divbase-cli 0.1.0.dev2__py3-none-any.whl → 0.1.0.dev4__py3-none-any.whl

divbase_cli/cli_commands/query_cli.py

@@ -17,13 +17,11 @@ TODO:
 """
 
 import logging
-from pathlib import Path
 
 import typer
 from rich import print
 
-from divbase_cli.cli_commands.user_config_cli import CONFIG_FILE_OPTION
-from divbase_cli.cli_commands.version_cli import PROJECT_NAME_OPTION
+from divbase_cli.cli_commands.shared_args_options import PROJECT_NAME_OPTION
 from divbase_cli.cli_config import cli_settings
 from divbase_cli.config_resolver import resolve_project
 from divbase_cli.user_auth import make_authenticated_request
@@ -75,7 +73,6 @@ def sample_metadata_query(
     ),
     metadata_tsv_name: str = METADATA_TSV_ARGUMENT,
     project: str | None = PROJECT_NAME_OPTION,
-    config_file: Path = CONFIG_FILE_OPTION,
 ) -> None:
     """
     Query the tsv sidecar metadata file for the VCF files in the project's data store on DivBase.
@@ -86,7 +83,7 @@ def sample_metadata_query(
     TODO: handle when the name of the sample column is something other than Sample_ID
     """
 
-    project_config = resolve_project(project_name=project, config_path=config_file)
+    project_config = resolve_project(project_name=project)
 
     request_data = SampleMetadataQueryRequest(tsv_filter=filter, metadata_tsv_name=metadata_tsv_name)
 
@@ -100,14 +97,23 @@ def sample_metadata_query(
 
     results = SampleMetadataQueryTaskResult(**response.json())
 
+    if results.warnings:
+        print("[yellow]Warnings:[/yellow]")
+        for warning in results.warnings:
+            print(f"  • {warning}")
+        print()
+
     if show_sample_results:
         print("[bright_blue]Name and file for each sample in query results:[/bright_blue]")
         for sample in results.sample_and_filename_subset:
             print(f"Sample ID: '{sample['Sample_ID']}', Filename: '{sample['Filename']}'")
 
     print(f"The results for the query ([bright_blue]{results.query_message}[/bright_blue]):")
-    print(f"Unique Sample IDs: {results.unique_sample_ids}")
-    print(f"Unique filenames: {results.unique_filenames}\n")
+
+    unique_sample_ids = results.unique_sample_ids or []
+    unique_filenames = results.unique_filenames or []
+    print(f"Unique Sample IDs: {unique_sample_ids}")
+    print(f"Unique filenames: {unique_filenames}\n")
 
 
 @query_app.command("bcftools-pipe")
@@ -116,7 +122,6 @@ def pipe_query(
     command: str = BCFTOOLS_ARGUMENT,
     metadata_tsv_name: str = METADATA_TSV_ARGUMENT,
     project: str | None = PROJECT_NAME_OPTION,
-    config_file: Path = CONFIG_FILE_OPTION,
 ) -> None:
     """
     Submit a query to run on the DivBase API. A single, merged VCF file will be added to the project on success.
@@ -129,7 +134,7 @@ def pipe_query(
     TODO consider handling the bcftools command whitelist checks also on the CLI level since the error messages are nicer looking?
     TODO consider moving downloading of missing files elsewhere, since this is now done before the celery task
     """
-    project_config = resolve_project(project_name=project, config_path=config_file)
+    project_config = resolve_project(project_name=project)
 
     request_data = BcftoolsQueryRequest(tsv_filter=tsv_filter, command=command, metadata_tsv_name=metadata_tsv_name)
 

divbase_cli/cli_commands/shared_args_options.py

@@ -0,0 +1,23 @@
+"""
+To avoid potential problems with circular imports, we can put shared typer args + options (etc...) here
+
+If you have something that is only used in one of the cli subcommands, don't move it here.
+"""
+
+import typer
+
+PROJECT_NAME_OPTION = typer.Option(
+    None,
+    "--project",
+    "-p",
+    help="Name of the DivBase project, if not provided uses the default in your DivBase config file",
+    show_default=False,
+)
+
+
+FORMAT_AS_TSV_OPTION = typer.Option(
+    False,
+    "--tsv",
+    "-t",
+    help="If set, will print the output in .TSV format for easier programmatic parsing.",
+)

