dds-cli 2.13.0__tar.gz → 2.14.0__tar.gz

{dds_cli-2.13.0 → dds_cli-2.14.0}/PKG-INFO

@@ -1,17 +1,16 @@
 Metadata-Version: 2.4
 Name: dds_cli
-Version: 2.13.0
+Version: 2.14.0
 Summary: A command line tool to manage data and projects in the SciLifeLab Data Delivery System.
 Home-page: https://github.com/ScilifelabDataCentre/dds_cli
 Author: SciLifeLab Data Centre
 License: MIT
 Classifier: Development Status :: 4 - Beta
 Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: boto3==1.24.73
@@ -23,17 +22,17 @@ Requires-Dist: immutabledict==2.2.1
 Requires-Dist: jwcrypto==1.5.6
 Requires-Dist: prettytable==3.7.0
 Requires-Dist: prompt-toolkit==3.0.40
-Requires-Dist: PyNaCl==1.5.0
+Requires-Dist: PyNaCl==1.6.2
 Requires-Dist: pytz==2022.2.1
 Requires-Dist: PyYAML==6.0.2
-Requires-Dist: questionary==1.10.0
+Requires-Dist: questionary==2.1.1
 Requires-Dist: requests==2.32.4
 Requires-Dist: rich==13.6.0
 Requires-Dist: rich-click==1.5.2
 Requires-Dist: simplejson==3.17.6
 Requires-Dist: tzlocal==4.2
 Requires-Dist: zstandard==0.23.0
-Requires-Dist: textual==2.1.2
+Requires-Dist: legacy-cgi==2.6.1; python_version >= "3.13"
 Dynamic: author
 Dynamic: classifier
 Dynamic: description

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/__main__.py

@@ -8,61 +8,60 @@
 import concurrent.futures
 import itertools
 import logging
+import pathlib
 import sys
 
 # Installed
-import pathlib
-import rich_click as click
+
 import click_pathlib
+import questionary
 import rich
 import rich.logging
 import rich.markup
 import rich.progress
 import rich.prompt
-import questionary
+import rich_click as click
 
 # Own modules
 import dds_cli
 import dds_cli.account_manager
-import dds_cli.unit_manager
-import dds_cli.motd_manager
-import dds_cli.superadmin_helper
+import dds_cli.auth
 import dds_cli.data_getter
 import dds_cli.data_lister
 import dds_cli.data_putter
 import dds_cli.data_remover
 import dds_cli.directory
+import dds_cli.message_helper
+import dds_cli.motd_manager
 import dds_cli.project_creator
-import dds_cli.auth
-import dds_cli.project_status
 import dds_cli.project_info
+import dds_cli.project_status
+import dds_cli.superadmin_helper
+import dds_cli.unit_manager
 import dds_cli.user
 import dds_cli.utils
-import dds_cli.message_helper
 from dds_cli.options import (
+    break_on_fail_flag,
     destination_option,
     email_arg,
     email_option,
     folder_option,
+    json_flag,
+    nomail_flag,
     num_threads_option,
     project_option,
+    silent_flag,
+    size_flag,
     sort_projects_option,
     source_option,
     source_path_file_option,
     token_path_option,
-    username_option,
-    break_on_fail_flag,
-    json_flag,
-    nomail_flag,
-    silent_flag,
-    size_flag,
     tree_flag,
     usage_flag,
+    username_option,
     users_flag,
 )
 
-# import dds_cli.dds_gui.app
-
 ####################################################################################################
 # START LOGGING CONFIG ###################################################### START LOGGING CONFIG #
 ####################################################################################################
@@ -209,21 +208,6 @@ def dds_main(click_ctx, verbose, force_no_log, log_file, no_prompt, token_path):
                 click_ctx.obj.update({"DEFAULT_LOG": False})
 
 
-### GUI COMMAND ###
-
-# TODO: Should totp be passed to the gui?
-
-
-# @dds_main.command(name="gui")
-# @click.pass_obj
-# def gui(click_ctx):
-#     """Start the DDS GUI."""
-#     gui_app = dds_cli.dds_gui.app.DDSApp(token_path=click_ctx.get("TOKEN_PATH"))
-#     gui_app.title = "SciLifeLab Data Delivery System"
-#     gui_app.sub_title = "CLI Version: " + dds_cli.__version__
-#     gui_app.run()
-
-
 # ************************************************************************************************ #
 # MAIN DDS COMMANDS ************************************************************ MAIN DDS COMMANDS #
 # ************************************************************************************************ #
@@ -383,6 +367,7 @@ def list_projects_and_contents(
         dds_cli.exceptions.AuthenticationError,
         dds_cli.exceptions.ApiResponseError,
         dds_cli.exceptions.ApiRequestError,
+        dds_cli.exceptions.DDSCLIException,
     ) as err:
         LOG.error(err)
         sys.exit(1)
@@ -544,13 +529,14 @@ def configure():
             "Which method would you like to use?", choices=["Email", "Authenticator App", "Cancel"]
         ).ask()
 
