divbase-cli 0.1.0a12__tar.gz → 0.1.0a15__tar.gz

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/.gitignore

@@ -50,9 +50,10 @@ docker/logs/*
 #MacOS artifacts
 .DS_Store
 
-# mkdocs build cache
+# mkdocs/zensical build cache
 .cache/
-# mkdocs auto generated files
+site/
+# documentation site's auto generated files
 docs/cli/_auto_generated/*.md
 docs/releases/index.md
 

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.4
+Metadata-Version: 2.5
 Name: divbase-cli
-Version: 0.1.0a12
+Version: 0.1.0a15
 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==0.1.0a12
-Requires-Dist: keyring>=25.7.0
-Requires-Dist: typer==0.26.7
+Requires-Dist: divbase-lib==0.1.0a15
+Requires-Dist: keyring==25.7.0
+Requires-Dist: typer==0.26.8
 Description-Content-Type: text/markdown
 
 # divbase-cli

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/pyproject.toml

@@ -8,9 +8,9 @@ authors = [
 ]
 requires-python = ">=3.12"
 dependencies = [
-    "typer==0.26.7",
-    "keyring>=25.7.0",
-    "divbase-lib==0.1.0a12",
+    "typer==0.26.8",
+    "keyring==25.7.0",
+    "divbase-lib==0.1.0a15",
 ]
 dynamic = ["version"]
 

divbase_cli-0.1.0a15/src/divbase_cli/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.1.0a15"

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_commands/auth_cli.py

@@ -4,7 +4,6 @@ CLI subcommand for managing user auth with DivBase server.
 
 import logging
 import time
-from datetime import datetime
 
 import typer
 from pydantic import SecretStr
@@ -31,6 +30,7 @@ from divbase_cli.user_auth import (
 )
 from divbase_cli.user_config import load_user_config
 from divbase_lib.divbase_constants import PAT_TOKEN_PREFIX
+from divbase_lib.utils import format_unix_timestamp_for_cli
 
 logger = logging.getLogger(__name__)
 
@@ -63,7 +63,7 @@ def login(
         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)}")
+            print(f"Session expires: {format_unix_timestamp_for_cli(unix_timestamp=session_expires_at)}")
 
             if not typer.confirm("Do you want to login again? This will replace your current session."):
                 print("Login cancelled.")

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_commands/dimensions_cli.py

@@ -1,5 +1,6 @@
 import csv
 import logging
+from datetime import datetime
 from pathlib import Path
 
 import typer
@@ -8,7 +9,7 @@ from rich import print
 from rich.table import Table
 
 from divbase_cli.cli_commands.shared_args_options import PROJECT_NAME_OPTION
-from divbase_cli.config_resolver import ensure_logged_in, resolve_project
+from divbase_cli.config_resolver import resolve_and_authenticate_project
 from divbase_cli.user_auth import make_authenticated_request
 from divbase_cli.utils import print_rich_table_as_tsv
 from divbase_lib.api_schemas.vcf_dimensions import (
@@ -18,6 +19,7 @@ from divbase_lib.api_schemas.vcf_dimensions import (
     DimensionsVCFFilesResult,
 )
 from divbase_lib.metadata_validator import SharedMetadataValidator
+from divbase_lib.utils import format_datetime_for_cli
 
 logger = logging.getLogger(__name__)
 
@@ -32,10 +34,8 @@ dimensions_app = typer.Typer(
 def update_dimensions_index(
     project: str | None = PROJECT_NAME_OPTION,
 ) -> None:
-    """Calculate and add the dimensions of all VCF files in the project to the dimensions index in the project."""
-
-    project_config = resolve_project(project_name=project)
-
+    """Calculate and add the dimensions of all VCF files in the project to the dimensions cache in the project."""
+    project_config = resolve_and_authenticate_project(project_name=project)
     response = make_authenticated_request(
         method="PUT",
         divbase_base_url=project_config.divbase_url,
@@ -96,19 +96,17 @@ def show_dimensions_index(
     project: str | None = PROJECT_NAME_OPTION,
 ) -> None:
     """
-    Show the dimensions index file for a project.
+    Show the dimensions cache file for a project.
     When running --unique-scaffolds, the sorting separates between numeric and non-numeric scaffold names.
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
     if sample_names_output and sample_names_stdout:
         raise typer.BadParameter("Use only one of --sample-names-output or --sample-names-stdout.")
 