divbase_cli/cli_commands/task_history_cli.py

@@ -6,11 +6,9 @@ Submits a query for fetching the Celery task history for the user to the DivBase
 """
 
 import logging
-from pathlib import Path
 
 import typer
 
-from divbase_cli.cli_commands.user_config_cli import CONFIG_FILE_OPTION
 from divbase_cli.cli_exceptions import AuthenticationError
 from divbase_cli.display_task_history import TaskHistoryDisplayManager
 from divbase_cli.user_auth import make_authenticated_request
@@ -28,7 +26,6 @@ task_history_app = typer.Typer(
 
 @task_history_app.command("user")
 def list_task_history_for_user(
-    config_file: Path = CONFIG_FILE_OPTION,
     limit: int = typer.Option(10, help="Maximum number of tasks to display in the terminal. Sorted by recency."),
     project: str | None = typer.Option(
         None, help="Optional project name to filter the user's task history by project."
@@ -40,7 +37,7 @@ def list_task_history_for_user(
 
     # TODO add option to sort ASC/DESC by task timestamp
 
-    config = load_user_config(config_file)
+    config = load_user_config()
     logged_in_url = config.logged_in_url
 
     if not logged_in_url:
@@ -73,13 +70,12 @@ def list_task_history_for_user(
 @task_history_app.command("id")
 def task_history_by_id(
     task_id: int | None = typer.Argument(..., help="Task ID to check the status of a specific query job."),
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """
     Check status of a specific task submitted by the user by its task ID.
     """
 
-    config = load_user_config(config_file)
+    config = load_user_config()
     logged_in_url = config.logged_in_url
 
     if not logged_in_url:
@@ -104,7 +100,6 @@ def task_history_by_id(
 
 @task_history_app.command("project")
 def list_task_history_for_project(
-    config_file: Path = CONFIG_FILE_OPTION,
     limit: int = typer.Option(10, help="Maximum number of tasks to display in the terminal. Sorted by recency."),
     project: str = typer.Argument(..., help="Project name to check the task history for."),
 ):
@@ -115,7 +110,7 @@ def list_task_history_for_project(
     # TODO add option to sort ASC/DESC by task timestamp
     # TODO use default project from config if not --project specified
 
-    config = load_user_config(config_file)
+    config = load_user_config()
     logged_in_url = config.logged_in_url
 
     if not logged_in_url:

divbase_cli/cli_commands/user_config_cli.py

@@ -4,8 +4,6 @@ config subcommand for the divbase-cli package.
 Controls the user config file stored at "~/.config/.divbase_tools.yaml" (unless specified otherwise).
 """
 
-from pathlib import Path
-
 import typer
 from rich import print
 from rich.console import Console
@@ -13,34 +11,12 @@ from rich.table import Table
 
 from divbase_cli.cli_config import cli_settings
 from divbase_cli.user_config import (
-    create_user_config,
     load_user_config,
 )
 
-CONFIG_FILE_OPTION = typer.Option(
-    cli_settings.CONFIG_PATH,
-    "--config",
-    "-c",
-    help="Path to your user configuration file. If you didn't specify a custom path when you created it, you don't need to set this.",
-)
-
 config_app = typer.Typer(help="Manage your user configuration file for the DivBase CLI.", no_args_is_help=True)
 
