dds-cli 0.0__tar.gz

dds_cli-0.0/LICENSE

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+MIT License
+
+Copyright (c) 2019 SciLifeLab Data Centre
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

dds_cli-0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: dds_cli
+Version: 0.0
+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
+Author-email: datacentre@scilifelab.se
+License: MIT
+Keywords: data delivery research science scilifelab
+Platform: UNKNOWN
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.7
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Requires-Python: >=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# SciLifeLab Data Delivery System - Command line interface
+
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/dds_cli/)
+
+> **A command line tool `dds` to manage data and projects in the SciLifeLab Data Delivery Service.**
+
+This will be used for data delivery within larger projects and/or projects resulting in the production of large amounts of data, for example next-generation sequencing data and imaging.
+
+This tool is written and maintained by the [SciLifeLab Data Centre](https://www.scilifelab.se/data).
+
+## Table of contents
+
+* [Installation](#installation)
+* [Overview of commands](#overview-of-commands)
+
+## Installation
+
+### Python Package Index
+
+> :warning: Not available yet - coming soon after first release :warning:
+
+The `dds-cli` package can be installed from [PyPI](https://pypi.python.org/pypi/dds_cli/) using pip as follows:
+
+```bash
+pip install dds_cli
+```
+
+### Development version
+
+If you would like the latest development version of tools, the command is:
+
+```bash
+pip install --upgrade --force-reinstall git+https://github.com/ScilifelabDataCentre/dds_cli.git@dev
+```
+
+If you intend to make edits to the code, first make a fork of the repository and then clone it locally.
+Go to the cloned directory and install with pip (also installs development requirements):
+
+```bash
+pip install --upgrade -r requirements-dev.txt -e .
+```
+
+## Overview of commands
+
+Once installed you can use the command `dds` in a terminal session. This has the following subcommands:
+
+* `get` - Download specified files from the cloud and restore the original format.
+* `ls` - List the projects and the files within projects.
+* `put` - Process and upload specified files to the cloud.
+* `rm` - Delete files within a project.
+
+

dds_cli-0.0/README.md

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+# SciLifeLab Data Delivery System - Command line interface
+
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![install with PyPI](https://img.shields.io/badge/install%20with-PyPI-blue.svg)](https://pypi.org/project/dds_cli/)
+
+> **A command line tool `dds` to manage data and projects in the SciLifeLab Data Delivery Service.**
+
+This will be used for data delivery within larger projects and/or projects resulting in the production of large amounts of data, for example next-generation sequencing data and imaging.
+
+This tool is written and maintained by the [SciLifeLab Data Centre](https://www.scilifelab.se/data).
+
+## Table of contents
+
+* [Installation](#installation)
+* [Overview of commands](#overview-of-commands)
+
+## Installation
+
+### Python Package Index
+
+> :warning: Not available yet - coming soon after first release :warning:
+
+The `dds-cli` package can be installed from [PyPI](https://pypi.python.org/pypi/dds_cli/) using pip as follows:
+
+```bash
+pip install dds_cli
+```
+
+### Development version
+
+If you would like the latest development version of tools, the command is:
+
+```bash
+pip install --upgrade --force-reinstall git+https://github.com/ScilifelabDataCentre/dds_cli.git@dev
+```
+
+If you intend to make edits to the code, first make a fork of the repository and then clone it locally.
+Go to the cloned directory and install with pip (also installs development requirements):
+
+```bash
+pip install --upgrade -r requirements-dev.txt -e .
+```
+
+## Overview of commands
+
+Once installed you can use the command `dds` in a terminal session. This has the following subcommands:
+
+* `get` - Download specified files from the cloud and restore the original format.
+* `ls` - List the projects and the files within projects.
+* `put` - Process and upload specified files to the cloud.
+* `rm` - Delete files within a project.

dds_cli-0.0/dds_cli/__init__.py

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+"""DDS CLI."""
+
+import datetime
+import os
+import pathlib
+import pkg_resources
+import prompt_toolkit
+import rich.console
+
+
+###############################################################################
+# PROJECT SPEC ################################################# PROJECT SPEC #
+###############################################################################
+
+__title__ = "Data Delivery System"
+__version__ = pkg_resources.get_distribution("dds_cli").version
+__url__ = "https://www.scilifelab.se/data"
+__author__ = "SciLifeLab Data Centre"
+__author_email__ = "datacentre@scilifelab.se"
+__license__ = "MIT"
+__all__ = [
+    "DDS_METHODS",
+    "DDS_DIR_REQUIRED_METHODS",
+    "DDS_KEYS_REQUIRED_METHODS",
+    "DDSEndpoint",
+    "FileSegment",
+    "dds_questionary_styles",
+]
+
+
+###############################################################################
+# VARIABLES ####################################################### VARIABLES #
+###############################################################################
+
+# Keep track of all allowed methods
+DDS_METHODS = ["put", "get", "ls", "rm", "create", "add", "delete"]
+
+# Methods to which a directory created by DDS
+DDS_DIR_REQUIRED_METHODS = ["put", "get"]
+
+# Methods which require a project ID
+DDS_KEYS_REQUIRED_METHODS = ["put", "get"]
+
+# Token related variables
+TOKEN_FILE = pathlib.Path(os.path.expanduser("~/.dds_cli_token"))
+TOKEN_MAX_AGE = datetime.timedelta(days=2)
+TOKEN_WARNING_AGE = datetime.timedelta(days=1, hours=18)
+
+
+###############################################################################
+# CLASSES ########################################################### CLASSES #
+###############################################################################
+
+
+class DDSEndpoint:
+    """Defines all DDS urls."""
+
+    # Base url - local or remote
+    BASE_ENDPOINT_LOCAL = "http://127.0.0.1:5000/api/v1"
+    BASE_ENDPOINT_REMOTE = "https://dds.dckube.scilifelab.se/api/v1"
+    BASE_ENDPOINT = (
+        BASE_ENDPOINT_LOCAL if os.getenv("DDS_CLI_ENV") == "development" else BASE_ENDPOINT_REMOTE
+    )
+
+    # User management
+    USER_ADD = BASE_ENDPOINT + "/user/add"
+    USER_DELETE = BASE_ENDPOINT + "/user/delete"
+    USER_DELETE_SELF = BASE_ENDPOINT + "/user/delete_self"
+    REVOKE_PROJECT_ACCESS = BASE_ENDPOINT + "/user/access/revoke"
+    DISPLAY_USER_INFO = BASE_ENDPOINT + "/user/info"
+    USER_ACTIVATION = BASE_ENDPOINT + "/user/activation"
+
+    # Authentication - user and project
+    ENCRYPTED_TOKEN = BASE_ENDPOINT + "/user/encrypted_token"
+    SECOND_FACTOR = BASE_ENDPOINT + "/user/second_factor"
+
+    # S3Connector keys
+    S3KEYS = BASE_ENDPOINT + "/s3/proj"
+
+    # File related urls
+    FILE_NEW = BASE_ENDPOINT + "/file/new"
+    FILE_MATCH = BASE_ENDPOINT + "/file/match"
+    FILE_INFO = BASE_ENDPOINT + "/file/info"
+    FILE_INFO_ALL = BASE_ENDPOINT + "/file/all/info"
+    FILE_UPDATE = BASE_ENDPOINT + "/file/update"
+
+    # Project specific urls
+
+    # Listing urls
+    LIST_PROJ = BASE_ENDPOINT + "/proj/list"
+    LIST_FILES = BASE_ENDPOINT + "/files/list"
+    LIST_PROJ_USERS = BASE_ENDPOINT + "/proj/users"
+
+    # Deleting urls
+    REMOVE_PROJ_CONT = BASE_ENDPOINT + "/proj/rm"
+    REMOVE_FILE = BASE_ENDPOINT + "/file/rm"
+    REMOVE_FOLDER = BASE_ENDPOINT + "/file/rmdir"
+
+    # Encryption keys
+    PROJ_PUBLIC = BASE_ENDPOINT + "/proj/public"
+    PROJ_PRIVATE = BASE_ENDPOINT + "/proj/private"
+
+    # Display facility usage
+    USAGE = BASE_ENDPOINT + "/usage"
+    INVOICE = BASE_ENDPOINT + "/invoice"
+
+    # Project creation urls
+    CREATE_PROJ = BASE_ENDPOINT + "/proj/create"
+
+    # Project status updation
+    UPDATE_PROJ_STATUS = BASE_ENDPOINT + "/proj/status"
+
+    TIMEOUT = 5
+
+
+class FileSegment:
+    """Defines information on signatures, file chunks, etc."""
+
+    DDS_SIGNATURE = b"DelSys"
+    SEGMENT_SIZE_RAW = 65536  # Size of chunk to read from raw file
+    SEGMENT_SIZE_CIPHER = SEGMENT_SIZE_RAW + 16  # Size of chunk to read from encrypted file
+
+
+# Custom styles for questionary
+dds_questionary_styles = prompt_toolkit.styles.Style(
+    [
+        ("qmark", "fg:ansiblue bold"),  # token in front of the question
+        ("question", "bold"),  # question text
+        ("answer", "fg:ansigreen nobold bg:"),  # submitted answer text behind the question
+        ("pointer", "fg:ansiyellow bold"),  # pointer used in select and checkbox prompts
+        ("highlighted", "fg:ansiblue bold"),  # pointed-at choice in select and checkbox prompts
+        ("selected", "fg:ansiyellow noreverse bold"),  # style for a selected item of a checkbox
+        ("separator", "fg:ansiblack"),  # separator in lists
+        ("instruction", ""),  # user instructions for select, rawselect, checkbox
+        ("text", ""),  # plain text
+        ("disabled", "fg:gray italic"),  # disabled choices for select and checkbox prompts
+        ("choice-default", "fg:ansiblack"),
+        ("choice-default-changed", "fg:ansiyellow"),
+        ("choice-required", "fg:ansired"),
+    ]
+)
+
+# Determine if the user is on an old terminal without proper Unicode support
+dds_on_legacy_console = rich.console.detect_legacy_windows()