+    project_config = resolve_and_authenticate_project(project_name=project)
     if unique_samples:
         response = make_authenticated_request(
             method="GET",
-            divbase_base_url=logged_in_url,
+            divbase_base_url=project_config.divbase_url,
             api_route=f"v1/vcf-dimensions/projects/{project_config.name}/samples",
         )
         unique_sample_names_sorted = DimensionsSamplesResult(**response.json()).unique_samples
@@ -236,7 +234,7 @@ def _format_api_response_for_display_in_terminal(api_response: DimensionsShowRes
         dimensions_entry = {
             "filename": entry["vcf_file_s3_key"],
             "file_version_ID_in_bucket": entry["s3_version_id"],
-            "last_updated": entry.get("updated_at"),
+            "last_updated": format_datetime_for_cli(datetime.fromisoformat(entry["updated_at"])),
             "dimensions": {
                 "scaffold_count": len(sorted_scaffolds),
                 "scaffolds": sorted_scaffolds,
@@ -278,12 +276,10 @@ def create_metadata_template_with_project_samples_names(
     """
     Create a template sample metadata file (TSV format) pre-filled with the sample names from the project's VCF files based on the information stored in the project's VCF dimensions cache. Tip: run 'divbase-cli dimensions update' first to ensure that the VCF dimensions are up-to-date.
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     response = make_authenticated_request(
         method="GET",
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         api_route=f"v1/vcf-dimensions/projects/{project_config.name}/samples",
     )
     unique_sample_names_sorted = DimensionsSamplesResult(**response.json()).unique_samples
@@ -294,7 +290,7 @@ def create_metadata_template_with_project_samples_names(
     )
 
     if sample_count == 0:
-        # Fallback in case there are no samples in the dimensions index. If no dimensions entry for the project
+        # Fallback in case there are no samples in the dimensions cache. If no dimensions entry for the project
         # VCFDimensionsEntryMissingError will be returned. But for some reason, there are no samples in the VCF, this will catch that.
         print("No samples found for this project. No file written.")
         return
@@ -341,17 +337,14 @@ def validate_metadata_template_versus_dimensions_and_formatting_constraints(
     """
     # Client-side validation of a sidecar metadata TSV file, intended to be run before upload to DivBase.
     # Uses the SharedMetadataValidator (that is also used on the server-side) which checks for formatting errors and also validates that the sample names
-    # in the TSV file match the sample names in the dimensions index for the project
-
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    # in the TSV file match the sample names in the dimensions cache for the project
+    project_config = resolve_and_authenticate_project(project_name=project)
     print(f"Validating local metadata file: {input_path}")
     print(f"Project: {project_config.name}\n")
 
     response = make_authenticated_request(
         method="GET",
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         api_route=f"v1/vcf-dimensions/projects/{project_config.name}/samples",
     )
     unique_sample_names = DimensionsSamplesResult(**response.json()).unique_samples

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_commands/file_cli.py

@@ -3,10 +3,8 @@ Command line interface for managing files in a DivBase project's store on DivBas
 """
 
 from collections import defaultdict
-from datetime import datetime
 from glob import glob
 from pathlib import Path
-from zoneinfo import ZoneInfo
 
 import typer
 from rich import print
@@ -24,7 +22,11 @@ from divbase_cli.cli_exceptions import (
     ShellExpandedGlobError,
     UnsupportedCharactersError,
 )
-from divbase_cli.config_resolver import ensure_logged_in, resolve_download_dir, resolve_project
+from divbase_cli.config_resolver import (
+    resolve_and_authenticate_project,
+    resolve_download_dir,
+)
+from divbase_cli.services.pre_signed_urls import DownloadOutcome
 from divbase_cli.services.project_versions import get_version_details_command
 from divbase_cli.services.s3_files import (
     ToDownload,
@@ -48,14 +50,13 @@ from divbase_lib.divbase_constants import (
     UNSUPPORTED_CHARACTERS_DISPLAY,
     UNSUPPORTED_CHARACTERS_IN_FILENAMES,
 )
-from divbase_lib.utils import format_file_size
+from divbase_lib.utils import format_datetime_for_cli, format_file_size
 
 file_app = typer.Typer(no_args_is_help=True, help="Download/upload/list files to/from the project's store on DivBase.")
 
 NO_FILES_SPECIFIED_MSG = "No files specified for the command, exiting..."
 NO_UPLOAD_MATCHES_MSG = "The following file paths or glob patterns did not match any existing files:"
 
-
 PREFIX_ARGUMENT = typer.Argument(
     None,
     help="Optional prefix to filter on. Use a '/' to specify a folder. e.g. 'vcfs/'",
@@ -143,12 +144,11 @@ def list_files(
     if detailed and format_output_as_tsv:
         raise typer.BadParameter(message="The --detailed option and --tsv option cannot be used together.")
 
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
+    project_config = resolve_and_authenticate_project(project_name=project)
 
     if show_deleted_files:
         files = list_soft_deleted_files_command(
-            divbase_base_url=logged_in_url,
+            divbase_base_url=project_config.divbase_url,
             project_name=project_config.name,
             prefix=prefix,
         )
@@ -159,17 +159,17 @@ def list_files(
 
         print(f"Soft deleted files for the project '{project_config.name}':")
         for file_details in files:
-            cet_timestamp = _format_time_stamp(file_details.last_modified)
+            deleted_at = format_datetime_for_cli(dt=file_details.last_modified)
             if file_details.name.endswith("/"):
-                print(f"- [bold blue]'{file_details.name}'[/bold blue] (deleted at: '{cet_timestamp}')")
+                print(f"- [bold blue]'{file_details.name}'[/bold blue] (deleted at: '{deleted_at}')")
             else:
-                print(f"- '{file_details.name}' (deleted at: '{cet_timestamp}')")
+                print(f"- '{file_details.name}' (deleted at: '{deleted_at}')")
         print("\nTo restore a soft deleted file, use the 'divbase-cli files restore' command.")
         print("To get more information about one of the soft deleted files, use the 'divbase-cli files info' command.")
         return
 
     files, folders = list_files_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         prefix=prefix,
         include_results_files=include_results_files,
@@ -211,17 +211,14 @@ def tree_files(
     - Show the tree starting from the 'vcfs/' folder:
         divbase-cli files tree vcfs/
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     files, _ = list_files_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         prefix=prefix,
         include_results_files=include_results_files,
         file_system_view=False,
     )
-
     if not files:
         print("No files found in the project's store on DivBase.")
         return
@@ -247,16 +244,14 @@ def file_info(
     - Get information about a specific file in the project:
         divbase-cli files info my_file.vcf.gz
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
     if file_name.endswith("/"):
         raise typer.BadParameter(
             message="The 'info' command is only for files, not folders. Please provide a file name without a trailing '/'."
         )
 
+    project_config = resolve_and_authenticate_project(project_name=project)
     file_info = get_file_info_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         object_name=file_name,
     )
@@ -278,16 +273,16 @@ def file_info(
         caption="Versions shown are ordered with the latest/current version first/at the top",
     )
     table.add_column("File size", justify="left", style="magenta", no_wrap=True)
-    table.add_column("Upload date (CET)", justify="left", style="green", no_wrap=True)
+    table.add_column("Upload date", justify="left", style="green", no_wrap=True)
     table.add_column("MD5 checksum", justify="left", style="yellow")
     table.add_column("Version ID", justify="left", style="cyan")
 
     for version in file_info.versions:
-        cet_timestamp = _format_time_stamp(version.last_modified)
+        upload_date = format_datetime_for_cli(dt=version.last_modified)
         file_size = format_file_size(size_bytes=version.size)
         table.add_row(
             file_size,
-            cet_timestamp,
+            upload_date,
             version.etag,
             version.version_id,
         )
@@ -336,27 +331,26 @@ def download_files(
     - Mix latest and versioned files in one command:
         divbase-cli files download file1.vcf.gz "file2.tsv:VERSION_ID"
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-    download_dir_path = resolve_download_dir(download_dir=download_dir)
-
     if project_version == "":
         raise typer.BadParameter(
             "It seems like you provided an empty string for --project-version. \n"
             "Please provide a valid project version or omit the flag."
         )
 
+    project_config = resolve_and_authenticate_project(project_name=project)
+    download_dir_path = resolve_download_dir(download_dir=download_dir)
+
     raw_files_input = _resolve_file_inputs(files=files, file_list=file_list)
     raw_files_input = _expand_folder_prefixes(
         files=raw_files_input,
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
     )
     if flatten:
         check_no_overlap_on_flattened_downloads(to_download=raw_files_input)
 
     download_results = download_files_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         raw_files_input=raw_files_input,
         download_dir=download_dir_path,
@@ -416,14 +410,15 @@ def download_all_files(
             "Please provide a valid project version or omit the flag."
         )
 
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
+    project_config = resolve_and_authenticate_project(project_name=project)
     download_dir_path = resolve_download_dir(download_dir=download_dir)
 
     all_files: list[ToDownload] = []
     if project_version:
         version_details = get_version_details_command(
-            project_name=project_config.name, divbase_base_url=logged_in_url, version_name=project_version
+            project_name=project_config.name,
+            divbase_base_url=project_config.divbase_url,
+            version_name=project_version,
         )
         for version_name, file_details in version_details.files.items():
             all_files.append(
@@ -437,7 +432,7 @@ def download_all_files(
 
     else:
         files, _ = list_files_command(
-            divbase_base_url=logged_in_url,
+            divbase_base_url=project_config.divbase_url,
             project_name=project_config.name,
             prefix=None,
             include_results_files=False,
@@ -502,7 +497,7 @@ def download_all_files(
     else:
         raw_files_input = [file.s3_key for file in files_to_download]
     download_results = download_files_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         raw_files_input=raw_files_input,
         download_dir=download_dir_path,
@@ -542,11 +537,9 @@ def stream_file(
     - Run a bcftools command (the "-" tells bcftools to read from standard input):
         divbase-cli files stream my_file.vcf.gz | bcftools view -h -
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     stream_file_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         file_name=file_name,
         version_id=version_id,
@@ -621,19 +614,15 @@ def upload_files(
     - Upload from a text file list (one file path per line):
         divbase-cli files upload --file-list files_to_upload.txt --to experiment1/
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
     if bool(files) + bool(file_list) > 1:
         raise typer.BadParameter("You cannot specify files as arguments and provide a --file-list.")
-
     if skip_existing and disable_safe_mode:
         raise typer.BadParameter(
             "The --skip-existing and --disable-safe-mode options cannot be used together.\n"
             "Safe mode calculates file checksums, "
             "and these checksums are needed for --skip-existing to know what files to skip uploading."
         )
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     to_upload = _resolve_user_upload_inputs(
         files=files,
         file_list=file_list,
@@ -645,7 +634,7 @@ def upload_files(
 