 
-@config_app.command("create")
-def create_user_config_command(
-    config_file: Path = typer.Option(
-        cli_settings.CONFIG_PATH,
-        "--config",
-        "-c",
-        help="Where to store your config file locally on your pc.",
-    ),
-):
-    """Create a user configuration file for divbase-cli."""
-    create_user_config(config_path=config_file)
-    print(f"User configuration file created at {config_file.resolve()}.")
-
-
 @config_app.command("add")
 def add_project_command(
     name: str = typer.Argument(..., help="Name of the project to add to your config file."),
@@ -56,17 +32,16 @@ def add_project_command(
         "-d",
         help="Set this project as the default project in your config file.",
     ),
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """Add a new project to your user configuration file."""
-    config = load_user_config(config_file)
+    config = load_user_config()
     project = config.add_project(
         name=name,
         divbase_url=divbase_url,
         is_default=make_default,
     )
 
-    print(f"Project: '{project.name}' added to your config file located at {config_file.resolve()}.")
+    print(f"Project: '{project.name}' added to your config.")
     print(f"The URL: {project.divbase_url} was set as the DivBase API URL for this project.")
 
     if make_default:
@@ -75,17 +50,16 @@ def add_project_command(
         print(f"To make '{project.name}' your default project you can run: 'divbase config set-default {project.name}'")
 
 
-@config_app.command("remove")
+@config_app.command("rm")
 def remove_project_command(
     name: str = typer.Argument(..., help="Name of the project to remove from your user configuration file."),
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """Remove a project from your user configuration file."""
-    config = load_user_config(config_file)
+    config = load_user_config()
     removed_project = config.remove_project(name)
 
     if not removed_project:
-        print(f"The project '{name}' was not found in your config file located at {config_file.resolve()}.")
+        print(f"Nothing to do, the project '{name}' was not found in your user config")
     else:
         print(f"The project '{removed_project}' was removed from your config.")
 
@@ -93,20 +67,17 @@ def remove_project_command(
 @config_app.command("set-default")
 def set_default_project_command(
     name: str = typer.Argument(..., help="Name of the project to add to the user configuration file."),
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """Set your default project to use in all divbase-cli commands."""
-    config = load_user_config(config_file)
+    config = load_user_config()
     default_project_name = config.set_default_project(name=name)
     print(f"Default project is now set to '{default_project_name}'.")
 
 
 @config_app.command("show-default")
-def show_default_project_command(
-    config_file: Path = CONFIG_FILE_OPTION,
-) -> None:
+def show_default_project_command() -> None:
     """Print the currently set default project to the console."""
-    config = load_user_config(config_file)
+    config = load_user_config()
 
     if config.default_project:
         print(config.default_project)
@@ -123,10 +94,9 @@ def set_default_dload_dir_command(
         You can specify an absolute path. 
         You can use '.' to refer to the directory you run the command from.""",
     ),
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """Set the default download dir"""
-    config = load_user_config(config_file)
+    config = load_user_config()
     dload_dir = config.set_default_download_dir(download_dir=download_dir)
     if dload_dir == ".":
         print("The default download directory will be whereever you run the command from.")
@@ -135,14 +105,14 @@ def set_default_dload_dir_command(
 
 
 @config_app.command("show")
-def show_user_config(
-    config_file: Path = CONFIG_FILE_OPTION,
-):
+def show_user_config():
     """Pretty print the contents of your current config file."""
-    config = load_user_config(config_file)
+    config = load_user_config()
     console = Console()
 
-    console.print(f"[bold]Your DivBase user configuration file's contents located at:[/bold] '{config_file}'")
+    console.print(
+        f"[bold]Your DivBase user configuration file's contents located at:[/bold] '{cli_settings.CONFIG_PATH.resolve()}'\n"
+    )
 
     if not config.default_download_dir:
         dload_dir_info = "Not specified, meaning the working directory of wherever you run the download command from."

divbase_cli/cli_commands/version_cli.py

@@ -1,28 +1,23 @@
 """CLI commands for managing project versions in DivBase."""
 
 from datetime import datetime
-from pathlib import Path
 from zoneinfo import ZoneInfo
 
 import typer
 from rich import print
-from rich.console import Console
 from rich.table import Table
 
-from divbase_cli.cli_commands.user_config_cli import CONFIG_FILE_OPTION
+from divbase_cli.cli_commands.shared_args_options import FORMAT_AS_TSV_OPTION, PROJECT_NAME_OPTION
 from divbase_cli.config_resolver import ensure_logged_in, resolve_project
-from divbase_cli.services import (
+from divbase_cli.services.project_versions import (
     add_version_command,
     delete_version_command,
     get_version_details_command,
     list_versions_command,
+    update_version_command,
 )
-
-PROJECT_NAME_OPTION = typer.Option(
-    None,
-    help="Name of the DivBase project, if not provided uses the default in your DivBase config file",
-    show_default=False,
-)
+from divbase_cli.utils import print_rich_table_as_tsv
+from divbase_lib.utils import format_file_size
 
 version_app = typer.Typer(
     no_args_is_help=True,
@@ -42,11 +37,10 @@ def add_version(
     name: str = typer.Argument(help="Name of the version (e.g., semantic version).", show_default=False),
     description: str = typer.Option("", help="Optional description of the version."),
     project: str | None = PROJECT_NAME_OPTION,
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """Add a new project version entry which specifies the current state of all files in the project at the current timestamp."""
-    project_config = resolve_project(project_name=project, config_path=config_file)
-    logged_in_url = ensure_logged_in(config_path=config_file, desired_url=project_config.divbase_url)
+    project_config = resolve_project(project_name=project)
+    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
 
     add_version_response = add_version_command(
         name=name,
@@ -57,11 +51,58 @@ def add_version(
     print(f"New version: '{add_version_response.name}' added to the project: '{project_config.name}'")
 
 
-@version_app.command("list")
+@version_app.command("update")
+def update_version(
+    version_name: str = typer.Argument(help="Name of the existing version you want to modify", show_default=False),
+    new_name: str | None = typer.Option(
+        None, "--new-name", "-n", help="New name for the version. If not specified, the name will remain unchanged."
+    ),
+    new_description: str | None = typer.Option(
+        None,
+        "--new-description",
+        "-d",
+        help="Optional new description of the version. If not specified, the description will remain unchanged.",
+    ),
+    project: str | None = PROJECT_NAME_OPTION,
+):
+    """
+    Update an existing project version entry's name and/or description.
+
+    The files and timestamp associated with a version entry are immutable and cannot be changed.
+    This is by design to ensure version entries are representations of the project's state at the timepoint they were created at.
+    You can create a new version entry to capture the current state of the project instead.
+
+    To see your current version entries run: `divbase-cli version ls`
+    """
+    if not new_name and not new_description:
+        print(
+            "No updates specified. Please provide a new name (--new-name) and/or description (--new-description) to update for this entry."
+        )
+        return
+
+    project_config = resolve_project(project_name=project)
+    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
+
+    updated_version = update_version_command(
+        project_name=project_config.name,
+        divbase_base_url=logged_in_url,
+        version_name=version_name,
+        new_name=new_name,
+        new_description=new_description,
+    )
+    if new_name and new_name != version_name:
+        print(f"Version '{version_name}' renamed to '{updated_version.name}' in project: '{project_config.name}'")
+    else:
+        print(f"Version '{updated_version.name}' updated in project: '{project_config.name}'")
+    if new_description:
+        print(f"New description: '{updated_version.description}'")
+
+
+@version_app.command("ls")
 def list_versions(
     project: str | None = PROJECT_NAME_OPTION,
-    config_file: Path = CONFIG_FILE_OPTION,
     include_deleted: bool = typer.Option(False, help="Include soft-deleted versions in the listing."),
+    format_output_as_tsv: bool = FORMAT_AS_TSV_OPTION,
 ):
     """
     List all entries in the project versioning file.
@@ -70,8 +111,8 @@ def list_versions(
     If you specify --include-deleted, soft-deleted versions will also be shown.
     Soft-deleted versions can be restored by a DivBase admin within 30 days of deletion.
     """
-    project_config = resolve_project(project_name=project, config_path=config_file)
-    logged_in_url = ensure_logged_in(config_path=config_file, desired_url=project_config.divbase_url)
+    project_config = resolve_project(project_name=project)
+    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
 
     versions_info = list_versions_command(
         project_name=project_config.name, include_deleted=include_deleted, divbase_base_url=logged_in_url
@@ -81,7 +122,6 @@ def list_versions(
         print(f"No versions found for project: {project_config.name}.")
         return
 