+        auth_method: str | None = None  # type hint, initialized
         if auth_method_choice == "Cancel":
             LOG.info("Two-factor authentication method not configured.")
             sys.exit(0)
         elif auth_method_choice == "Authenticator App":
-            auth_method: str = "totp"
+            auth_method = "totp"
         elif auth_method_choice == "Email":
-            auth_method: str = "hotp"
+            auth_method = "hotp"
 
         with dds_cli.auth.Auth(authenticate=True, force_renew_token=False) as authenticator:
             authenticator.twofactor(auth_method=auth_method)
@@ -885,6 +871,8 @@ def activate_user(click_ctx, email):
     Super Admins: All users
     Unit Admins: Unit Admins / Personnel
     """
+    proceed_activation = False  # default assignment
+
     if click_ctx.get("NO_PROMPT", False):
         pass
     else:
@@ -925,6 +913,8 @@ def deactivate_user(click_ctx, email):
     Super Admins: All users
     Unit Admins: Unit Admins / Personnel
     """
+    proceed_deactivation = False  # default assignment
+
     if click_ctx.get("NO_PROMPT", False):
         pass
     else:
@@ -1166,6 +1156,13 @@ def display_project_status(click_ctx, project, show_history):
         sys.exit(1)
 
 
+def validate_deadline(_ctx, _param, value):
+    """Validate that the deadline is a positive number of days between 1 and 90."""
+    if value is not None and value not in range(1, 91):
+        raise click.BadParameter("Deadline must be a positive number of days between 1 and 90.")
+    return value
+
+
 # -- dds project status release -- #
 @project_status.command(name="release", no_args_is_help=True)
 # Options
@@ -1174,7 +1171,8 @@ def display_project_status(click_ctx, project, show_history):
     "--deadline",
     required=False,
     type=int,
-    help="Deadline in days when releasing a project.",
+    callback=validate_deadline,
+    help="Deadline in days when releasing a project. Must be a positive number of days (maximum 90 days).",
 )
 @nomail_flag(help_message="Do not send e-mail notifications regarding project updates.")
 @click.pass_obj
@@ -1315,7 +1313,8 @@ def delete_project(click_ctx, project: str):
     "--new-deadline",
     required=False,
     type=int,
-    help="Number of days to extend the deadline.",
+    callback=validate_deadline,
+    help="Number of days to extend the deadline. Must be a positive number of days (maximum 90 days).",
 )
 @click.pass_obj
 def extend_deadline(click_ctx, project: str, new_deadline: int):
@@ -1739,6 +1738,7 @@ def put_data(
         dds_cli.exceptions.ApiRequestError,
         dds_cli.exceptions.NoKeyError,
         dds_cli.exceptions.NoDataError,
+        dds_cli.exceptions.DDSCLIException,
     ) as err:
         LOG.error(err)
         sys.exit(1)
@@ -2269,6 +2269,7 @@ def get_stats(click_ctx):
         dds_cli.exceptions.AuthenticationError,
         dds_cli.exceptions.ApiResponseError,
         dds_cli.exceptions.ApiRequestError,
+        dds_cli.exceptions.DDSCLIException,
     ) as err:
         LOG.error(err)
         sys.exit(1)

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/custom_decorators.py

@@ -154,6 +154,8 @@ def removal_spinner(func):
             SpinnerColumn(spinner_name="dots12", style="white"),
             console=dds_cli.utils.stderr_console,
         ) as progress:
+
+            description: str | None = None  # type hint, initialized
             # Determine spinner text
             if func.__name__ == "remove_all":
                 description = f"Removing all files in project {self.project}"

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/data_getter.py

@@ -101,8 +101,17 @@ class DataGetter(base.DDSBaseClass):
 
             if not self.filehandler.data:
                 if self.temporary_directory and self.temporary_directory.is_dir():
-                    LOG.debug("Deleting temporary folder '%s'.", self.temporary_directory)
-                    dds_cli.utils.delete_folder(self.temporary_directory)
+                    LOG.debug("Deleting staging directory '%s'.", self.temporary_directory)
+                    try:
+                        dds_cli.utils.delete_folder(self.temporary_directory)
+                    except OSError as err:
+                        # Folder deletion may fail if log file is still being written to
+                        # This is not critical - the important thing is to show the error message
+                        LOG.error(
+                            "Could not delete staging directory %s: %s",
+                            self.temporary_directory,
+                            err,
+                        )
                 raise dds_cli.exceptions.DownloadError("No files to download.")
 
             self.status = self.filehandler.create_download_status_dict()

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/data_lister.py

@@ -5,26 +5,24 @@
 ###############################################################################
 
 # Standard library
-from dataclasses import dataclass
-import logging
-from typing import Tuple, Union, List
 import datetime
+import logging
 import pathlib
+from dataclasses import dataclass
+from typing import List, Tuple, Union
 
 # Installed
-from rich.padding import Padding
+import pytz
+import tzlocal
 from rich.markup import escape
+from rich.padding import Padding
 from rich.table import Table
 from rich.tree import Tree
-import pytz
-import tzlocal
 
 # Own modules
-from dds_cli import base
-from dds_cli import exceptions
-import dds_cli.utils
-from dds_cli import DDSEndpoint
+from dds_cli import DDSEndpoint, base, exceptions
 from dds_cli import text_handler as th
+import dds_cli.utils
 
 
 ###############################################################################
@@ -268,7 +266,11 @@ class DataLister(base.DDSBaseClass):
             # Get max length of size string
             max_size = max(
                 (
-                    len(x["size"].split(" ")[0])
+                    len(
+                        dds_cli.utils.format_api_response(
+                            response=x["size"], key="Size", binary=self.binary
+                        ).split(" ", maxsplit=1)[0]
+                    )
                     for x in sorted_files_folders
                     if show_size and "size" in x
                 ),
@@ -280,9 +282,12 @@ class DataLister(base.DDSBaseClass):
                 is_folder = item.pop("folder")
 
                 if not is_folder:
-                    tree.subtrees.append(
-                        (escape(item["name"]), item.get("size") if show_size else None)
-                    )
+                    formatted_size = None
+                    if show_size and "size" in item:
+                        formatted_size = dds_cli.utils.format_api_response(
+                            response=item["size"], key="Size", binary=self.binary
+                        )
+                    tree.subtrees.append((escape(item["name"]), formatted_size))
                 else:
                     subtree, _max_string, _max_size = __construct_file_tree(
                         pathlib.Path(folder, item["name"]).as_posix() if folder else item["name"],
@@ -348,15 +353,7 @@ class DataLister(base.DDSBaseClass):
                             string_len=len(node[0]),
                             max_string_len=max_str - 4 * depth,
                         )
-                        line += f"{tab}{node[1].split()[0]}"
-
-                        # Define space between number and size format
-                        tabs_bf_format = th.TextHandler.format_tabs(
-                            string_len=len(node[1].split()[1]),
-                            max_string_len=max_size,
-                            tab_len=2,
-                        )
-                        line += f"{tabs_bf_format}{node[1].split()[1]}"
+                        line += f"{tab}{node[1].split()[0]} {node[1].split()[1]}"
                     tree.add(line)
 
             return tree, tree_length

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/data_putter.py

@@ -7,30 +7,28 @@
 # Standard library
 import concurrent.futures
 import itertools
+import json
 import logging
 import pathlib
-import json
 
 # Installed
 import boto3
 import botocore
 from rich.markup import escape
-from rich.progress import Progress, SpinnerColumn, BarColumn
+from rich.progress import BarColumn, Progress, SpinnerColumn
 
 # Own modules
-from dds_cli import base
-from dds_cli import exceptions
+import dds_cli
+import dds_cli.directory
+import dds_cli.utils
+from dds_cli import DDSEndpoint, base
 from dds_cli import data_remover as dr
-from dds_cli import DDSEndpoint
+from dds_cli import exceptions
 from dds_cli import file_encryptor as fe
 from dds_cli import file_handler_local as fhl
 from dds_cli import status
 from dds_cli import text_handler as txt
-from dds_cli.custom_decorators import verify_proceed, update_status, subpath_required
-
-import dds_cli
-import dds_cli.directory
-import dds_cli.utils
+from dds_cli.custom_decorators import subpath_required, update_status, verify_proceed
 
 ###############################################################################
 # START LOGGING CONFIG ################################# START LOGGING CONFIG #
@@ -274,7 +272,16 @@ class DataPutter(base.DDSBaseClass):
         if not self.filehandler.data:
             if self.temporary_directory and self.temporary_directory.is_dir():
                 LOG.debug("Deleting temporary folder %s.", self.temporary_directory)
-                dds_cli.utils.delete_folder(self.temporary_directory)
+                try:
+                    dds_cli.utils.delete_folder(self.temporary_directory)
+                except OSError as err:
+                    # Folder deletion may fail if log file is still being written to
+                    # This is not critical - the important thing is to show the error message
+                    LOG.debug(
+                        "Could not delete staging directory %s: %s",
+                        self.temporary_directory,
+                        err,
+                    )
             raise exceptions.UploadError(
                 "The specified data has already been uploaded. If you wish to redo the upload, "
                 "use the '--overwrite' flag. Please use with caution as previously uploaded data "

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/file_compressor.py

@@ -104,8 +104,7 @@ class Compressor:
                     #     if not chunk:
                     #         break
                     #     yield
-                    for chunk in iter(lambda: compressor.read(chunk_size), b""):
-                        yield chunk
+                    yield from iter(lambda: compressor.read(chunk_size), b"")
         except Exception as err:  # pylint: disable=broad-exception-caught
             LOG.warning(str(err))
         else:

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/file_handler_local.py

@@ -92,8 +92,7 @@ class LocalFileHandler(fh.FileHandler):
 
         try:
             with file.open(mode="rb") as infile:
-                for chunk in iter(lambda: infile.read(chunk_size), b""):
-                    yield chunk
+                yield from iter(lambda: infile.read(chunk_size), b"")
         except OSError as err:
             LOG.warning(str(err))
 
@@ -278,11 +277,10 @@ class LocalFileHandler(fh.FileHandler):
             # LOG.debug(
             #     "Test: %s",
             # )
-            for chunk in fc.Compressor.compress_file(file=file_info["path_raw"]):
-                # LOG.debug("Chunk type: %s", type(chunk))
-                # checksum.update(chunk)
-                # break
-                yield chunk
+            yield from fc.Compressor.compress_file(file=file_info["path_raw"])
+            # LOG.debug("Chunk type: %s", type(chunk))
+            # checksum.update(chunk)
+            # break
 
         # LOG.debug("Streaming file finished.")
         # Add checksum to file info

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/project_status.py

@@ -102,6 +102,9 @@ class ProjectStatusManager(base.DDSBaseClass):
     def update_status(self, new_status, deadline=None, is_aborted=False, no_mail=False):
         """Update project status"""
 
+        if deadline is not None and deadline <= 0:
+            raise exceptions.DDSCLIException("Deadline must be a positive number of days.")
+
         extra_params = {"new_status": new_status, "send_email": not no_mail}
         if deadline:
             extra_params["deadline"] = deadline
@@ -219,7 +222,7 @@ class ProjectStatusManager(base.DDSBaseClass):
         dds_cli.utils.console.print(print_info)
 
         # If it wasnt provided during the command click, ask the user for the new deadline
-        if not new_deadline:
+        if new_deadline is None:
             # Question number of days to extend the deadline
             prompt_question = (
                 "How many days would you like to extend the project deadline with? "
@@ -227,6 +230,12 @@ class ProjectStatusManager(base.DDSBaseClass):
             )
             new_deadline = rich.prompt.IntPrompt.ask(prompt_question, default=default_unit_days)
 
+        # Validate that the deadline extension is positive
+        if new_deadline <= 0:
+            raise exceptions.DDSCLIException(
+                "Deadline extension must be a positive number of days."
+            )
+
         # Confirm operation question
         new_deadline_date = parse(current_deadline) + datetime.timedelta(days=new_deadline)
         new_deadline_date = new_deadline_date.strftime("%a,%d %b %Y %H:%M:%S")

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli/version.py

@@ -2,4 +2,4 @@
 
 # Do not change bump the major version unless absolutely necessary - makes incompatible with API
 # If mid or minor version reaches 9, continue to 10, 11 etc.
-__version__ = "2.13.0"
+__version__ = "2.14.0"

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli.egg-info/PKG-INFO

@@ -1,17 +1,16 @@
 Metadata-Version: 2.4
 Name: dds_cli
-Version: 2.13.0
+Version: 2.14.0
 Summary: A command line tool to manage data and projects in the SciLifeLab Data Delivery System.
 Home-page: https://github.com/ScilifelabDataCentre/dds_cli
 Author: SciLifeLab Data Centre
 License: MIT
 Classifier: Development Status :: 4 - Beta
 Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: boto3==1.24.73
@@ -23,17 +22,17 @@ Requires-Dist: immutabledict==2.2.1
 Requires-Dist: jwcrypto==1.5.6
 Requires-Dist: prettytable==3.7.0
 Requires-Dist: prompt-toolkit==3.0.40
-Requires-Dist: PyNaCl==1.5.0
+Requires-Dist: PyNaCl==1.6.2
 Requires-Dist: pytz==2022.2.1
 Requires-Dist: PyYAML==6.0.2
-Requires-Dist: questionary==1.10.0
+Requires-Dist: questionary==2.1.1
 Requires-Dist: requests==2.32.4
 Requires-Dist: rich==13.6.0
 Requires-Dist: rich-click==1.5.2
 Requires-Dist: simplejson==3.17.6
 Requires-Dist: tzlocal==4.2
 Requires-Dist: zstandard==0.23.0
-Requires-Dist: textual==2.1.2
+Requires-Dist: legacy-cgi==2.6.1; python_version >= "3.13"
 Dynamic: author
 Dynamic: classifier
 Dynamic: description

dds_cli-2.14.0/dds_cli.egg-info/SOURCES.txt

@@ -0,0 +1,62 @@
+LICENSE
+README.md
+pyproject.toml
+setup.py
+dds_cli/__init__.py
+dds_cli/__main__.py
+dds_cli/account_manager.py
+dds_cli/auth.py
+dds_cli/base.py
+dds_cli/constants.py
+dds_cli/custom_decorators.py
+dds_cli/data_getter.py
+dds_cli/data_lister.py
+dds_cli/data_putter.py
+dds_cli/data_remover.py
+dds_cli/directory.py
+dds_cli/exceptions.py
+dds_cli/file_compressor.py
+dds_cli/file_encryptor.py
+dds_cli/file_handler.py
+dds_cli/file_handler_local.py
+dds_cli/file_handler_remote.py
+dds_cli/message_helper.py
+dds_cli/motd_manager.py
+dds_cli/options.py
+dds_cli/project_creator.py
+dds_cli/project_info.py
+dds_cli/project_status.py
+dds_cli/s3_connector.py
+dds_cli/status.py
+dds_cli/superadmin_helper.py
+dds_cli/text_handler.py
+dds_cli/timestamp.py
+dds_cli/unit_manager.py
+dds_cli/user.py
+dds_cli/utils.py
+dds_cli/version.py
+dds_cli.egg-info/PKG-INFO
+dds_cli.egg-info/SOURCES.txt
+dds_cli.egg-info/dependency_links.txt
+dds_cli.egg-info/entry_points.txt
+dds_cli.egg-info/not-zip-safe
+dds_cli.egg-info/requires.txt
+dds_cli.egg-info/top_level.txt
+tests/__init__.py
+tests/test_account_manager.py
+tests/test_auth.py
+tests/test_base.py
+tests/test_commands.py
+tests/test_data_getter.py
+tests/test_data_putter.py
+tests/test_data_remover.py
+tests/test_decorators.py
+tests/test_file_compressor.py
+tests/test_file_encryptor.py
+tests/test_file_handler_local.py
+tests/test_motd_manager.py
+tests/test_project_status.py
+tests/test_s3_connector.py
+tests/test_superadmin_helper.py
+tests/test_user.py
+tests/test_utils.py

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli.egg-info/requires.txt

@@ -7,14 +7,16 @@ immutabledict==2.2.1
 jwcrypto==1.5.6
 prettytable==3.7.0
 prompt-toolkit==3.0.40
-PyNaCl==1.5.0
+PyNaCl==1.6.2
 pytz==2022.2.1
 PyYAML==6.0.2
-questionary==1.10.0
+questionary==2.1.1
 requests==2.32.4
 rich==13.6.0
 rich-click==1.5.2
 simplejson==3.17.6
 tzlocal==4.2
 zstandard==0.23.0
-textual==2.1.2
+
+[:python_version >= "3.13"]
+legacy-cgi==2.6.1

{dds_cli-2.13.0 → dds_cli-2.14.0}/dds_cli.egg-info/top_level.txt

@@ -1,3 +1,2 @@
 dds_cli
-gui_build
 tests

{dds_cli-2.13.0 → dds_cli-2.14.0}/setup.py

@@ -24,11 +24,10 @@ setup(
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: MIT License",
-        "Programming Language :: Python :: 3.8",
-        "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
         "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
     ],
     url="https://github.com/ScilifelabDataCentre/dds_cli",
     author="SciLifeLab Data Centre",