     uploaded_results = upload_files_command(
         project_name=project_config.name,
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         all_files=to_upload,
         safe_mode=not disable_safe_mode,
         skip_existing=skip_existing,
@@ -697,13 +686,12 @@ def make_directory(
     - Create multiple directories at once:
         divbase-cli files mkdir vcfs metadata results
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     cleaned_dir_names = _sanitize_directory_names(directories)
+
     dirs_created = make_directories_command(
         directories=cleaned_dir_names,
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
     )
     if dirs_created.created:
@@ -741,13 +729,12 @@ def remove_directory(
     - Remove multiple directories at once:
         divbase-cli files rmdir vcfs/ metadata/
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     directories = _sanitize_directory_names(directories)
+
     for dir in directories:
         files, _ = list_files_command(
-            divbase_base_url=logged_in_url,
+            divbase_base_url=project_config.divbase_url,
             project_name=project_config.name,
             prefix=dir,
             include_results_files=True,
@@ -763,7 +750,7 @@ def remove_directory(
 
     # NOTE: as dirs are just empty files which end with "/", we can just do a regular soft delete on them.
     deleted_dirs = soft_delete_objects_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         all_files=directories,
     )
@@ -800,9 +787,7 @@ def remove_files(
     - Run a dry run to see what files would be deleted without actually deleting them:
         divbase-cli files rm file1.vcf.gz file2.tsv --dry-run
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     all_files = _resolve_file_inputs(files=files, file_list=file_list)
 
     if dry_run:
@@ -812,7 +797,7 @@ def remove_files(
         return
 
     deleted_files = soft_delete_objects_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         all_files=all_files,
     )
@@ -845,13 +830,11 @@ def restore_soft_deleted_files(
     - Restore files from a text file list (one file name per line):
         divbase-cli files restore --file-list files_to_restore.txt
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     all_files = _resolve_file_inputs(files=files, file_list=file_list)
 
     restored_objects_response = restore_objects_command(
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         project_name=project_config.name,
         all_files=all_files,
     )
@@ -923,8 +906,8 @@ def _print_ls_tsv_format(files: list[ObjectDetails], folders: list[str]) -> None
     for folder in folders:
         print(f"{markup_escape(folder)}\t-\t-")
     for f in files:
-        cet = _format_time_stamp(f.last_modified)
-        print(f"{markup_escape(f.name)}\t{format_file_size(f.size)}\t{cet}")
+        last_modified = format_datetime_for_cli(dt=f.last_modified)
+        print(f"{markup_escape(f.name)}\t{format_file_size(f.size)}\t{last_modified}")
 
 
 def _print_ls_detailed(files: list[ObjectDetails], folders: list[str]) -> None:
@@ -934,8 +917,8 @@ def _print_ls_detailed(files: list[ObjectDetails], folders: list[str]) -> None:
         console.print(f"[bold blue]{markup_escape(folder)}[/bold blue]")
     for f in files:
         size_str = format_file_size(f.size).rjust(10)
-        cet = _format_time_stamp(f.last_modified)
-        console.print(f"{markup_escape(f.name)} [magenta]{size_str}[/magenta]  [green]{cet}[/green]")
+        last_modified = format_datetime_for_cli(dt=f.last_modified)
+        console.print(f"{markup_escape(f.name)} [magenta]{size_str}[/magenta]  [green]{last_modified}[/green]")
 
 
 def _resolve_file_inputs(files: list[str] | None, file_list: Path | None) -> list[str]:
@@ -1191,7 +1174,7 @@ def _sanitize_directory_names(directories: list[str]) -> list[str]:
     return cleaned_dir_names
 
 
-def _pretty_print_download_results(download_results):
+def _pretty_print_download_results(download_results: DownloadOutcome) -> None:
     """Helper fn used by download and download all commands to print the results of the download in a nice format."""
     if download_results.successful:
         print("\n[green bold]Successfully downloaded the following files:[/green bold]")
@@ -1203,8 +1186,3 @@ def _pretty_print_download_results(download_results):
         for failed in download_results.failed:
             print(f"[red]- '{failed.object_name}': [/red] Exception: '{failed.exception}'")
         raise typer.Exit(1)
-
-
-def _format_time_stamp(time_stamp: datetime) -> str:
-    """Helper fn to format a datetime object into a string for printing."""
-    return time_stamp.astimezone(ZoneInfo("CET")).strftime("%Y-%m-%d %H:%M %Z")

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_commands/query_cli.py

@@ -23,9 +23,8 @@ from divbase_cli.cli_commands.shared_args_options import DOWNLOAD_DIR_OPTION, PR
 from divbase_cli.cli_config import cli_settings
 from divbase_cli.cli_exceptions import PolledTaskNotFinalError, QueryTaskFailedError
 from divbase_cli.config_resolver import (
-    ensure_logged_in,
+    resolve_and_authenticate_project,
     resolve_download_dir,
-    resolve_project,
 )
 from divbase_cli.retries import (
     retry_polling_until_final_or_retryable_api_errors,
@@ -110,19 +109,16 @@ def sample_metadata_query(
     Query the tsv sidecar metadata file for the VCF files in the project's data store on DivBase.
     Returns the sample IDs and filenames that match the query.
     """
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     request_data = SampleMetadataQueryRequest(tsv_filter=tsv_filter, metadata_tsv_name=metadata_tsv_name)
 
     response = make_authenticated_request(
         method="POST",
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         api_route=f"v1/query/sample-metadata/projects/{project_config.name}",
         json=request_data.model_dump(),
         timeout=20,  # This is longer than default (5), as api call response is query result, not a task-id.
     )
-
     results = SampleMetadataQueryTaskResult(**response.json())
 
     if results.warnings:
@@ -211,9 +207,7 @@ def vcf_query(
             print(f"  • {warning}")
         print()
 