-    console = Console()
     table = Table(title=f"Versions for {project_config.name}")
     table.add_column("Version", style="cyan", no_wrap=True)
     table.add_column("Created ", style="magenta")
@@ -99,49 +139,70 @@ def list_versions(
         else:
             table.add_row(name, created_at, desc)
 
-    console.print(table)
+    if not format_output_as_tsv:
+        print(table)
+    else:
+        print_rich_table_as_tsv(table=table)
 
 
 @version_app.command("info")
 def get_version_info(
     version: str = typer.Argument(help="Specific version to retrieve information for"),
     project: str | None = PROJECT_NAME_OPTION,
-    config_file: Path = CONFIG_FILE_OPTION,
+    format_output_as_tsv: bool = FORMAT_AS_TSV_OPTION,
 ):
-    """Provide detailed information about a user specified project version, including all files present and their unique hashes."""
-    project_config = resolve_project(project_name=project, config_path=config_file)
-    logged_in_url = ensure_logged_in(config_path=config_file, desired_url=project_config.divbase_url)
+    """
+    Provide detailed information about a user specified project version, including all files present and their unique hashes.
+    """
+    project_config = resolve_project(project_name=project)
+    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
 
     version_details = get_version_details_command(
         project_name=project_config.name, divbase_base_url=logged_in_url, version_name=version
     )
 
-    print(f"Project version entry for project: '{project_config.name}' with name: '{version_details.name}'")
-    print(f"Entry created at: {format_timestamp(version_details.created_at)}")
-    if version_details.description:
-        print(f"Description: {version_details.description}")
-    if version_details.is_deleted:
-        print(
-            "[red]WARNING: This version has been soft-deleted and will soon be permanently deleted unless restored - Contact a DivBase admin to prevent this.[/red]"
+    table = Table(title=f"Project version files for {project_config.name}")
+    table.add_column("Name", style="cyan", no_wrap=True)
+    table.add_column("Version ID", style="magenta")
+    table.add_column("MD5 Checksum", style="green")
+    table.add_column("Size", style="yellow")
+    for object_name, file_details in version_details.files.items():
+        file_size = format_file_size(file_details["size"])
+
+        table.add_row(
+            object_name,
+            file_details["version_id"],
+            file_details["etag"],
+            file_size,
         )
-    print("Files at this version:")
-    for object_name, hash in version_details.files.items():
-        print(f"- '{object_name}' : '{hash}'")
+
+    if not format_output_as_tsv:
+        print(f"Project version entry for project: '{project_config.name}' with name: '{version_details.name}'")
+        print(f"Entry created at: {format_timestamp(version_details.created_at)}")
+        if version_details.description:
+            print(f"Description: {version_details.description}")
+        if version_details.is_deleted:
+            print(
+                "[red]WARNING: This version has been soft-deleted and will soon be permanently deleted unless restored - Contact a DivBase admin to prevent this.[/red]"
+            )
+        print(table)
+    else:
+        print_rich_table_as_tsv(table=table)
 
 
-@version_app.command("delete")
+@version_app.command("rm")
 def delete_version(
     name: str = typer.Argument(help="Name of the version (e.g., semantic version).", show_default=False),
     project: str | None = PROJECT_NAME_OPTION,
-    config_file: Path = CONFIG_FILE_OPTION,
 ):
     """
     Delete a version entry in the project versioning table. This does not delete the files themselves.
+
     Deleted version entries older than 30 days will be permanently deleted.
     You can ask a DivBase admin to restore a deleted version within that time period.
     """
-    project_config = resolve_project(project_name=project, config_path=config_file)
-    logged_in_url = ensure_logged_in(config_path=config_file, desired_url=project_config.divbase_url)
+    project_config = resolve_project(project_name=project)
+    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
 
     deleted_version = delete_version_command(
         project_name=project_config.name, divbase_base_url=logged_in_url, version_name=name

divbase_cli/cli_config.py

@@ -2,16 +2,31 @@
 Settings for DivBase CLI.
 
 This class creates a single 'settings' object at module load time that can be imported and used throughout the entire package.
+
+The user config and tokens are stored in the users local app dir:
+https://typer.tiangolo.com/tutorial/app-dir/
 """
 
 import os
 from dataclasses import dataclass
 from pathlib import Path
 
-DEFAULT_CONFIG_PATH = Path.home() / ".config" / "divbase" / "config.yaml"
-DEFAULT_TOKENS_PATH = Path.home() / ".config" / "divbase" / ".secrets"
+import typer
+
+APP_NAME = "divbase-cli"
+APP_DIR = Path(typer.get_app_dir(APP_NAME))
 DEFAULT_METADATA_TSV_NAME = "sample_metadata.tsv"
-DEFAULT_DIVBASE_API_URL = "http://localhost:8000/api"  # TODO - change to production URL when time comes
+DEFAULT_LOG_LEVEL = "INFO"
+DEV_MODE = os.getenv("DIVBASE_DEV", "0") == "1"
+CONFIG_PATH = APP_DIR / "config.yaml"
+TOKENS_PATH = APP_DIR / ".secrets"
+
+if DEV_MODE:
+    DEFAULT_DIVBASE_API_URL = "http://localhost:8000/api"
+    DEFAULT_LOGGING_ON = "1"
+else:
+    DEFAULT_DIVBASE_API_URL = "https://divbase-dev.scilifelab-2-dev.sys.kth.se/api"  # TODO - prod url when time
+    DEFAULT_LOGGING_ON = "0"
 
 
 @dataclass
@@ -19,21 +34,24 @@ class DivBaseCLISettings:
     """
     Settings for DivBase CLI.
 
-    NOTE: Do not create an instance of this class yourself,
-    import the 'settings' instance created at this module's load time.
+    You do not need to create an instance of this class yourself,
+    instead, import the 'cli_settings' instance created at this module's load time.
     """
 
-    CONFIG_PATH: Path = Path(os.getenv("DIVBASE_CONFIG_PATH", DEFAULT_CONFIG_PATH))
-    TOKENS_PATH: Path = Path(os.getenv("DIVBASE_TOKENS_PATH", DEFAULT_TOKENS_PATH))
+    CONFIG_PATH: Path = Path(os.getenv("DIVBASE_CLI_CONFIG_PATH", CONFIG_PATH))
+    TOKENS_PATH: Path = Path(os.getenv("DIVBASE_CLI_TOKENS_PATH", TOKENS_PATH))
     DIVBASE_API_URL: str = os.getenv("DIVBASE_API_URL", DEFAULT_DIVBASE_API_URL)
     METADATA_TSV_NAME: str = os.getenv("DIVBASE_METADATA_TSV_NAME", DEFAULT_METADATA_TSV_NAME)
-    LOGGING_ON: bool = bool(os.getenv("DIVBASE_LOGGING_ON", "True") == "True")
-    LOG_LEVEL: str = os.getenv("DIVBASE_LOG_LEVEL", "INFO").upper()
+    LOGGING_ON: bool = os.getenv("DIVBASE_LOGGING_ON", DEFAULT_LOGGING_ON) == "1"
+    LOG_LEVEL: str = os.getenv("DIVBASE_LOG_LEVEL", DEFAULT_LOG_LEVEL).upper()
 
     def __post_init__(self):
         valid_levels = ["CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG", "NOTSET"]
         if self.LOG_LEVEL not in valid_levels:
             raise ValueError(f"Invalid LOG_LEVEL: {self.LOG_LEVEL}. Must be one of {valid_levels}.")
 
+        if self.DIVBASE_API_URL.endswith("/"):
+            self.DIVBASE_API_URL = self.DIVBASE_API_URL[:-1]
+
 
 cli_settings = DivBaseCLISettings()