From cca0459443ff16d7e291f8c07cd647a88fe80f8b Mon Sep 17 00:00:00 2001 From: Aishling Cooke Date: Mon, 29 Jul 2024 13:49:52 +0100 Subject: [PATCH 01/37] DDS-2023: Add the testing page to the navigation links - Currently, the testing page does not appear in the navigation panel. This makes it hard to find and users often don't. --- docs/index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/index.rst b/docs/index.rst index 27bbf8f82..638712547 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -200,6 +200,7 @@ Command documentation and guide unit motd changelog + testing Indices and tables ================== From 2b57960ccc588b3cd7c6ac7bc385f02168238af6 Mon Sep 17 00:00:00 2001 From: Aishling Cooke Date: Mon, 29 Jul 2024 14:57:10 +0100 Subject: [PATCH 02/37] DDS-2023: Remove references to TestPyPi - The instructions as is do not work. Explain that incompatibilities can happen. - Add ID to installation.rst so can reference it. --- docs/installation.rst | 2 ++ docs/testing.rst | 21 +++++++++------------ 2 files changed, 11 insertions(+), 12 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index b7162ce49..fba24e22e 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -1,3 +1,5 @@ +.. _installation: + Installation guide #################### diff --git a/docs/testing.rst b/docs/testing.rst index ef9eabac0..b1c1acde3 100644 --- a/docs/testing.rst +++ b/docs/testing.rst @@ -26,8 +26,8 @@ This page will give you information on: If your testing account has the role "Researcher", you can skip this section. -* First and foremost, **no sensitive data** is allowed to be delivered within this test instance. -* In order to create projects, which is required in order to test the upload / download functionality: +* First and foremost, this is not a production instance and will get releases without warning. **No sensitive data** is allowed to be delivered within this instance. +* In order to create projects, which is required in order to test the upload / download functionality: * You must have the account role "Unit Admin" or "Unit Personnel" * Your unit must have at least two "Unit Admins" * When listing your projects you will see your projects, and yours only. However, in order to not create a large number of separate storage locations for testing purposes, the actual storage location is shared by all units in the test setup. In the production instance, there's always a separate storage location per SciLifeLab unit. @@ -61,20 +61,17 @@ This page will give you information on: .. _test-install: -3. How to install the test version of the CLI +3. How to install the CLI ================================================ -You need to install the test version of the CLI from TestPyPi. Run this command in the terminal. - -.. code-block:: bash - - pip install -i https://test.pypi.org/simple/ dds-cli +Install the CLI as described in the :ref:`installation guide`. .. note:: - - This is **not** the same command as shown in the installation guide. - - You can install the released version of the CLI by following the installation guide, however you will not have the latest version or any of the features that are currently being implemented. There may also be unexpected errors since the released CLI and the DDS test instance may not be completely compatible. + Rarely, backwards incompatible releases will break the integration between the CLI and the API. As we + release the web application to test during the development process, there can be small windows of time + where the production CLI is not compatible with the DDS instance deployed to test. + + These windows of time will be kept as small as possible and we will notify test users. .. _test-config: From 4333abebdc60ae8f154eba6a6a665084b903c687 Mon Sep 17 00:00:00 2001 From: Aishling Cooke Date: Mon, 29 Jul 2024 15:00:30 +0100 Subject: [PATCH 03/37] DDS-2023: Update SPRINTLOG.md --- SPRINTLOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index 4b6f52799..b678087fd 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -360,3 +360,7 @@ _Empty sprint_ # 2024-06-17 - 2024-06-28 - Update documentation to have correct executable name ([#702](https://github.com/ScilifelabDataCentre/dds_cli/pull/702)) + +# 2024-07-29 - 2024-08-09 + +- Improve docs related to the testing instance ([#705](https://github.com/ScilifelabDataCentre/dds_cli/pull/705)) From e6abf6c41f1e40951105b69ece0a774b43b9a8ae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?= Date: Wed, 28 Aug 2024 10:20:19 +0200 Subject: [PATCH 04/37] unpinned pyinstaller --- requirements-dev.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements-dev.txt b/requirements-dev.txt index 4dfa0e048..670a73ee2 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,7 +2,7 @@ black==24.1.1 Sphinx==5.0.2 sphinx-rtd-theme==1.0.0 sphinx-click==4.0.0 -pyinstaller==4.1 +pyinstaller # version not pinned due to latest used by release procedure pylint==2.17.3 sphinx-copybutton==0.5.1 sphinxcontrib-svg2pdfconverter==1.2.2 \ No newline at end of file From aea5486fd2baaa4f49f77a7f1d4b8c5473a719f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?= Date: Wed, 28 Aug 2024 10:45:27 +0200 Subject: [PATCH 05/37] sprintlog --- SPRINTLOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index b678087fd..45b5d7ed5 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -364,3 +364,7 @@ _Empty sprint_ # 2024-07-29 - 2024-08-09 - Improve docs related to the testing instance ([#705](https://github.com/ScilifelabDataCentre/dds_cli/pull/705)) + +# 2024-08-26 - 2024-09-06 + +- Remove pinned version in requirements-dev.txt to resolve CVE ([#706](https://github.com/ScilifelabDataCentre/dds_cli/pull/706)) From 9f90e67ec25162d06d725a00c3f8c6b656d5ba07 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?= Date: Wed, 28 Aug 2024 11:11:41 +0200 Subject: [PATCH 06/37] codeowners file --- .github/CODEOWNERS | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 .github/CODEOWNERS diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 000000000..466e9d4d1 --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,2 @@ +# Team Hermes are the owners of all files in this repository +* @ScilifelabDataCentre/teamhermes From ed4829e28f1af47fe54c0cd43189adcea2a908d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?= Date: Wed, 28 Aug 2024 11:18:26 +0200 Subject: [PATCH 07/37] sprintlog --- SPRINTLOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index b678087fd..485928355 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -364,3 +364,11 @@ _Empty sprint_ # 2024-07-29 - 2024-08-09 - Improve docs related to the testing instance ([#705](https://github.com/ScilifelabDataCentre/dds_cli/pull/705)) + +# 2024-08-12 - 2024-08-23 + +_Empty sprint_ + +# 2024-08-26 - 2024-09-06 + +- Add CODEOWNERS file in order to define Team Hermes as owners of all files in repository ([#707](https://github.com/ScilifelabDataCentre/dds_cli/pull/707)) From 89b5d06b20a51c1a8c49fe9333b3c3fc0270b441 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 10:53:38 +0200 Subject: [PATCH 08/37] Started process to bump python in client --- WINDOWS.md | 4 ++-- docs/installation.rst | 4 ++-- requirements.txt | 14 +++++++------- setup.py | 3 ++- 4 files changed, 13 insertions(+), 12 deletions(-) diff --git a/WINDOWS.md b/WINDOWS.md index e584b0e9e..af0ba4a19 100644 --- a/WINDOWS.md +++ b/WINDOWS.md @@ -1,6 +1,6 @@ # How to install the DDS CLI on Windows -## 1. Download and install Python > 3.7 +## 1. Download and install Python > 3.8 ### 1.1. Go to https://www.python.org/downloads/windows/ @@ -42,7 +42,7 @@ ![Powershell 1](docs/_static/windows/powershell_top-1.png) -> **Note:** Upon entering `python --version` the version of the previously installed Python distribution should be shown. If a version number < 3.7 is shown or Python is not found, please consult the :ref:`Troubleshooting` section below. +> **Note:** Upon entering `python --version` the version of the previously installed Python distribution should be shown. If a version number < 3.8 is shown or Python is not found, please consult the :ref:`Troubleshooting` section below. ### 2.3. Python ships with a helper program called **pip** to install additional packages. In the next step, this software should be upgraded to its current version. diff --git a/docs/installation.rst b/docs/installation.rst index fba24e22e..65022a53a 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -29,7 +29,7 @@ As mentioned above, you can install ``dds-cli`` from PyPI or via an executable. Install from **PyPI** ----------------------- -1. To perform these steps you need to have Python version 3.7 or higher installed. +1. To perform these steps you need to have Python version 3.8 or higher installed. * First check which Python version you have @@ -39,7 +39,7 @@ Install from **PyPI** .. image:: ../img/python3-version.svg - If this does not return ``Python 3.7.x`` or higher, you will need to `install Python `_. + If this does not return ``Python 3.8.x`` or higher, you will need to `install Python `_. .. warning:: diff --git a/requirements.txt b/requirements.txt index 5b4d0dc75..5bb7795cd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,15 +5,15 @@ click-pathlib==2020.3.13.0 cryptography==42.0.4 immutabledict==2.2.1 jwcrypto==1.5.6 -prettytable==3.4.1 -prompt-toolkit==3.0.31 +prettytable==3.7.0 +prompt-toolkit==3.0.40 PyNaCl==1.5.0 pytz==2022.2.1 -PyYAML==6.0.1 -questionary==1.10.0 -requests==2.32.0 -rich==12.5.1 +PyYAML==6.0.2 +questionary==1.10.0 # not mantained since 2018, can break anytime +requests==2.32.2 +rich==13.6.0 rich-click==1.5.2 simplejson==3.17.6 tzlocal==4.2 -zstandard==0.19.0 +zstandard==0.22.0 \ No newline at end of file diff --git a/setup.py b/setup.py index 8298f4540..88a664cc9 100644 --- a/setup.py +++ b/setup.py @@ -24,10 +24,11 @@ classifiers=[ "Development Status :: 4 - Beta", "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3.7", "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", ], url="https://github.com/ScilifelabDataCentre/dds_cli", author="SciLifeLab Data Centre", From 85a312ab3d3a9361413651ef49a0e37271e4a342 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:08:47 +0200 Subject: [PATCH 09/37] sprintlog --- SPRINTLOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index f33c43685..4b43df84f 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -373,3 +373,4 @@ _Empty sprint_ - Remove pinned version in requirements-dev.txt to resolve CVE ([#706](https://github.com/ScilifelabDataCentre/dds_cli/pull/706)) - Add CODEOWNERS file in order to define Team Hermes as owners of all files in repository ([#707](https://github.com/ScilifelabDataCentre/dds_cli/pull/707)) +- Update documentation and related libraries for pyton 3.12, dropped support for python 3.7 ([#709](https://github.com/ScilifelabDataCentre/dds_cli/pull/709)) From 0343c81970b09ad339d47c1b31964e506a7906b8 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:25:22 +0200 Subject: [PATCH 10/37] update workflows to match pyton version --- .github/workflows/pytest-cli.yml | 4 ++-- .github/workflows/release-cli.