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     request_data = BcftoolsQueryRequest(
         tsv_filter=tsv_filter,
         command=command,
@@ -221,10 +215,9 @@ def vcf_query(
         samples=normalized_samples,
         all_samples=all_samples,
     )
-
     response = make_authenticated_request(
         method="POST",
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         api_route=f"v1/query/vcf/projects/{project_config.name}",
         json=request_data.model_dump(),
     )
@@ -260,11 +253,12 @@ def get_results_from_query_job_by_task_id(
             f"--max-wait-mins must be between 1 and {MAX_WAIT_MINS_HARD_LIMIT} minutes, got {max_wait_mins}."
         )
 
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
+    project_config = resolve_and_authenticate_project(project_name=project)
 
     task_status = poll_task_until_final_state_reached(
-        divbase_url=logged_in_url, task_id=task_id, timeout_mins=max_wait_mins
+        divbase_url=project_config.divbase_url,
+        task_id=task_id,
+        timeout_mins=max_wait_mins,
     )
 
     resolved_download_dir = resolve_download_dir(download_dir=download_dir)
@@ -273,7 +267,7 @@ def get_results_from_query_job_by_task_id(
     if task_status == "SUCCESS":
         result_filename = f"{QUERY_RESULTS_FILE_PREFIX}{task_id}.vcf.gz"
         download_results = download_files_command(
-            divbase_base_url=logged_in_url,
+            divbase_base_url=project_config.divbase_url,
             project_name=project_config.name,
             raw_files_input=[result_filename],
             download_dir=resolved_download_dir,
@@ -328,7 +322,7 @@ def poll_task_until_final_state_reached(divbase_url: str, task_id: int, timeout_
                     f"Task {task_id} has unsupported task type '{task_results.name}'. Only VCF query jobs are supported for this CLI command."
                 )
 
-            if task_results.status in FINAL_STATES:
+            if task_results.status and task_results.status in FINAL_STATES:
                 return task_results.status
 
             raise PolledTaskNotFinalError(f"Task {task_id} state is {task_results.status}")

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_commands/task_history_cli.py

@@ -10,7 +10,10 @@ import logging
 import typer
 
 from divbase_cli.cli_commands.shared_args_options import FORMAT_AS_TSV_OPTION
-from divbase_cli.config_resolver import ensure_logged_in, resolve_project, resolve_url_for_non_project_specific_commands
+from divbase_cli.config_resolver import (
+    resolve_and_authenticate_project,
+    resolve_url_for_non_project_specific_commands,
+)
 from divbase_cli.display_task_history import TaskHistoryDisplayManager
 from divbase_cli.user_auth import make_authenticated_request
 from divbase_cli.user_config import load_user_config
@@ -104,15 +107,13 @@ def list_task_history_for_project(
     Check status of all tasks submitted for a project. Requires a manager role in the project. Displays the latest 10 tasks by default, unless --limit is specified.
     """
     # TODO add option to sort ASC/DESC by task timestamp
-    project_config = resolve_project(project_name=project)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
+    project_config = resolve_and_authenticate_project(project_name=project)
 
     task_history_response = make_authenticated_request(
         method="GET",
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         api_route=f"v1/task-history/projects/{project_config.name}",
     )
-
     task_history_data = [TaskHistoryResult(**item) for item in task_history_response.json()]
 
     TaskHistoryDisplayManager(

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_commands/version_cli.py

@@ -1,14 +1,11 @@
 """CLI commands for managing project versions in DivBase."""
 
-from datetime import datetime
-from zoneinfo import ZoneInfo
-
 import typer
 from rich import print
 from rich.table import Table
 
 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.config_resolver import resolve_and_authenticate_project
 from divbase_cli.services.project_versions import (
     add_version_command,
     delete_version_command,
@@ -17,7 +14,7 @@ from divbase_cli.services.project_versions import (
     update_version_command,
 )
 from divbase_cli.utils import print_rich_table_as_tsv
-from divbase_lib.utils import format_file_size
+from divbase_lib.utils import format_datetime_for_cli, format_file_size
 
 version_app = typer.Typer(
     no_args_is_help=True,
@@ -25,13 +22,6 @@ version_app = typer.Typer(
 )
 
 
-def format_timestamp(timestamp_str: str) -> str:
-    """Format ISO timestamp to Europe/Stockholm format with timezone"""
-    dt = datetime.fromisoformat(timestamp_str)
-    cet_dt = dt.astimezone(ZoneInfo("Europe/Stockholm"))
-    return cet_dt.strftime("%d/%m/%Y %H:%M:%S %Z")
-
-
 @version_app.command("add")
 def add_version(
     name: str = typer.Argument(help="Name of the version (e.g., semantic version).", show_default=False),
@@ -39,14 +29,12 @@ def add_version(
     project: str | None = PROJECT_NAME_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)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     add_version_response = add_version_command(
         name=name,
         description=description,
         project_name=project_config.name,
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
     )
     print(f"New version: '{add_version_response.name}' added to the project: '{project_config.name}'")
 
@@ -75,17 +63,14 @@ def update_version(
     To see your current version entries run: `divbase-cli version ls`
     """
     if not new_name and not new_description:
-        print(
+        raise typer.BadParameter(
             "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)
 
+    project_config = resolve_and_authenticate_project(project_name=project)
     updated_version = update_version_command(
         project_name=project_config.name,
-        divbase_base_url=logged_in_url,
+        divbase_base_url=project_config.divbase_url,
         version_name=version_name,
         new_name=new_name,
         new_description=new_description,
@@ -111,11 +96,11 @@ 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)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     versions_info = list_versions_command(
-        project_name=project_config.name, include_deleted=include_deleted, divbase_base_url=logged_in_url
+        project_name=project_config.name,
+        include_deleted=include_deleted,
+        divbase_base_url=project_config.divbase_url,
     )
 
     if not versions_info:
@@ -125,6 +110,7 @@ def list_versions(
     table = Table(title=f"Versions for {project_config.name}")
     table.add_column("Version", style="cyan", no_wrap=True)
     table.add_column("Created ", style="magenta")
+    table.add_column("Last Updated", style="blue")
     table.add_column("Description", style="green")
     if include_deleted:
         table.add_column("Soft Deleted", style="red")
@@ -132,12 +118,13 @@ def list_versions(
     for version in versions_info:
         name = version.name
         desc = version.description or "No description provided"
-        created_at = format_timestamp(version.created_at)
+        created_at = format_datetime_for_cli(dt=version.created_at)
+        updated_at = format_datetime_for_cli(dt=version.updated_at)
         if include_deleted:
             soft_deleted = "Yes" if version.is_deleted else "No"
-            table.add_row(name, created_at, desc, soft_deleted)
+            table.add_row(name, created_at, updated_at, desc, soft_deleted)
         else:
-            table.add_row(name, created_at, desc)
+            table.add_row(name, created_at, updated_at, desc)
 
     if not format_output_as_tsv:
         print(table)
@@ -154,11 +141,11 @@ def get_version_info(
     """
     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)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     version_details = get_version_details_command(
-        project_name=project_config.name, divbase_base_url=logged_in_url, version_name=version
+        project_name=project_config.name,
+        divbase_base_url=project_config.divbase_url,
+        version_name=version,
     )
 
     table = Table(title=f"Project version files for {project_config.name}")
@@ -178,7 +165,8 @@ def get_version_info(
 
     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)}")
+        print(f"Entry created at: {format_datetime_for_cli(dt=version_details.created_at)}")
+        print(f"Entry last updated at: {format_datetime_for_cli(dt=version_details.updated_at)}")
         if version_details.description:
             print(f"Description: {version_details.description}")
         if version_details.is_deleted:
@@ -201,14 +189,14 @@ def delete_version(
     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)
-    logged_in_url = ensure_logged_in(desired_url=project_config.divbase_url)
-
+    project_config = resolve_and_authenticate_project(project_name=project)
     deleted_version = delete_version_command(
-        project_name=project_config.name, divbase_base_url=logged_in_url, version_name=name
+        project_name=project_config.name,
+        divbase_base_url=project_config.divbase_url,
+        version_name=name,
     )
     if deleted_version.already_deleted:
-        date_deleted = format_timestamp(deleted_version.date_deleted)
+        date_deleted = format_datetime_for_cli(dt=deleted_version.date_deleted)
         print(f"The version: '{deleted_version.name}' has already been soft-deleted on {date_deleted}.")
     else:
         print(f"The version: '{deleted_version.name}' was deleted from the project: '{project_config.name}'")

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/cli_exceptions.py

@@ -2,8 +2,6 @@
 Custom exceptions for the divbase CLI.
 """
 
-from pathlib import Path
-
 
 class DivBaseCLIError(Exception):
     """Base exception for all divbase CLI errors."""
@@ -173,13 +171,12 @@ class ProjectNotInConfigError(DivBaseCLIError):
     But info about the project could not be obtained from the user config file.
     """
 
-    def __init__(self, config_path: Path, project_name: str):
-        self.config_path = config_path
+    def __init__(self, project_name: str):
         self.project_name = project_name
         error_message = (
             f"Couldn't get information about the project named: '{project_name}' \n"
-            f"Please check the project is included in '{config_path.resolve()}'.\n"
-            f"you can run 'divbase-cli config show' to view the contents of your config file.\n"
+            f"Use the command 'divbase-cli config add <project_name>' to add the project to your config.\n"
+            f"You can run 'divbase-cli config show' to view the contents of your config file.\n"
         )
         super().__init__(error_message)
 

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/config_resolver.py

@@ -14,22 +14,33 @@ from divbase_cli.user_auth import get_pat_for_authentication
 from divbase_cli.user_config import ProjectConfig, load_user_config
 
 
-def ensure_logged_in(desired_url: str | None = None) -> str:
+def resolve_and_authenticate_project(project_name: str | None) -> ProjectConfig:
     """
-    Ensure the user is logged in by checking the logged_in_url value in the user config.
+    Helper function that resolves the project to use for a CLI command and ensures
+    the user is logged in to the correct DivBase API URL for that project.
 
-    Optionally checks the logged_in_url matches the desired_url (e.g. for project-specific commands) if provided.
+    Returns the ProjectConfig object for the resolved project, will raise errors otherwise.
     """
-    config = load_user_config()
-    if config.logged_in_url:
-        if desired_url and config.logged_in_url != desired_url:
+    user_config = load_user_config()
+    if not project_name:
+        project_name = user_config.default_project
+    if not project_name:
+        raise ProjectNameNotSpecifiedError()
+
+    project_config = user_config.project_info(project_name)
+
+    if user_config.logged_in_url:
+        if project_config.divbase_url != user_config.logged_in_url:
             raise AuthenticationError(
-                f"You are not logged in to the correct DivBase URL: {desired_url}. Please log in again."
+                f"You are trying to run a command for the project '{project_name}' which has the DivBase URL: {project_config.divbase_url} \n"
+                f"You are however logged in to this URL: {user_config.logged_in_url} \n"
+                "Please log in again."
             )
-        return config.logged_in_url
+        return project_config
 
     if get_pat_for_authentication():
-        return desired_url or cli_settings.DIVBASE_API_URL
+        # if a user has a PAT, we will assume the PAT is for the correct URL
+        return project_config
 
     raise AuthenticationError("You are not logged in. Please log in with 'divbase-cli auth login [EMAIL]'.")
 
@@ -54,22 +65,6 @@ def resolve_url_for_non_project_specific_commands() -> str:
     raise AuthenticationError("You are not logged in. Please log in with 'divbase-cli auth login [EMAIL]'.")
 
 
-def resolve_project(project_name: str | None) -> ProjectConfig:
-    """
-    Helper function to resolve the project to use for a CLI command.
-    Falls back to the default project set in the user config if not explicitly provided.
-
-    Once the project is resolved a ProjectConfig object is returned,
-    which contains the name and API URL of the project.
-    """
-    config = load_user_config()
-    if not project_name:
-        project_name = config.default_project
-    if not project_name:
-        raise ProjectNameNotSpecifiedError()
-    return config.project_info(project_name)
-
-
 def resolve_download_dir(download_dir: str | None) -> Path:
     """
     Helper function to resolve the download directory to use for a CLI command involving downloading files.

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/display_task_history.py

@@ -1,6 +1,4 @@
 import logging
-from datetime import datetime
-from zoneinfo import ZoneInfo
 
 from rich.console import Console
 from rich.table import Table
@@ -12,6 +10,7 @@ from divbase_lib.api_schemas.task_history import (
     SampleMetadataQueryTaskResult,
     TaskHistoryResult,
 )
+from divbase_lib.utils import format_datetime_for_cli
 
 logger = logging.getLogger(__name__)
 
@@ -53,7 +52,7 @@ class TaskHistoryDisplayManager:
     def print_task_history(self) -> None:
         """Display the task history fetched from the results backend in a formatted table."""
 
-        sorted_tasks = sorted(self.task_items, key=lambda x: x.created_at or "", reverse=True)
+        sorted_tasks = sorted(self.task_items, key=lambda x: x.created_at, reverse=True)
         display_limit = self.display_limit
         limited_tasks = sorted_tasks[:display_limit]
 
@@ -72,16 +71,16 @@ class TaskHistoryDisplayManager:
                 colour = self.STATE_COLOURS.get(state, "white")
                 state_with_colour = f"[{colour}]{state}[/{colour}]"
 
-            submitter = task.submitter_email or "Unknown"
+            submitter = task.submitter_email
             result = self._format_result(task, state)
 
             table.add_row(
                 submitter,
                 str(task.id),
                 state_with_colour,
-                self._to_cet(task.created_at),
-                self._to_cet(task.started_at),
-                str(task.runtime if task.runtime is not None else "N/A"),
+                format_datetime_for_cli(task.created_at),
+                format_datetime_for_cli(task.started_at) if task.started_at else "N/A",
+                f"{task.runtime:.2f}" if task.runtime is not None else "N/A",
                 result,
             )
 
@@ -91,7 +90,7 @@ class TaskHistoryDisplayManager:
             console = Console()
             console.print(table)
 
-    def _create_task_history_table(self):
+    def _create_task_history_table(self) -> Table:
         """
         Use the Rich library to initiate a table for displaying task history.
         """
@@ -119,7 +118,7 @@ class TaskHistoryDisplayManager:
         table.add_column("Result", style="white", width=35, overflow="fold")
         return table
 
-    def _format_result(self, task, state):
+    def _format_result(self, task: TaskHistoryResult, state: str) -> str:
         """
         Format the result message based on the task state and type.
         """
@@ -156,7 +155,7 @@ class TaskHistoryDisplayManager:
 
         elif isinstance(task.result, DimensionUpdateTaskResult):
             result_message = (
-                f"VCF file dimensions index added or updated:\n  {task.result.VCF_files_added}\n"
+                f"VCF file dimensions cache added or updated:\n  {task.result.VCF_files_added}\n"
                 f"VCF files skipped by this job (previous DivBase-generated result VCFs):\n  {task.result.VCF_files_skipped}\n"
                 f"VCF files that have been deleted from the project and now are dropped from the index:\n  {task.result.VCF_files_deleted}"
             )
@@ -182,16 +181,3 @@ class TaskHistoryDisplayManager:
         if self.format_output_as_tsv:
             return text
         return f"[{colour}]{text}[/{colour}]"
-
-    def _to_cet(self, timestamp_str):
-        """
-        Convert a UTC timestamp string in '%Y-%m-%d %H:%M:%S UTC' format to CET.
-        """
-        if not timestamp_str or timestamp_str == "N/A":
-            return "N/A"
-        try:
-            dt = datetime.strptime(timestamp_str, "%Y-%m-%d %H:%M:%S %Z")
-            cet_dt = dt.astimezone(ZoneInfo("Europe/Stockholm"))
-            return cet_dt.strftime("%Y-%m-%d %H:%M:%S %Z")
-        except Exception:
-            return timestamp_str

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/services/s3_files.py

@@ -267,7 +267,7 @@ def download_files_command(
     else:
         # parse raw file inputs to see if any specific version ids were provided using format:
         # file_name:version_id (not possible when using project_version)
-        json_data = []
+        json_data: list[dict[str, str | None]] = []
         for file_input in raw_files_input:
             if ":" in file_input:
                 name, version_id = file_input.split(sep=":", maxsplit=1)

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/user_auth.py

@@ -18,7 +18,6 @@ import os
 import time
 import warnings
 from dataclasses import dataclass
-from datetime import datetime
 from json import JSONDecodeError
 from pathlib import Path
 from typing import Any
@@ -34,9 +33,10 @@ from divbase_cli import __version__ as cli_version
 from divbase_cli.cli_config import cli_settings
 from divbase_cli.cli_exceptions import AuthenticationError, DivBaseAPIConnectionError, DivBaseAPIError
 from divbase_cli.retries import retry_only_on_retryable_divbase_api_errors
-from divbase_cli.user_config import load_user_config
+from divbase_cli.user_config import UserConfig, load_user_config
 from divbase_lib.api_schemas.auth import LogoutRequest
 from divbase_lib.divbase_constants import CLI_VERSION_HEADER_KEY
+from divbase_lib.utils import format_unix_timestamp_for_cli
 
 LOGIN_AGAIN_MESSAGE = "Your session has expired. Please log in again with 'divbase-cli auth login [EMAIL]'."
 PERSONAL_ACCESS_TOKEN_EXPIRED_MESSAGE = (
@@ -113,15 +113,15 @@ class PATData:
 
     def is_pat_expired(self) -> bool:
         """Check if the PAT is expired"""
-        cutoff = time.time() + 10  # 10 second buffer to account for clock skew or time delay
-        return self.pat_expires_at is not None and self.pat_expires_at <= cutoff
+        if self.pat_expires_at is None:
+            return False
+        return self.pat_expires_at <= time.time() + 10  # 10 second buffer to account for clock skew or time delay
 
     def pat_expiry_formatted(self) -> str:
         """Returns the token's expiry time in a human readable format in user's current timezone."""
         if self.pat_expires_at is None:
             return "Never"
-        expiry = datetime.fromtimestamp(self.pat_expires_at).astimezone()
-        return expiry.strftime("%Y-%m-%d %H:%M:%S %Z")
+        return format_unix_timestamp_for_cli(unix_timestamp=self.pat_expires_at)
 
 
 def delete_stored_pat(pat_path: Path = cli_settings.PATS_FALLBACK_PATH) -> None:
@@ -131,7 +131,7 @@ def delete_stored_pat(pat_path: Path = cli_settings.PATS_FALLBACK_PATH) -> None:
     pat_path.unlink(missing_ok=True)
 
 
-def check_existing_session(divbase_url: str, config) -> int | None:
+def check_existing_session(divbase_url: str, config: UserConfig) -> int | None:
     """
     Check if a user is already logged in to DivBase.
     Used to prevent unnecessary multiple logins.

{divbase_cli-0.1.0a12 → divbase_cli-0.1.0a15}/src/divbase_cli/user_config.py

@@ -128,7 +128,7 @@ class UserConfig:
         for project in self.projects:
             if project.name == name:
                 return project
-        raise ProjectNotInConfigError(config_path=self.config_path, project_name=name)
+        raise ProjectNotInConfigError(project_name=name)
 
     def set_login_status(self, url: str | None, email: str | None) -> None:
         """

divbase_cli-0.1.0a12/src/divbase_cli/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.1.0a12"