is developed in the [DivBase repository](https://github.com/ScilifelabDataCentre/divbase) by Scilifelab Data Centre.

divbase_cli-0.1.0a1/pyproject.toml

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+[project]
+name = "divbase-cli"
+description = "Command Line Interface for Divbase"
+readme = "README.md"
+license = "MIT"
+authors = [
+    { name = "SciLifeLab Data Centre", email = "datacentre@scilifelab.se" },
+]
+requires-python = ">=3.12"
+dependencies = [
+    "typer==0.24.1",
+    "keyring>=25.7.0",
+    "divbase-lib==0.1.0a1",
+]
+dynamic = ["version"]
+
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Environment :: Console",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+]
+
+[project.urls]
+Homepage = "https://divbase.scilifelab-2-prod.sys.kth.se"
+Documentation = "https://scilifelabdatacentre.github.io/divbase"
+Repository = "https://github.com/ScilifelabDataCentre/divbase"
+Issues = "https://github.com/ScilifelabDataCentre/divbase/issues"
+
+[project.scripts]
+divbase-cli = "divbase_cli.divbase_cli:main"
+
+[build-system]
+requires = ["hatchling >= 1.26"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+path = "src/divbase_cli/__init__.py"
+
+[tool.uv.sources]
+divbase-lib = { workspace = true }
+
+[tool.ruff]
+extend = "../../ruff.toml"
+
+[tool.ruff.lint.flake8-tidy-imports.banned-api]
+"divbase_api" = { msg = "divbase-cli cannot use code from divbase-api. Move shared code to divbase-lib." }

divbase_cli-0.1.0a1/src/divbase_cli/__init__.py

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+__version__ = "0.1.0a1"

divbase_cli-0.1.0a1/src/divbase_cli/cli_commands/__init__.py

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+# File: /divbase/divbase/packages/divbase-cli/src/divbase_cli/commands/__init__.py
+"""
+This file initializes the commands subpackage for the divbase-cli package.
+"""

divbase_cli-0.1.0a1/src/divbase_cli/cli_commands/auth_cli.py

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+"""
+CLI subcommand for managing user auth with DivBase server.
+"""
+
+import logging
+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 (
+    check_existing_session,
+    login_to_divbase,
+    logout_of_divbase,
+    make_authenticated_request,
+)
+from divbase_cli.user_config import load_user_config
+
+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.
+    """
+    logout_of_divbase()
+    print("Logged out successfully.")
+
+
+@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']})")