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pytest-cli.yml b/.github/workflows/pytest-cli.yml index f7fce4aaa..9d08f8032 100644 --- a/.github/workflows/pytest-cli.yml +++ b/.github/workflows/pytest-cli.yml @@ -17,10 +17,10 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Set up Python 3.10.4 + - name: Set up Python 3.12 uses: actions/setup-python@v2 with: - python-version: 3.10.4 + python-version: 3.12 - name: Install dds_cli run: | diff --git a/.github/workflows/release-cli.yml b/.github/workflows/release-cli.yml index 5184afa21..54ac8fe4e 100644 --- a/.github/workflows/release-cli.yml +++ b/.github/workflows/release-cli.yml @@ -18,10 +18,10 @@ jobs: - uses: actions/checkout@v3 name: Check out source-code repository - - name: Set up Python 3.9 + - name: Set up Python 3.12 uses: actions/setup-python@v4 with: - python-version: 3.9 + python-version: 3.12 - name: Install python dependencies run: | From 60f101de2644dc23a1a480d4ca9adc852c23e6b5 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:28:30 +0200 Subject: [PATCH 11/37] bump libraty --- tests/requirements-test.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/requirements-test.txt b/tests/requirements-test.txt index 5d1964f9f..997ff3f78 100644 --- a/tests/requirements-test.txt +++ b/tests/requirements-test.txt @@ -2,5 +2,5 @@ Flask==2.0.2 requests-mock==1.9.3 pytest==7.1.2 pytest-cov==3.0.0 -pyfakefs==4.5.5 +pyfakefs==5.3.0 Werkzeug==2.2.3 \ No newline at end of file From 662bfa81632e28ed387be80bca9069fe0ce5dd9c Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:30:07 +0200 Subject: [PATCH 12/37] bump libraty --- tests/requirements-test.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/requirements-test.txt b/tests/requirements-test.txt index 997ff3f78..71ffe35f0 100644 --- a/tests/requirements-test.txt +++ b/tests/requirements-test.txt @@ -1,4 +1,4 @@ -Flask==2.0.2 +Flask==2.2.5 requests-mock==1.9.3 pytest==7.1.2 pytest-cov==3.0.0 From 44d4ca989739f815363141f1a6e4279ea0995c90 Mon Sep 17 00:00:00 2001 From: Wojciech Potrzebowski Date: Wed, 4 Sep 2024 09:33:09 +0200 Subject: [PATCH 13/37] Update __main__.py --- dds_cli/__main__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dds_cli/__main__.py b/dds_cli/__main__.py index fafc964d6..63d01db34 100644 --- a/dds_cli/__main__.py +++ b/dds_cli/__main__.py @@ -1185,7 +1185,7 @@ def retract_project(click_ctx, project): required=False, is_flag=True, default=False, - help="Something has one wrong in the project.", + help="Something has gone wrong in the project.", ) @click.pass_obj def archive_project(click_ctx, project: str, abort: bool = False): From bc3a8f98145f9981b6e086e5ef3dcd6f9a7f0f9f Mon Sep 17 00:00:00 2001 From: valyo <582646+valyo@users.noreply.github.com> Date: Thu, 12 Sep 2024 14:19:19 +0200 Subject: [PATCH 14/37] added list of passwd managers --- docs/password.rst | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/docs/password.rst b/docs/password.rst index 11315a600..3208c8886 100644 --- a/docs/password.rst +++ b/docs/password.rst @@ -8,12 +8,17 @@ Securing your password Your Data Delivery System (DDS) password will be used to protect your data from any unauthorized parties. Choosing a secure password is therefore essential since the password's complexity will determine how easy it is to guess the password and thereby gain access to your data. Remembering a number of different passwords for different services can be difficult, and many people resort to using the same or similar password for all, or saving them in insecure ways where they are easily lost or/and read by others. -Due to this, we highly recommend that you use a password manager to store your passwords. An example of this is `Bitwarden `_ which is also used by the SciLifeLab Data Centre team. +Due to this, we highly recommend that you use a password manager to store your passwords. Some common password management services are `Bitwarden `, `LastPass `, `1Password `_. How to use password managers, e.g. Bitwarden ============================================= -Using a password manager such as Bitwarden means that you need to keep track of a single password: The password you set for the password manager. The rest are stored within the password manager, allowing you to have different complex ones for each service you use. Many of these tools have mobile apps and plugins for different browsers, which simplifies password management significantly. +Using a password manager means that you need to keep track of a single password: +The password you set for the password manager. +The rest are stored within the password manager, +allowing you to have different complex ones for each service you use. +Many of these tools have mobile apps and plugins for different browsers, +which simplifies password management significantly. The following is an example of how to start using Bitwarden. From 305a28806d22cdbd3c02d80b486f634aeb3d360b Mon Sep 17 00:00:00 2001 From: valyo <582646+valyo@users.noreply.github.com> Date: Thu, 12 Sep 2024 14:22:33 +0200 Subject: [PATCH 15/37] fix links --- docs/password.rst | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/docs/password.rst b/docs/password.rst index 3208c8886..c33028773 100644 --- a/docs/password.rst +++ b/docs/password.rst @@ -6,9 +6,16 @@ Securing your password ================================= -Your Data Delivery System (DDS) password will be used to protect your data from any unauthorized parties. Choosing a secure password is therefore essential since the password's complexity will determine how easy it is to guess the password and thereby gain access to your data. Remembering a number of different passwords for different services can be difficult, and many people resort to using the same or similar password for all, or saving them in insecure ways where they are easily lost or/and read by others. +Your Data Delivery System (DDS) password will be used to protect your data from any +unauthorized parties. Choosing a secure password is therefore essential since the +password's complexity will determine how easy it is to guess the password and thereby +gain access to your data. Remembering a number of different passwords for different +services can be difficult, and many people resort to using the same or similar +password for all, or saving them in insecure ways where they are easily lost or/and +read by others. -Due to this, we highly recommend that you use a password manager to store your passwords. Some common password management services are `Bitwarden `, `LastPass `, `1Password `_. +Due to this, we highly recommend that you use a password manager to store your passwords. +Some common password management services are `Bitwarden `_, `LastPass `_, `1Password `_. How to use password managers, e.g. Bitwarden ============================================= From 1136c653a5bd5a183aa51d555a9154b1c8d1a358 Mon Sep 17 00:00:00 2001 From: valyo <582646+valyo@users.noreply.github.com> Date: Mon, 16 Sep 2024 16:07:39 +0200 Subject: [PATCH 16/37] added clarification regarding Bitwarden --- docs/password.rst | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) diff --git a/docs/password.rst b/docs/password.rst index c33028773..68a3968fc 100644 --- a/docs/password.rst +++ b/docs/password.rst @@ -15,19 +15,22 @@ password for all, or saving them in insecure ways where they are easily lost or/ read by others. Due to this, we highly recommend that you use a password manager to store your passwords. -Some common password management services are `Bitwarden `_, `LastPass `_, `1Password `_. +Some common password management services are `Bitwarden `_, +`LastPass `_, `1Password `_. How to use password managers, e.g. Bitwarden ============================================= Using a password manager means that you need to keep track of a single password: -The password you set for the password manager. -The rest are stored within the password manager, +the password you set for the password manager. +All your other passwords are stored within the password manager, allowing you to have different complex ones for each service you use. -Many of these tools have mobile apps and plugins for different browsers, +Many of the password management services have mobile apps and plugins for different browsers, which simplifies password management significantly. -The following is an example of how to start using Bitwarden. +Data Centre does not provide a password manager service and we do not specifically recommend +any of the mentioned ones. For illustrative purposes only, we provide +detailed instructions on how to begin using Bitwarden to demonstrate the concept: 1. Go to https://bitwarden.com/ 2. Create an account. At the time of writing, this is done by clicking ``Get Started`` in the top right corner. Fill in your information and click Create account at the bottom. Remember to choose a complex password, that you can remember. Do not share this password with anyone. From 85b351c353a205fa6c815dce1b14637e06fd65c0 Mon Sep 17 00:00:00 2001 From: valyo <582646+valyo@users.noreply.github.com> Date: Mon, 16 Sep 2024 16:15:34 +0200 Subject: [PATCH 17/37] sprintlog --- SPRINTLOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index f33c43685..dc325fc81 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -373,3 +373,7 @@ _Empty sprint_ - Remove pinned version in requirements-dev.txt to resolve CVE ([#706](https://github.com/ScilifelabDataCentre/dds_cli/pull/706)) - Add CODEOWNERS file in order to define Team Hermes as owners of all files in repository ([#707](https://github.com/ScilifelabDataCentre/dds_cli/pull/707)) + +# 2024-09-09 - 2024-09-20 + +- Clarify documentation about password managers ([#711](https://github.com/ScilifelabDataCentre/dds_cli/pull/711)) From 40723f78e4aab86fbc3a30f3c33e394654b5108d Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 10:53:38 +0200 Subject: [PATCH 18/37] Started process to bump python in client --- WINDOWS.md | 4 ++-- docs/installation.rst | 4 ++-- requirements.txt | 14 +++++++------- setup.py | 3 ++- 4 files changed, 13 insertions(+), 12 deletions(-) diff --git a/WINDOWS.md b/WINDOWS.md index e584b0e9e..af0ba4a19 100644 --- a/WINDOWS.md +++ b/WINDOWS.md @@ -1,6 +1,6 @@ # How to install the DDS CLI on Windows -## 1. Download and install Python > 3.7 +## 1. Download and install Python > 3.8 ### 1.1. Go to https://www.python.org/downloads/windows/ @@ -42,7 +42,7 @@ ![Powershell 1](docs/_static/windows/powershell_top-1.png) -> **Note:** Upon entering `python --version` the version of the previously installed Python distribution should be shown. If a version number < 3.7 is shown or Python is not found, please consult the :ref:`Troubleshooting` section below. +> **Note:** Upon entering `python --version` the version of the previously installed Python distribution should be shown. If a version number < 3.8 is shown or Python is not found, please consult the :ref:`Troubleshooting` section below. ### 2.3. Python ships with a helper program called **pip** to install additional packages. In the next step, this software should be upgraded to its current version. diff --git a/docs/installation.rst b/docs/installation.rst index fba24e22e..65022a53a 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -29,7 +29,7 @@ As mentioned above, you can install ``dds-cli`` from PyPI or via an executable. Install from **PyPI** ----------------------- -1. To perform these steps you need to have Python version 3.7 or higher installed. +1. To perform these steps you need to have Python version 3.8 or higher installed. * First check which Python version you have @@ -39,7 +39,7 @@ Install from **PyPI** .. image:: ../img/python3-version.svg - If this does not return ``Python 3.7.x`` or higher, you will need to `install Python `_. + If this does not return ``Python 3.8.x`` or higher, you will need to `install Python `_. .. warning:: diff --git a/requirements.txt b/requirements.txt index 5b4d0dc75..5bb7795cd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,15 +5,15 @@ click-pathlib==2020.3.13.0 cryptography==42.0.4 immutabledict==2.2.1 jwcrypto==1.5.6 -prettytable==3.4.1 -prompt-toolkit==3.0.31 +prettytable==3.7.0 +prompt-toolkit==3.0.40 PyNaCl==1.5.0 pytz==2022.2.1 -PyYAML==6.0.1 -questionary==1.10.0 -requests==2.32.0 -rich==12.5.1 +PyYAML==6.0.2 +questionary==1.10.0 # not mantained since 2018, can break anytime +requests==2.32.2 +rich==13.6.0 rich-click==1.5.2 simplejson==3.17.6 tzlocal==4.2 -zstandard==0.19.0 +zstandard==0.22.0 \ No newline at end of file diff --git a/setup.py b/setup.py index 8298f4540..88a664cc9 100644 --- a/setup.py +++ b/setup.py @@ -24,10 +24,11 @@ classifiers=[ "Development Status :: 4 - Beta", "License :: OSI Approved :: MIT License", - "Programming Language :: Python :: 3.7", "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", ], url="https://github.com/ScilifelabDataCentre/dds_cli", author="SciLifeLab Data Centre", From 2f490015d05c23411f8bb9b7979447574a071ff4 Mon Sep 17 00:00:00 2001 From: valyo <582646+valyo@users.noreply.github.com> Date: Mon, 16 Sep 2024 16:20:33 +0200 Subject: [PATCH 19/37] sprintlog --- SPRINTLOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index dc325fc81..eb821ce91 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -373,6 +373,7 @@ _Empty sprint_ - Remove pinned version in requirements-dev.txt to resolve CVE ([#706](https://github.com/ScilifelabDataCentre/dds_cli/pull/706)) - Add CODEOWNERS file in order to define Team Hermes as owners of all files in repository ([#707](https://github.com/ScilifelabDataCentre/dds_cli/pull/707)) +- Update documentation and related libraries for pyton 3.12, dropped support for python 3.7 ([#709](https://github.com/ScilifelabDataCentre/dds_cli/pull/709)) # 2024-09-09 - 2024-09-20 From aa1b3b542766b1af70c95e462880053e24fe3fd2 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:25:22 +0200 Subject: [PATCH 20/37] update workflows to match pyton version --- .github/workflows/pytest-cli.yml | 4 ++-- .github/workflows/release-cli.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/pytest-cli.yml b/.github/workflows/pytest-cli.yml index f7fce4aaa..9d08f8032 100644 --- a/.github/workflows/pytest-cli.yml +++ b/.github/workflows/pytest-cli.yml @@ -17,10 +17,10 @@ jobs: steps: - uses: actions/checkout@v3 - - name: Set up Python 3.10.4 + - name: Set up Python 3.12 uses: actions/setup-python@v2 with: - python-version: 3.10.4 + python-version: 3.12 - name: Install dds_cli run: | diff --git a/.github/workflows/release-cli.yml b/.github/workflows/release-cli.yml index 5184afa21..54ac8fe4e 100644 --- a/.github/workflows/release-cli.yml +++ b/.github/workflows/release-cli.yml @@ -18,10 +18,10 @@ jobs: - uses: actions/checkout@v3 name: Check out source-code repository - - name: Set up Python 3.9 + - name: Set up Python 3.12 uses: actions/setup-python@v4 with: - python-version: 3.9 + python-version: 3.12 - name: Install python dependencies run: | From 73b675ab253395dc9e641fc172c631f3897ce285 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:28:30 +0200 Subject: [PATCH 21/37] bump libraty --- tests/requirements-test.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/requirements-test.txt b/tests/requirements-test.txt index 5d1964f9f..997ff3f78 100644 --- a/tests/requirements-test.txt +++ b/tests/requirements-test.txt @@ -2,5 +2,5 @@ Flask==2.0.2 requests-mock==1.9.3 pytest==7.1.2 pytest-cov==3.0.0 -pyfakefs==4.5.5 +pyfakefs==5.3.0 Werkzeug==2.2.3 \ No newline at end of file From 3c0db7f8e4d986da46e97a33beb80bcb455881da Mon Sep 17 00:00:00 2001 From: rv0lt Date: Mon, 2 Sep 2024 11:30:07 +0200 Subject: [PATCH 22/37] bump libraty --- tests/requirements-test.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/requirements-test.txt b/tests/requirements-test.txt index 997ff3f78..71ffe35f0 100644 --- a/tests/requirements-test.txt +++ b/tests/requirements-test.txt @@ -1,4 +1,4 @@ -Flask==2.0.2 +Flask==2.2.5 requests-mock==1.9.3 pytest==7.1.2 pytest-cov==3.0.0 From 9ea47f3725cf0b9491da1e805062f6fc7e3015fd Mon Sep 17 00:00:00 2001 From: rv0lt Date: Wed, 18 Sep 2024 11:52:46 +0200 Subject: [PATCH 23/37] added dev endpoint --- dds_cli/__init__.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/dds_cli/__init__.py b/dds_cli/__init__.py index 507fc6906..104122086 100644 --- a/dds_cli/__init__.py +++ b/dds_cli/__init__.py @@ -61,12 +61,15 @@ class DDSEndpoint: BASE_ENDPOINT_DOCKER = "http://dds_backend:5000/api/v1" BASE_ENDPOINT_REMOTE = "https://delivery.scilifelab.se/api/v1" BASE_ENDPOINT_REMOTE_TEST = "https://testing.delivery.scilifelab.se/api/v1" + BASE_ENDPOINT_REMOTE_DEV = "https://dev.delivery.scilifelab.se/api/v1" if os.getenv("DDS_CLI_ENV") == "development": BASE_ENDPOINT = BASE_ENDPOINT_LOCAL elif os.getenv("DDS_CLI_ENV") == "docker-dev": BASE_ENDPOINT = BASE_ENDPOINT_DOCKER elif os.getenv("DDS_CLI_ENV") == "test-instance": BASE_ENDPOINT = BASE_ENDPOINT_REMOTE_TEST + elif os.getenv("DDS_CLI_ENV") == "development-instance": + BASE_ENDPOINT = BASE_ENDPOINT_REMOTE_DEV else: BASE_ENDPOINT = BASE_ENDPOINT_REMOTE From 6740c9082e90accfeb2ce8bc5f5318f8df4a0622 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Wed, 18 Sep 2024 11:59:57 +0200 Subject: [PATCH 24/37] sprintlog --- SPRINTLOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index 4b43df84f..a7a11a1bb 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -374,3 +374,7 @@ _Empty sprint_ - Remove pinned version in requirements-dev.txt to resolve CVE ([#706](https://github.com/ScilifelabDataCentre/dds_cli/pull/706)) - Add CODEOWNERS file in order to define Team Hermes as owners of all files in repository ([#707](https://github.com/ScilifelabDataCentre/dds_cli/pull/707)) - Update documentation and related libraries for pyton 3.12, dropped support for python 3.7 ([#709](https://github.com/ScilifelabDataCentre/dds_cli/pull/709)) + +# 2024-09-09 - 2024-09-20 + +- Added new dev instance url to cli config ([#712](https://github.com/ScilifelabDataCentre/dds_cli/pull/712)) From 96623dfd7e6e31d998311445513a9528d0f20909 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=81lvaro=20Revuelta?= <46089290+rv0lt@users.noreply.github.com> Date: Thu, 19 Sep 2024 10:59:26 +0200 Subject: [PATCH 25/37] Update dds_cli/__init__.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Ina Odén Österbo <35953392+i-oden@users.noreply.github.com> --- dds_cli/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dds_cli/__init__.py b/dds_cli/__init__.py index 104122086..d7cdafa51 100644 --- a/dds_cli/__init__.py +++ b/dds_cli/__init__.py @@ -68,7 +68,7 @@ class DDSEndpoint: BASE_ENDPOINT = BASE_ENDPOINT_DOCKER elif os.getenv("DDS_CLI_ENV") == "test-instance": BASE_ENDPOINT = BASE_ENDPOINT_REMOTE_TEST - elif os.getenv("DDS_CLI_ENV") == "development-instance": + elif os.getenv("DDS_CLI_ENV") == "dev-instance": BASE_ENDPOINT = BASE_ENDPOINT_REMOTE_DEV else: BASE_ENDPOINT = BASE_ENDPOINT_REMOTE From 6348e772640b669523e43f58a33dfe8c1f13c52d Mon Sep 17 00:00:00 2001 From: rv0lt Date: Thu, 19 Sep 2024 11:15:25 +0200 Subject: [PATCH 26/37] new versjk --- dds_cli/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dds_cli/version.py b/dds_cli/version.py index f5e94b471..0fcff0475 100644 --- a/dds_cli/version.py +++ b/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__ = "2.7.1" +__version__ = "2.7.1-pentest" From 66c44be8813bbb048e5aa0744cdfcc9ea48e584f Mon Sep 17 00:00:00 2001 From: rv0lt Date: Thu, 19 Sep 2024 11:19:42 +0200 Subject: [PATCH 27/37] new version --- dds_cli/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dds_cli/version.py b/dds_cli/version.py index 0fcff0475..652ce9fa8 100644 --- a/dds_cli/version.py +++ b/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__ = "2.7.1-pentest" +__version__ = "2.7.1.pentest" From 837d9dca869a5fb8766e1aead8c5138655498cea Mon Sep 17 00:00:00 2001 From: rv0lt Date: Thu, 19 Sep 2024 11:22:23 +0200 Subject: [PATCH 28/37] new version --- dds_cli/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dds_cli/version.py b/dds_cli/version.py index 652ce9fa8..cdda9b3a4 100644 --- a/dds_cli/version.py +++ b/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__ = "2.7.1.pentest" +__version__ = "2.7.1.dev0" From ff5d59b31c0f4de4020b2e48a607d5b1fea378b2 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Fri, 20 Sep 2024 09:10:32 +0200 Subject: [PATCH 29/37] undo version change --- dds_cli/version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dds_cli/version.py b/dds_cli/version.py index cdda9b3a4..f5e94b471 100644 --- a/dds_cli/version.py +++ b/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__ = "2.7.1.dev0" +__version__ = "2.7.1" From fd4d52f26a4f29cb1b76b73e3dbf62d957c39847 Mon Sep 17 00:00:00 2001 From: valyo <582646+valyo@users.noreply.github.com> Date: Fri, 20 Sep 2024 11:01:11 +0200 Subject: [PATCH 30/37] review suggestions --- docs/password.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/password.rst b/docs/password.rst index 68a3968fc..7ea1475da 100644 --- a/docs/password.rst +++ b/docs/password.rst @@ -28,8 +28,8 @@ allowing you to have different complex ones for each service you use. Many of the password management services have mobile apps and plugins for different browsers, which simplifies password management significantly. -Data Centre does not provide a password manager service and we do not specifically recommend -any of the mentioned ones. For illustrative purposes only, we provide +Data Centre does not provide a password management service and we do not specifically recommend +any of the ones mentioned above. For illustrative purposes only, we provide detailed instructions on how to begin using Bitwarden to demonstrate the concept: 1. Go to https://bitwarden.com/ From a44ef1fcacaa6a053248794010f611fc78f09a86 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 24 Sep 2024 07:53:56 +0000 Subject: [PATCH 31/37] Generate new screengrabs with rich-codex --- img/dds-auth.svg | 106 ++++++++--------- img/dds-data-get.svg | 194 +++++++++++++++---------------- img/dds-data-put.svg | 198 ++++++++++++++++---------------- img/dds-data.svg | 88 +++++++------- img/dds-help-1.svg | 174 ++++++++++++++-------------- img/dds-help-2.svg | 174 ++++++++++++++-------------- img/dds-project-status-help.svg | 102 ++++++++-------- img/dds-project.svg | 92 +++++++-------- img/dds-user.svg | 100 ++++++++-------- img/python-version.svg | 18 +-- img/python3-version.svg | 18 +-- 11 files changed, 632 insertions(+), 632 deletions(-) diff --git a/img/dds-auth.svg b/img/dds-auth.svg index f3d10db3d..07e96574d 100644 --- a/img/dds-auth.svg +++ b/img/dds-auth.svg @@ -19,90 +19,90 @@ font-weight: 700; } - .terminal-1830499860-matrix { + .terminal-1237076098-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1830499860-title { + .terminal-1237076098-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1830499860-r1 { fill: #c5c8c6 } -.terminal-1830499860-r2 { fill: #868887;font-style: italic; } -.terminal-1830499860-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-1830499860-r4 { fill: #d0b344;font-weight: bold } -.terminal-1830499860-r5 { fill: #68a0b3;font-weight: bold } -.terminal-1830499860-r6 { fill: #868887 } -.terminal-1830499860-r7 { fill: #4e707b;font-weight: bold } + .terminal-1237076098-r1 { fill: #c5c8c6 } +.terminal-1237076098-r2 { fill: #868887;font-style: italic; } +.terminal-1237076098-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-1237076098-r4 { fill: #d0b344;font-weight: bold } +.terminal-1237076098-r5 { fill: #68a0b3;font-weight: bold } +.terminal-1237076098-r6 { fill: #868887 } +.terminal-1237076098-r7 { fill: #4e707b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -114,30 +114,30 @@ - + - - $ dds auth -[..truncated..] - -Usage: dds auth [OPTIONS] COMMAND [ARGS]... - - Group command for creating and managing authenticated sessions (valid for 7 days).                  -Authenticate yourself once and run multiple commands within a certain amount of time without  -specifying your user credentials. If you do not authenticate yourself and start a new session, you -will need to provide your DDS username when running the other commands. -All subcommands are usable by all user roles. - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--help      Show this message and exit.                                                          │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│info       Display information about ongoing authenticated session.                             │ -│login      Start or renew an authenticated session.                                             │ -│logout     End authenticated session.                                                           │ -│twofactor  Group command for configuring and deactivating methods of two factor authentication. │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds auth +[..truncated..] + +Usage: dds auth [OPTIONS] COMMAND [ARGS]... + + Group command for creating and managing authenticated sessions (valid for 7 days).                  +Authenticate yourself once and run multiple commands within a certain amount of time without  +specifying your user credentials. If you do not authenticate yourself and start a new session, you +will need to provide your DDS username when running the other commands. +All subcommands are usable by all user roles. + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--help      Show this message and exit.                                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│info       Display information about ongoing authenticated session.                             │ +│login      Start or renew an authenticated session.                                             │ +│logout     End authenticated session.                                                           │ +│twofactor  Group command for configuring and deactivating methods of two factor authentication. │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-data-get.svg b/img/dds-data-get.svg index 39e38e333..3566f41db 100644 --- a/img/dds-data-get.svg +++ b/img/dds-data-get.svg @@ -19,154 +19,154 @@ font-weight: 700; } - .terminal-2316791639-matrix { + .terminal-316438670-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2316791639-title { + .terminal-316438670-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2316791639-r1 { fill: #c5c8c6 } -.terminal-2316791639-r2 { fill: #868887;font-style: italic; } -.terminal-2316791639-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-2316791639-r4 { fill: #d0b344;font-weight: bold } -.terminal-2316791639-r5 { fill: #68a0b3;font-weight: bold } -.terminal-2316791639-r6 { fill: #868887 } -.terminal-2316791639-r7 { fill: #4e707b;font-weight: bold } -.terminal-2316791639-r8 { fill: #cc555a } -.terminal-2316791639-r9 { fill: #98a84b;font-weight: bold } -.terminal-2316791639-r10 { fill: #8a4346 } -.terminal-2316791639-r11 { fill: #8d7b39;font-weight: bold } + .terminal-316438670-r1 { fill: #c5c8c6 } +.terminal-316438670-r2 { fill: #868887;font-style: italic; } +.terminal-316438670-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-316438670-r4 { fill: #d0b344;font-weight: bold } +.terminal-316438670-r5 { fill: #68a0b3;font-weight: bold } +.terminal-316438670-r6 { fill: #868887 } +.terminal-316438670-r7 { fill: #4e707b;font-weight: bold } +.terminal-316438670-r8 { fill: #cc555a } +.terminal-316438670-r9 { fill: #98a84b;font-weight: bold } +.terminal-316438670-r10 { fill: #8a4346 } +.terminal-316438670-r11 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -178,50 +178,50 @@ - + - - $ dds data get --help -[..truncated..] -Usage: dds data get [OPTIONS] - - Download data from a project.                                                                       -To download the data to a specific destination, use the `--destination` option. This cannot be an  -existing directory, for security reasons. This will be improved on in future releases. -Following to the download, the DDS decrypts the files, checks if the files are compressed and if  -so decompresses them. -NB! The current setup requires decryption and decompression to be performed locally. Make sure you -have enough space. This will be improved on in future releases. The default number of files to  -download, decrypt and decompress at a time is four. This can be changed by altering the  -`--num-threads` option, but whether or not it works depends on the machine you are running the CLI -on. -The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  -finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  -yourself before downloading data. - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│*--project-pTEXT                      Project ID from which you're downloading  │ -│                                                        data.                                     │ -│[required]                               │ -│--num-threads-ntINTEGER RANGE [1<=x<=32]  Number of parallel threads to perform the │ -│                                                        delivery                                  │ -│[default: 4; 1<=x<=32]                   │ -│--source-sTEXT                      Path to file or directory. Use the option │ -│                                                        multiple times to specify more than one   │ -│                                                        source [multiple]                         │ -│--source-path-file-spfPATH                      File containing path to files or          │ -│                                                        directories.                              │ -│--destination-dDIRECTORY                 Destination of downloaded data.           │ -│--break-on-fail  Cancel download of all files if one       │ -│                                                        fails.                                    │ -│--silent  Turn off progress bar for each individual │ -│                                                        file. Summary bars still visible.         │ -│--get-all-a  Download all project contents.            │ -│--verify-checksum  Perform SHA-256 checksum verification     │ -│                                                        after download (slower).                  │ -│--help  Show this message and exit.               │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds data get --help +[..truncated..] +Usage: dds data get [OPTIONS] + + Download data from a project.                                                                       +To download the data to a specific destination, use the `--destination` option. This cannot be an  +existing directory, for security reasons. This will be improved on in future releases. +Following to the download, the DDS decrypts the files, checks if the files are compressed and if  +so decompresses them. +NB! The current setup requires decryption and decompression to be performed locally. Make sure you +have enough space. This will be improved on in future releases. The default number of files to  +download, decrypt and decompress at a time is four. This can be changed by altering the  +`--num-threads` option, but whether or not it works depends on the machine you are running the CLI +on. +The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  +finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  +yourself before downloading data. + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│*--project-pTEXT                      Project ID from which you're downloading  │ +│                                                        data.                                     │ +│[required]                               │ +│--num-threads-ntINTEGER RANGE [1<=x<=32]  Number of parallel threads to perform the │ +│                                                        delivery                                  │ +│[default: 4; 1<=x<=32]                   │ +│--source-sTEXT                      Path to file or directory. Use the option │ +│                                                        multiple times to specify more than one   │ +│                                                        source [multiple]                         │ +│--source-path-file-spfPATH                      File containing path to files or          │ +│                                                        directories.                              │ +│--destination-dDIRECTORY                 Destination of downloaded data.           │ +│--break-on-fail  Cancel download of all files if one       │ +│                                                        fails.                                    │ +│--silent  Turn off progress bar for each individual │ +│                                                        file. Summary bars still visible.         │ +│--get-all-a  Download all project contents.            │ +│--verify-checksum  Perform SHA-256 checksum verification     │ +│                                                        after download (slower).                  │ +│--help  Show this message and exit.               │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-data-put.svg b/img/dds-data-put.svg index c040bd6ef..3bf63e4f6 100644 --- a/img/dds-data-put.svg +++ b/img/dds-data-put.svg @@ -19,157 +19,157 @@ font-weight: 700; } - .terminal-510542596-matrix { + .terminal-4032580667-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-510542596-title { + .terminal-4032580667-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-510542596-r1 { fill: #c5c8c6 } -.terminal-510542596-r2 { fill: #868887;font-style: italic; } -.terminal-510542596-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-510542596-r4 { fill: #d0b344;font-weight: bold } -.terminal-510542596-r5 { fill: #68a0b3;font-weight: bold } -.terminal-510542596-r6 { fill: #868887 } -.terminal-510542596-r7 { fill: #4e707b;font-weight: bold } -.terminal-510542596-r8 { fill: #98a84b;font-weight: bold } -.terminal-510542596-r9 { fill: #cc555a } -.terminal-510542596-r10 { fill: #8a4346 } -.terminal-510542596-r11 { fill: #8d7b39;font-weight: bold } + .terminal-4032580667-r1 { fill: #c5c8c6 } +.terminal-4032580667-r2 { fill: #868887;font-style: italic; } +.terminal-4032580667-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-4032580667-r4 { fill: #d0b344;font-weight: bold } +.terminal-4032580667-r5 { fill: #68a0b3;font-weight: bold } +.terminal-4032580667-r6 { fill: #868887 } +.terminal-4032580667-r7 { fill: #4e707b;font-weight: bold } +.terminal-4032580667-r8 { fill: #98a84b;font-weight: bold } +.terminal-4032580667-r9 { fill: #cc555a } +.terminal-4032580667-r10 { fill: #8a4346 } +.terminal-4032580667-r11 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -181,51 +181,51 @@ - + - - $ dds data put --help -[..truncated..] -Usage: dds data put [OPTIONS] - - Upload data to a project.                                                                           -Limited to Unit Admins and Personnel. -To upload a file (with the same name) a second time, use the `--overwrite` flag. -Prior to the upload, the DDS checks if the files are compressed and if not compresses them,  -followed by encryption. After this the files are uploaded to the cloud. -NB! The current setup requires compression and encryption to be performed locally. Make sure you  -have enough space. This will be improved on in future releases. The default number of files to  -compress, encrypt and upload at a time is four. This can be changed by altering the  -`--num-threads` option, but whether or not it works depends on the machine you are running the CLI -on. -The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  -finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  -yourself before uploading data. - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--mount-dir-mdDIRECTORY                 New directory where the files will be     │ -│                                                        mounted before upload and any error log   │ -│                                                        files will be saved for a specific        │ -│                                                        upload.                                   │ -│*--project-pTEXT                      Project ID to which you're uploading      │ -│                                                        data.                                     │ -│[required]                               │ -│--source-sPATH                      Path to file or directory (local). Use    │ -│                                                        the option multiple times to specify more │ -│                                                        than one source [multiple]                │ -│--source-path-file-spfPATH                      File containing path to files or          │ -│                                                        directories.                              │ -│--num-threads-ntINTEGER RANGE [1<=x<=32]  Number of parallel threads to perform the │ -│                                                        delivery                                  │ -│[default: 4; 1<=x<=32]                   │ -│--destination-dTEXT                      Destination of uploaded data.             │ -│--overwrite  Overwrite files if already uploaded.      │ -│--break-on-fail  Cancel upload of all files if one fails.  │ -│--silent  Turn off progress bar for each individual │ -│                                                        file. Summary bars still visible.         │ -│--help  Show this message and exit.               │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds data put --help +[..truncated..] +Usage: dds data put [OPTIONS] + + Upload data to a project.                                                                           +Limited to Unit Admins and Personnel. +To upload a file (with the same name) a second time, use the `--overwrite` flag. +Prior to the upload, the DDS checks if the files are compressed and if not compresses them,  +followed by encryption. After this the files are uploaded to the cloud. +NB! The current setup requires compression and encryption to be performed locally. Make sure you  +have enough space. This will be improved on in future releases. The default number of files to  +compress, encrypt and upload at a time is four. This can be changed by altering the  +`--num-threads` option, but whether or not it works depends on the machine you are running the CLI +on. +The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  +finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  +yourself before uploading data. + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--mount-dir-mdDIRECTORY                 New directory where the files will be     │ +│                                                        mounted before upload and any error log   │ +│                                                        files will be saved for a specific        │ +│                                                        upload.                                   │ +│*--project-pTEXT                      Project ID to which you're uploading      │ +│                                                        data.                                     │ +│[required]                               │ +│--source-sPATH                      Path to file or directory (local). Use    │ +│                                                        the option multiple times to specify more │ +│                                                        than one source [multiple]                │ +│--source-path-file-spfPATH                      File containing path to files or          │ +│                                                        directories.                              │ +│--num-threads-ntINTEGER RANGE [1<=x<=32]  Number of parallel threads to perform the │ +│                                                        delivery                                  │ +│[default: 4; 1<=x<=32]                   │ +│--destination-dTEXT                      Destination of uploaded data.             │ +│--overwrite  Overwrite files if already uploaded.      │ +│--break-on-fail  Cancel upload of all files if one fails.  │ +│--silent  Turn off progress bar for each individual │ +│                                                        file. Summary bars still visible.         │ +│--help  Show this message and exit.               │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-data.svg b/img/dds-data.svg index 762899b13..9f3d522f8 100644 --- a/img/dds-data.svg +++ b/img/dds-data.svg @@ -19,77 +19,77 @@ font-weight: 700; } - .terminal-1452403837-matrix { + .terminal-3575578347-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1452403837-title { + .terminal-3575578347-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1452403837-r1 { fill: #c5c8c6 } -.terminal-1452403837-r2 { fill: #868887;font-style: italic; } -.terminal-1452403837-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-1452403837-r4 { fill: #d0b344;font-weight: bold } -.terminal-1452403837-r5 { fill: #68a0b3;font-weight: bold } -.terminal-1452403837-r6 { fill: #868887 } + .terminal-3575578347-r1 { fill: #c5c8c6 } +.terminal-3575578347-r2 { fill: #868887;font-style: italic; } +.terminal-3575578347-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-3575578347-r4 { fill: #d0b344;font-weight: bold } +.terminal-3575578347-r5 { fill: #68a0b3;font-weight: bold } +.terminal-3575578347-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -101,26 +101,26 @@ - + - - $ dds data -[..truncated..] - -Usage: dds data [OPTIONS] COMMAND [ARGS]... - - Group command for uploading, downloading and managing project data.                                 - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--help      Show this message and exit.                                                          │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│get   Download data from a project.                                                             │ -│ls    List project contents.                                                                    │ -│put   Upload data to a project.                                                                 │ -│rm    [Unit Admins and Personnel only] Delete data within a specific project.                   │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds data +[..truncated..] + +Usage: dds data [OPTIONS] COMMAND [ARGS]... + + Group command for uploading, downloading and managing project data.                                 + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--help      Show this message and exit.                                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│get   Download data from a project.                                                             │ +│ls    List project contents.                                                                    │ +│put   Upload data to a project.                                                                 │ +│rm    [Unit Admins and Personnel only] Delete data within a specific project.                   │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-help-1.svg b/img/dds-help-1.svg index 7b0b6614b..c2dafb98e 100644 --- a/img/dds-help-1.svg +++ b/img/dds-help-1.svg @@ -19,140 +19,140 @@ font-weight: 700; } - .terminal-4202155958-matrix { + .terminal-3099583012-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4202155958-title { + .terminal-3099583012-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4202155958-r1 { fill: #c5c8c6 } -.terminal-4202155958-r2 { fill: #868887;font-style: italic; } -.terminal-4202155958-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-4202155958-r4 { fill: #d0b344;font-weight: bold } -.terminal-4202155958-r5 { fill: #68a0b3;font-weight: bold } -.terminal-4202155958-r6 { fill: #868887 } -.terminal-4202155958-r7 { fill: #4e707b;font-weight: bold } -.terminal-4202155958-r8 { fill: #98a84b;font-weight: bold } -.terminal-4202155958-r9 { fill: #8d7b39;font-weight: bold } + .terminal-3099583012-r1 { fill: #c5c8c6 } +.terminal-3099583012-r2 { fill: #868887;font-style: italic; } +.terminal-3099583012-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-3099583012-r4 { fill: #d0b344;font-weight: bold } +.terminal-3099583012-r5 { fill: #68a0b3;font-weight: bold } +.terminal-3099583012-r6 { fill: #868887 } +.terminal-3099583012-r7 { fill: #4e707b;font-weight: bold } +.terminal-3099583012-r8 { fill: #98a84b;font-weight: bold } +.terminal-3099583012-r9 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -164,46 +164,46 @@ - + - - $ dds -     ︵  - ︵ (  )   ︵  -(  ) ) (  (  )   SciLifeLab Data Delivery System  - ︶  (  ) ) (    https://delivery.scilifelab.se/  -      ︶ (  )    CLI Version 2.7.1  -          ︶ -[..truncated..] -Usage: dds [OPTIONS] COMMAND [ARGS]... - - SciLifeLab Data Delivery System (DDS) command line interface.                                       -Access token is saved in a .dds_cli_token file in the home directory. -The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  -finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  -yourself before each delivery ('dds data put' / 'get'). - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--verbose-v  Print verbose output to the console.                              │ -│--log-file-l<filename>  Save a log to a file.                                             │ -│--no-prompt  Run without any interactive features.                             │ -│--token-path-tpTEXT        The path where the authentication token will be stored. For a     │ -│                                normal use-case, this should not be needed.                       │ -│--version  Display the version of this software.                             │ -│--help  List the options of any DDS subcommand and its default settings.  │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│auth         Group command for creating and managing authenticated sessions (valid for 7 days). │ -│data         Group command for uploading, downloading and managing project data.                │ -│ls           List the active projects you have access to or the project contents.               │ -│maintenance  [Super Admins only] Activate / Deactivate / Display status for Maintenance mode.   │ -│motd         [Super Admins only] Group command for managing Message of the Day within DDS.      │ -│project      Group command for creating and managing projects within the DDS.                   │ -│stats        Get statistics in the DDS.                                                         │ -│unit         [Super Admins only] Group command for managing units.                              │ -│user         Group command for managing user accounts, including your own.                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds +     ︵  + ︵ (  )   ︵  +(  ) ) (  (  )   SciLifeLab Data Delivery System  + ︶  (  ) ) (    https://delivery.scilifelab.se/  +      ︶ (  )    CLI Version 2.7.1  +          ︶ +[..truncated..] +Usage: dds [OPTIONS] COMMAND [ARGS]... + + SciLifeLab Data Delivery System (DDS) command line interface.                                       +Access token is saved in a .dds_cli_token file in the home directory. +The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  +finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  +yourself before each delivery ('dds data put' / 'get'). + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--verbose-v  Print verbose output to the console.                              │ +│--log-file-l<filename>  Save a log to a file.                                             │ +│--no-prompt  Run without any interactive features.                             │ +│--token-path-tpTEXT        The path where the authentication token will be stored. For a     │ +│                                normal use-case, this should not be needed.                       │ +│--version  Display the version of this software.                             │ +│--help  List the options of any DDS subcommand and its default settings.  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│auth         Group command for creating and managing authenticated sessions (valid for 7 days). │ +│data         Group command for uploading, downloading and managing project data.                │ +│ls           List the active projects you have access to or the project contents.               │ +│maintenance  [Super Admins only] Activate / Deactivate / Display status for Maintenance mode.   │ +│motd         [Super Admins only] Group command for managing Message of the Day within DDS.      │ +│project      Group command for creating and managing projects within the DDS.                   │ +│stats        Get statistics in the DDS.                                                         │ +│unit         [Super Admins only] Group command for managing units.                              │ +│user         Group command for managing user accounts, including your own.                      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-help-2.svg b/img/dds-help-2.svg index c06b5117e..ff6f511cd 100644 --- a/img/dds-help-2.svg +++ b/img/dds-help-2.svg @@ -19,140 +19,140 @@ font-weight: 700; } - .terminal-2328220121-matrix { + .terminal-3233145927-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2328220121-title { + .terminal-3233145927-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2328220121-r1 { fill: #c5c8c6 } -.terminal-2328220121-r2 { fill: #868887;font-style: italic; } -.terminal-2328220121-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-2328220121-r4 { fill: #d0b344;font-weight: bold } -.terminal-2328220121-r5 { fill: #68a0b3;font-weight: bold } -.terminal-2328220121-r6 { fill: #868887 } -.terminal-2328220121-r7 { fill: #4e707b;font-weight: bold } -.terminal-2328220121-r8 { fill: #98a84b;font-weight: bold } -.terminal-2328220121-r9 { fill: #8d7b39;font-weight: bold } + .terminal-3233145927-r1 { fill: #c5c8c6 } +.terminal-3233145927-r2 { fill: #868887;font-style: italic; } +.terminal-3233145927-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-3233145927-r4 { fill: #d0b344;font-weight: bold } +.terminal-3233145927-r5 { fill: #68a0b3;font-weight: bold } +.terminal-3233145927-r6 { fill: #868887 } +.terminal-3233145927-r7 { fill: #4e707b;font-weight: bold } +.terminal-3233145927-r8 { fill: #98a84b;font-weight: bold } +.terminal-3233145927-r9 { fill: #8d7b39;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -164,46 +164,46 @@ - + - - $ dds --help -     ︵  - ︵ (  )   ︵  -(  ) ) (  (  )   SciLifeLab Data Delivery System  - ︶  (  ) ) (    https://delivery.scilifelab.se/  -      ︶ (  )    CLI Version 2.7.1  -          ︶ -[..truncated..] -Usage: dds [OPTIONS] COMMAND [ARGS]... - - SciLifeLab Data Delivery System (DDS) command line interface.                                       -Access token is saved in a .dds_cli_token file in the home directory. -The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  -finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  -yourself before each delivery ('dds data put' / 'get'). - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--verbose-v  Print verbose output to the console.                              │ -│--log-file-l<filename>  Save a log to a file.                                             │ -│--no-prompt  Run without any interactive features.                             │ -│--token-path-tpTEXT        The path where the authentication token will be stored. For a     │ -│                                normal use-case, this should not be needed.                       │ -│--version  Display the version of this software.                             │ -│--help  List the options of any DDS subcommand and its default settings.  │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│auth         Group command for creating and managing authenticated sessions (valid for 7 days). │ -│data         Group command for uploading, downloading and managing project data.                │ -│ls           List the active projects you have access to or the project contents.               │ -│maintenance  [Super Admins only] Activate / Deactivate / Display status for Maintenance mode.   │ -│motd         [Super Admins only] Group command for managing Message of the Day within DDS.      │ -│project      Group command for creating and managing projects within the DDS.                   │ -│stats        Get statistics in the DDS.                                                         │ -│unit         [Super Admins only] Group command for managing units.                              │ -│user         Group command for managing user accounts, including your own.                      │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds --help +     ︵  + ︵ (  )   ︵  +(  ) ) (  (  )   SciLifeLab Data Delivery System  + ︶  (  ) ) (    https://delivery.scilifelab.se/  +      ︶ (  )    CLI Version 2.7.1  +          ︶ +[..truncated..] +Usage: dds [OPTIONS] COMMAND [ARGS]... + + SciLifeLab Data Delivery System (DDS) command line interface.                                       +Access token is saved in a .dds_cli_token file in the home directory. +The token is valid for 7 days. Make sure your token is valid long enough for the delivery to  +finish. To avoid that a delivery fails because of an expired token, we recommend reauthenticating  +yourself before each delivery ('dds data put' / 'get'). + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--verbose-v  Print verbose output to the console.                              │ +│--log-file-l<filename>  Save a log to a file.                                             │ +│--no-prompt  Run without any interactive features.                             │ +│--token-path-tpTEXT        The path where the authentication token will be stored. For a     │ +│                                normal use-case, this should not be needed.                       │ +│--version  Display the version of this software.                             │ +│--help  List the options of any DDS subcommand and its default settings.  │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│auth         Group command for creating and managing authenticated sessions (valid for 7 days). │ +│data         Group command for uploading, downloading and managing project data.                │ +│ls           List the active projects you have access to or the project contents.               │ +│maintenance  [Super Admins only] Activate / Deactivate / Display status for Maintenance mode.   │ +│motd         [Super Admins only] Group command for managing Message of the Day within DDS.      │ +│project      Group command for creating and managing projects within the DDS.                   │ +│stats        Get statistics in the DDS.                                                         │ +│unit         [Super Admins only] Group command for managing units.                              │ +│user         Group command for managing user accounts, including your own.                      │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-project-status-help.svg b/img/dds-project-status-help.svg index 2a5218f35..537176b6b 100644 --- a/img/dds-project-status-help.svg +++ b/img/dds-project-status-help.svg @@ -19,88 +19,88 @@ font-weight: 700; } - .terminal-346232205-matrix { + .terminal-2354063355-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-346232205-title { + .terminal-2354063355-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-346232205-r1 { fill: #c5c8c6 } -.terminal-346232205-r2 { fill: #868887;font-style: italic; } -.terminal-346232205-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-346232205-r4 { fill: #868887 } -.terminal-346232205-r5 { fill: #68a0b3;font-weight: bold } + .terminal-2354063355-r1 { fill: #c5c8c6 } +.terminal-2354063355-r2 { fill: #868887;font-style: italic; } +.terminal-2354063355-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-2354063355-r4 { fill: #868887 } +.terminal-2354063355-r5 { fill: #68a0b3;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -112,30 +112,30 @@ - + - - $ dds project status --help -[..truncated..] - - Manage project statuses.                                                                            -Display or change the status of a project. -Displaying the project status is available for all user roles. Changing the project status is  -limited to Unit Admins and Personnel. - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--help      Show this message and exit.                                                          │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│archive    Change the project status to 'Archived'.                                             │ -│busy       [Super Admins only] Returns the number of busy projects.                             │ -│delete     Delete an unreleased project (change project status to 'Deleted').                   │ -│display    Display the status of a specific project.                                            │ -│extend     Extend a project deadline by an specified number of days.                            │ -│release    Change project status to 'Available'.                                                │ -│retract    Change the project status to 'In Progress'.                                          │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds project status --help +[..truncated..] + + Manage project statuses.                                                                            +Display or change the status of a project. +Displaying the project status is available for all user roles. Changing the project status is  +limited to Unit Admins and Personnel. + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--help      Show this message and exit.                                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│archive    Change the project status to 'Archived'.                                             │ +│busy       [Super Admins only] Returns the number of busy projects.                             │ +│delete     Delete an unreleased project (change project status to 'Deleted').                   │ +│display    Display the status of a specific project.                                            │ +│extend     Extend a project deadline by an specified number of days.                            │ +│release    Change project status to 'Available'.                                                │ +│retract    Change the project status to 'In Progress'.                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-project.svg b/img/dds-project.svg index bdbe73e2e..d997c5748 100644 --- a/img/dds-project.svg +++ b/img/dds-project.svg @@ -19,80 +19,80 @@ font-weight: 700; } - .terminal-3993618841-matrix { + .terminal-4202290183-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3993618841-title { + .terminal-4202290183-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3993618841-r1 { fill: #c5c8c6 } -.terminal-3993618841-r2 { fill: #868887;font-style: italic; } -.terminal-3993618841-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-3993618841-r4 { fill: #d0b344;font-weight: bold } -.terminal-3993618841-r5 { fill: #68a0b3;font-weight: bold } -.terminal-3993618841-r6 { fill: #868887 } + .terminal-4202290183-r1 { fill: #c5c8c6 } +.terminal-4202290183-r2 { fill: #868887;font-style: italic; } +.terminal-4202290183-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-4202290183-r4 { fill: #d0b344;font-weight: bold } +.terminal-4202290183-r5 { fill: #68a0b3;font-weight: bold } +.terminal-4202290183-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -104,27 +104,27 @@ - + - - $ dds project -[..truncated..] - -Usage: dds project [OPTIONS] COMMAND [ARGS]... - - Group command for creating and managing projects within the DDS.                                    - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--help      Show this message and exit.                                                          │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│access     Manage specific users access to a project.                                           │ -│create     Create a project within the DDS.                                                     │ -│info       Manage project information.                                                          │ -│ls         List all active projects you have access to in the DDS.                              │ -│status     Manage project statuses.                                                             │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds project +[..truncated..] + +Usage: dds project [OPTIONS] COMMAND [ARGS]... + + Group command for creating and managing projects within the DDS.                                    + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--help      Show this message and exit.                                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│access     Manage specific users access to a project.                                           │ +│create     Create a project within the DDS.                                                     │ +│info       Manage project information.                                                          │ +│ls         List all active projects you have access to in the DDS.                              │ +│status     Manage project statuses.                                                             │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/dds-user.svg b/img/dds-user.svg index 9539375e0..bbfc15e26 100644 --- a/img/dds-user.svg +++ b/img/dds-user.svg @@ -19,86 +19,86 @@ font-weight: 700; } - .terminal-4021865309-matrix { + .terminal-4148092363-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4021865309-title { + .terminal-4148092363-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4021865309-r1 { fill: #c5c8c6 } -.terminal-4021865309-r2 { fill: #868887;font-style: italic; } -.terminal-4021865309-r3 { fill: #c5c8c6;font-weight: bold } -.terminal-4021865309-r4 { fill: #d0b344;font-weight: bold } -.terminal-4021865309-r5 { fill: #68a0b3;font-weight: bold } -.terminal-4021865309-r6 { fill: #868887 } + .terminal-4148092363-r1 { fill: #c5c8c6 } +.terminal-4148092363-r2 { fill: #868887;font-style: italic; } +.terminal-4148092363-r3 { fill: #c5c8c6;font-weight: bold } +.terminal-4148092363-r4 { fill: #d0b344;font-weight: bold } +.terminal-4148092363-r5 { fill: #68a0b3;font-weight: bold } +.terminal-4148092363-r6 { fill: #868887 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + @@ -110,29 +110,29 @@ - + - - $ dds user -[..truncated..] - -Usage: dds user [OPTIONS] COMMAND [ARGS]... - - Group command for managing user accounts, including your own.                                       - -╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ -│--help      Show this message and exit.                                                          │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ -╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ -│activate     Activate/Reactivate user accounts.                                                 │ -│add          Invite a new user to the DDS or add an existing one to a hosted project.           │ -│deactivate   Deactivate user accounts in the Data Delivery System.                              │ -│delete       Delete user accounts from the Data Delivery System.                                │ -│find         Check if a username is registered to an account in the DDS.                        │ -│info         Display information connected to your own DDS account.                             │ -│ls           List Unit Admins and Personnel connected to a specific unit.                       │ -╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ - + + $ dds user +[..truncated..] + +Usage: dds user [OPTIONS] COMMAND [ARGS]... + + Group command for managing user accounts, including your own.                                       + +╭─ Options ────────────────────────────────────────────────────────────────────────────────────────╮ +│--help      Show this message and exit.                                                          │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ +╭─ Commands ───────────────────────────────────────────────────────────────────────────────────────╮ +│activate     Activate/Reactivate user accounts.                                                 │ +│add          Invite a new user to the DDS or add an existing one to a hosted project.           │ +│deactivate   Deactivate user accounts in the Data Delivery System.                              │ +│delete       Delete user accounts from the Data Delivery System.                                │ +│find         Check if a username is registered to an account in the DDS.                        │ +│info         Display information connected to your own DDS account.                             │ +│ls           List Unit Admins and Personnel connected to a specific unit.                       │ +╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ + diff --git a/img/python-version.svg b/img/python-version.svg index 5206579ec..0135b4b17 100644 --- a/img/python-version.svg +++ b/img/python-version.svg @@ -19,27 +19,27 @@ font-weight: 700; } - .terminal-625154443-matrix { + .terminal-627251597-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-625154443-title { + .terminal-627251597-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-625154443-r1 { fill: #c5c8c6 } + .terminal-627251597-r1 { fill: #c5c8c6 } - + - + @@ -51,11 +51,11 @@ - + - - $ python --version -Python 3.12.4 + + $ python --version +Python 3.12.6 diff --git a/img/python3-version.svg b/img/python3-version.svg index fbb94e366..da66a23de 100644 --- a/img/python3-version.svg +++ b/img/python3-version.svg @@ -19,27 +19,27 @@ font-weight: 700; } - .terminal-936974782-matrix { + .terminal-939071936-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-936974782-title { + .terminal-939071936-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-936974782-r1 { fill: #c5c8c6 } + .terminal-939071936-r1 { fill: #c5c8c6 } - + - + @@ -51,11 +51,11 @@ - + - - $ python3 --version -Python 3.12.4 + + $ python3 --version +Python 3.12.6 From 96c9b167fdce82467ede03264ba0e92dca23b0de Mon Sep 17 00:00:00 2001 From: rv0lt Date: Tue, 24 Sep 2024 09:55:10 +0200 Subject: [PATCH 32/37] new version and changelog --- CHANGELOG.rst | 24 ++++++++++++++++++++++++ dds_cli/version.py | 2 +- 2 files changed, 25 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 49fb2a1af..4438e243c 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,6 +1,30 @@ Changelog ========== +.. _2.8.0: + +2.8.0 - 2024-09-24 +~~~~~~~~~~~~~~~~~~~ +- New features: + - Add CODEOWNERS file to the repository. + - Drop support for python 3.7 + - Added new dev instance url to cli config +- Dependencies: + - `prettytable` from `3.4.1` to `3.7.0` + - `prompt-toolkit` from `3.0.31` to `3.0.40` + - `pyYAML` from `6.0.1` to `6.0.2` + - `requests` from `2.32.0` to `2.32.2` + - `rich` from `12.5.1` to `13.6.0` + - `zstandard` from `0.19.0` to `0.22.0` +- Dependencies (tests): + - `flask` from `2.0.2` to `2.2.5` + - `pyfakefs` from `4.5.5` to `5.3.0` +- Fixes: + - Improve documentation related to the testing instance. + - Remove pinned version of pynstaller in requeriments-dev to solve cve. + - Clarify documentation about password management. + - Update documentation for python 3.12 + .. _2.7.1: 2.7.1 - 2024-06-27 diff --git a/dds_cli/version.py b/dds_cli/version.py index f5e94b471..9951ebcba 100644 --- a/dds_cli/version.py +++ b/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__ = "2.7.1" +__version__ = "2.8.0" From 10331eb0bf70722265ea1efd9dda6c651cefa4fa Mon Sep 17 00:00:00 2001 From: rv0lt Date: Tue, 24 Sep 2024 10:00:03 +0200 Subject: [PATCH 33/37] sprintlog --- SPRINTLOG.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index 4b43df84f..dd7eaa9c5 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -374,3 +374,11 @@ _Empty sprint_ - Remove pinned version in requirements-dev.txt to resolve CVE ([#706](https://github.com/ScilifelabDataCentre/dds_cli/pull/706)) - Add CODEOWNERS file in order to define Team Hermes as owners of all files in repository ([#707](https://github.com/ScilifelabDataCentre/dds_cli/pull/707)) - Update documentation and related libraries for pyton 3.12, dropped support for python 3.7 ([#709](https://github.com/ScilifelabDataCentre/dds_cli/pull/709)) + +# 2024-09-09 - 2024-09-20 + +_Empty sprint_ + +# 2024-09-24 - 2024-10-04 + +- New version and changelog([#714](https://github.com/ScilifelabDataCentre/dds_cli/pull/714)) From 8e952412238f63f5e5b3b7da8b25436ef15c1c77 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Tue, 24 Sep 2024 10:28:53 +0200 Subject: [PATCH 34/37] prettier --- SPRINTLOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/SPRINTLOG.md b/SPRINTLOG.md index 9ccb987f1..b3ca0baff 100644 --- a/SPRINTLOG.md +++ b/SPRINTLOG.md @@ -383,4 +383,3 @@ _Empty sprint_ # 2024-09-24 - 2024-10-04 - New version and changelog([#714](https://github.com/ScilifelabDataCentre/dds_cli/pull/714)) - From a01d373e9d2957ecf2f7140cdd14ba64fcf3de4f Mon Sep 17 00:00:00 2001 From: rv0lt Date: Tue, 24 Sep 2024 11:22:01 +0200 Subject: [PATCH 35/37] changelog --- CHANGELOG.rst | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 4438e243c..6b5780d30 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -5,10 +5,12 @@ Changelog 2.8.0 - 2024-09-24 ~~~~~~~~~~~~~~~~~~~ -- New features: - - Add CODEOWNERS file to the repository. +- Deprecations: - Drop support for python 3.7 +- New features: - Added new dev instance url to cli config +- Workflow: + - Add CODEOWNERS file to the repository. - Dependencies: - `prettytable` from `3.4.1` to `3.7.0` - `prompt-toolkit` from `3.0.31` to `3.0.40` @@ -19,11 +21,12 @@ Changelog - Dependencies (tests): - `flask` from `2.0.2` to `2.2.5` - `pyfakefs` from `4.5.5` to `5.3.0` -- Fixes: +- Documentation: - Improve documentation related to the testing instance. - - Remove pinned version of pynstaller in requeriments-dev to solve cve. - Clarify documentation about password management. - Update documentation for python 3.12 +- Fixes: + - Remove pinned version of pynstaller in requeriments-dev to solve cve. .. _2.7.1: From bc197c8523c93441f05431c4a25de3de9bdb3968 Mon Sep 17 00:00:00 2001 From: rv0lt Date: Tue, 24 Sep 2024 11:30:55 +0200 Subject: [PATCH 36/37] remove workflow from changelog --- CHANGELOG.rst | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 6b5780d30..9182d11a2 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -9,8 +9,6 @@ Changelog - Drop support for python 3.7 - New features: - Added new dev instance url to cli config -- Workflow: - - Add CODEOWNERS file to the repository. - Dependencies: - `prettytable` from `3.4.1` to `3.7.0` - `prompt-toolkit` from `3.0.31` to `3.0.40` From 017b2a8f5d1596b36e4bc7b69bb1c458cd798dae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ina=20Od=C3=A9n=20=C3=96sterbo?= Date: Tue, 24 Sep 2024 11:54:27 +0200 Subject: [PATCH 37/37] move in changelog --- CHANGELOG.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 9182d11a2..4cf26fc93 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -16,6 +16,7 @@ Changelog - `requests` from `2.32.0` to `2.32.2` - `rich` from `12.5.1` to `13.6.0` - `zstandard` from `0.19.0` to `0.22.0` + - `pyinstaller` version unpinned - Dependencies (tests): - `flask` from `2.0.2` to `2.2.5` - `pyfakefs` from `4.5.5` to `5.3.0` @@ -23,8 +24,6 @@ Changelog - Improve documentation related to the testing instance. - Clarify documentation about password management. - Update documentation for python 3.12 -- Fixes: - - Remove pinned version of pynstaller in requeriments-dev to solve cve. .. _2.7.1: