dtool-lookup-gui
================
.. image:: data/icons/22x22/dtool_logo.png
:height: 20px
:target: https://github.com/livMatS/dtool-lookup-gui
:alt: dtool-lookup-gui icon
.. image:: https://img.shields.io/github/actions/workflow/status/livMatS/dtool-lookup-gui/build-and-publish.yml?branch=master
:target: https://github.com/livMatS/dtool-lookup-gui/actions/workflows/build-and-publish.yml
:alt: GitHub Build Workflow Status
.. image:: https://img.shields.io/github/actions/workflow/status/livMatS/dtool-lookup-gui/test.yml?branch=master&label=tests
:alt: GitHub Tests Workflow Status
:target: https://github.com/livMatS/dtool-lookup-gui/actions/workflows/test.yml
.. image:: https://img.shields.io/github/v/release/livMatS/dtool-lookup-gui
:target: https://github.com/livMatS/dtool-lookup-gui/releases/latest
:alt: GitHub release (latest by date)
.. image:: https://badge.fury.io/py/dtool-lookup-gui.svg
:target: https://badge.fury.io/py/dtool-lookup-gui
:alt: PyPI package
dtool-lookup-gui is a graphical user interface for dtool_, the dtool-lookup-server_, the dtool-lookup-server-direct-mongo-plugin_ and the
dtool-lookup-server-dependency-graph-plugin_ written in Python_ and GTK_.
.. image:: data/screenshots/screenshot1.png
Quick start
-----------
Just download the pre-packaged binaries of the `latest release`_.
If the binaries won't run out-of-the-box on your system, continue below.
OS-specific notes
-----------------
Windows
^^^^^^^
The Windows executable comes in two variants, as a single portable file and an installer.
macOS
^^^^^
The app bundle requires MacOS 14.7 at least.
After downloading the `dmg` Apple Disk Image of the `latest release`_
and copying `dtool-lookup-gui` over to your `Applications` folder,
*macOS* will likely complain about `dtool-lookup-gui` being damaged
and refuse to execute it. This is due to the fact that we are no
Apple-verified developers. To run the app anyway, open a terminal and
remove Apple's quarantine attribute from the app with
.. code:: bash
sudo xattr -rds com.apple.quarantine /Applications/dtool-lookup-gui.app
That should enable you to launch the app as usual. Another option is to
call
.. code:: bash
/Applications/dtool-lookup-gui.app/Contents/MacOS/dtool-lookup-gui
directly from the command line.
Linux
^^^^^
After downloading and extracting the tar.gz-packaged Linux build, you may
run the bundled scripts :code:`set_launcher_icon.sh` and :code:`soft_link_launcher.sh`
subsequently to add this launcher icon to your desktop environment:
.. image:: data/screenshots/screenshot-ubuntu-launcher.png
This has been tested on Ubuntu 20.04 and GNOME 3.36.8.
The packaged Linux build will fail to launch out-of-the box under Wayland.
An error like this might arise:
.. code::
GLib-GIO-ERROR **: 11:26:50.444: Settings schema 'org.gnome.settings-daemon.plugins.xsettings' does not contain a key named 'antialiasing'
Trace/breakpoint trap (core dumped)
If unsure which display server is in use, check with
.. code:: bash
echo $XDG_SESSION_TYPE
This will likely output either :code:`x11` or :code:`wayland`.
If you are using Wayland, launch the app with environment variable
:code:`GDK_BACKEND=x11` set, e.g. via
.. code:: bash
GDK_BACKEND=x11 dtool-gui
Use
---
Searching
^^^^^^^^^
The app searches the index of a dtool-lookup-server. How exactly the index is searched depends on the implementation of the search plugin on the server side.
In the case of the reference search plugin, the `dtool-lookup-server-search-plugin-mongo`_, a word in the search field will search for exactly that word within all string fields stored in the underlying database.
This, of course, includes the content of the `README.yml` file attached to a dataset, but also matches against contents of the manifest (such as file names of the packaged items) and the basic set of administrative metadata, namely the fields
.. code:: json
{
"base_uri": "s3://test-bucket",
"created_at": 1683797360.056,
"creator_username": "jotelha",
"dtoolcore_version": "3.18.2",
"frozen_at": 1683797362.855,
"name": "test_dataset_2",
"number_of_items": 1,
"size_in_bytes": 19347,
"tags": [],
"type": "dataset",
"uri": "s3://test-bucket/26785c2a-e8f8-46bf-82a1-cec92dbdf28f",
"uuid": "26785c2a-e8f8-46bf-82a1-cec92dbdf28f"
}
The `dtool-lookup-server-search-plugin-mongo`_ README offers more information on the exact search mechanism.
If the `dtool-lookup-server-direct-mongo-plugin`_ is installed on the server side, very specific search queries that make use of operators from the MongoDB language are possible.
Enclose a MongoDB language query in curly brackets ``{...}`` and all fields in double quotes ``"..."`` to use this direct Mongo query functionality.
The query
.. code:: json
{
"creator_username": {
"$in": ["anna", "bert"]
},
"readme.description": {
"$regex": "toluene"
}
}
searches for all datasets created by users with the either the local user name "anna" or "bert" on the machine of dataset creation and with the word "toluene" included in the README field "description".
The regular expression operator can of course formulate more sophisticated criteria than a plain text search on the content of a specific field.
The `direct query`_ section of the `dtool-lookup-server-direct-mongo-plugin`_ README lists a few
other query examples.
Development
-----------
Please read the `contributing guidelines`_ before diving into the development process.
Requirements
^^^^^^^^^^^^
This application requires Gtk_ 3 and GtkSourceView_ 4.
On Ubuntu (20.04),
.. code:: bash
apt install -y gir1.2-gtksource-4
suffices to to install these dependencies from the standard system package repositories.
On recent macOS (>= 10.15) use homebrew,
.. code:: bash
brew install gtksourceview4 gnome-icon-theme
On earlie macOs, `MacPorts <https://www.macports.org/>`_ allows the installation of `gtksourceview4`
.. code:: bash
sudo port -v selfupdate
sudo port install xorg-server
sudo port install gtksourceview4 py-gobject3 py-pip py-numpy py-scipy
sudo port install adwaita-icon-theme
sudo port select --set python python310
sudo port select --set pip pip310
mkdir -p ~/venv
python -m venv --system-site-packages ~/venv/python-3.10
source ~/venv/python-3.10/bin/activate
pip install --upgrade pip
pip install wheel
pip install dtool-lookup-gui dtool-s3 dtool-smb
This has been tested on macOS 10.13.6.
On Windows, use `mingw64/msys2 <https://www.msys2.org>`_ and refer to the
`Using GTK from MSYS2 packages <https://www.gtk.org/docs/installations/windows#using-gtk-from-msys2-packages>`_
on the GTK project's pages.
Also refer to the build workflows `.github/workflows/build-on-[linux|macos|windows].yml` within this repository
for understanding the requirements for the different systems.
On Windows WSL, install
apt install gcc cmake python3-dev libcairo2-dev gir1.2-gtksource-4 libgirepository1.0-dev
to allow a development installation of the GUI as described below.
Installation
^^^^^^^^^^^^
For a locally editable install, clone this repository with
.. code:: console
git clone git+https://github.com/livMatS/dtool-lookup-gui.git
change into the repository directory,
.. code:: bash
cd dtool-lookup-gui
create and activate a clean virtual environment,
.. code:: bash
python -m venv venv
source venv/bin/activate
pip install --upgrade pip
and perform an editable install with
.. code:: bash
pip install -e .
Also run
.. code:: bash
glib-compile-schemas .
from within subdirectory ``dtool_lookup_gui``. Otherwise, GUI launch fails with
.. code::
gi.repository.GLib.Error: g-file-error-quark: Failed to open file “/path/to/repository/dtool_lookup_gui/gschemas.compiled”: open() failed: No such file or directory (4)
Running the GUI
---------------
After installation, run the GUI with:
.. code:: bash
dtool-gui
Note that when you run the GUI for the first time, you will need to configure
the URL of the lookup and the authentication server as well as provide a
username and a password. To do this, click on the "Burger" symbol and select
*Settings*.
Pinned requirements
^^^^^^^^^^^^^^^^^^^
``requirements.in`` contains unpinned dependencies. ``requirements.txt`` with pinned versions has been auto-generated with
.. code:: bash
pip install pip-tools
pip-compile --resolver=backtracking requirements.in > requirements.txt
GTK debugging
^^^^^^^^^^^^^
After
.. code-block:: bash
gsettings set org.gtk.Settings.Debug enable-inspector-keybinding true
use CTRL-SHIFT-D during execution to display the GTK inspector for interactive debugging.
GUI design
^^^^^^^^^^
The GUI uses custom Gtk widgets. To edit the the XML UI definition files with
Glade_, add the directory ``glade/catalog`` to `Extra Catalog & Template paths`
within Glade's preferences dialog.
Running unit tests
^^^^^^^^^^^^^^^^^^
Running the unit tests requires `pytest` and `pytest-asyncio`. Then, run all tests from repository root with `pytest`.
Funding
-------
This development has received funding from the Deutsche Forschungsgemeinschaft within the Cluster of Excellence livMatS_.
.. _contributing guidelines: CONTRIBUTING.md
.. _direct query: https://github.com/livMatS/dtool-lookup-server-direct-mongo-plugin#direct-query
.. _dtool: https://github.com/jic-dtool/dtool
.. _dtool-lookup-server: https://github.com/jic-dtool/dtool-lookup-server
.. _dtool-lookup-server-dependency-graph-plugin: https://github.com/livMatS/dtool-lookup-server-dependency-graph-plugin
.. _dtool-lookup-server-direct-mongo-plugin: https://github.com/livMatS/dtool-lookup-server-direct-mongo-plugin
.. _dtool-lookup-server-search-plugin-mongo: https://github.com/jic-dtool/dtool-lookup-server-search-plugin-mongo
.. _Glade: https://glade.gnome.org/
.. _GTK: https://www.gtk.org/
.. _GtkSourceView: https://wiki.gnome.org/Projects/GtkSourceView
.. _pip: https://pip.pypa.io/en/stable/
.. _Python: https://www.python.org/
.. _setuptools: https://setuptools.readthedocs.io/en/latest/
.. _livMatS: https://www.livmats.uni-freiburg.de/en
.. _latest release: https://github.com/livMatS/dtool-lookup-gui/releases/latest
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"description": "dtool-lookup-gui\n================\n\n.. image:: data/icons/22x22/dtool_logo.png\n :height: 20px\n :target: https://github.com/livMatS/dtool-lookup-gui\n :alt: dtool-lookup-gui icon\n.. image:: https://img.shields.io/github/actions/workflow/status/livMatS/dtool-lookup-gui/build-and-publish.yml?branch=master\n :target: https://github.com/livMatS/dtool-lookup-gui/actions/workflows/build-and-publish.yml\n :alt: GitHub Build Workflow Status\n.. image:: https://img.shields.io/github/actions/workflow/status/livMatS/dtool-lookup-gui/test.yml?branch=master&label=tests\n :alt: GitHub Tests Workflow Status\n :target: https://github.com/livMatS/dtool-lookup-gui/actions/workflows/test.yml\n.. image:: https://img.shields.io/github/v/release/livMatS/dtool-lookup-gui\n :target: https://github.com/livMatS/dtool-lookup-gui/releases/latest\n :alt: GitHub release (latest by date)\n.. image:: https://badge.fury.io/py/dtool-lookup-gui.svg\n :target: https://badge.fury.io/py/dtool-lookup-gui\n :alt: PyPI package\n\ndtool-lookup-gui is a graphical user interface for dtool_, the dtool-lookup-server_, the dtool-lookup-server-direct-mongo-plugin_ and the\ndtool-lookup-server-dependency-graph-plugin_ written in Python_ and GTK_.\n\n.. image:: data/screenshots/screenshot1.png\n\nQuick start\n-----------\n\nJust download the pre-packaged binaries of the `latest release`_.\n\nIf the binaries won't run out-of-the-box on your system, continue below.\n\nOS-specific notes\n-----------------\n\nWindows\n^^^^^^^\n\nThe Windows executable comes in two variants, as a single portable file and an installer.\n\nmacOS\n^^^^^\n\nThe app bundle requires MacOS 14.7 at least.\nAfter downloading the `dmg` Apple Disk Image of the `latest release`_\nand copying `dtool-lookup-gui` over to your `Applications` folder,\n*macOS* will likely complain about `dtool-lookup-gui` being damaged\nand refuse to execute it. This is due to the fact that we are no\nApple-verified developers. To run the app anyway, open a terminal and\nremove Apple's quarantine attribute from the app with\n\n.. code:: bash\n\n sudo xattr -rds com.apple.quarantine /Applications/dtool-lookup-gui.app\n\nThat should enable you to launch the app as usual. Another option is to\ncall\n\n.. code:: bash\n\n /Applications/dtool-lookup-gui.app/Contents/MacOS/dtool-lookup-gui\n\ndirectly from the command line.\n\nLinux\n^^^^^\n\nAfter downloading and extracting the tar.gz-packaged Linux build, you may\nrun the bundled scripts :code:`set_launcher_icon.sh` and :code:`soft_link_launcher.sh`\nsubsequently to add this launcher icon to your desktop environment:\n\n.. image:: data/screenshots/screenshot-ubuntu-launcher.png\n\nThis has been tested on Ubuntu 20.04 and GNOME 3.36.8.\n\nThe packaged Linux build will fail to launch out-of-the box under Wayland. \nAn error like this might arise:\n\n.. code::\n\n GLib-GIO-ERROR **: 11:26:50.444: Settings schema 'org.gnome.settings-daemon.plugins.xsettings' does not contain a key named 'antialiasing'\n Trace/breakpoint trap (core dumped)\n\nIf unsure which display server is in use, check with\n\n.. code:: bash\n\n echo $XDG_SESSION_TYPE\n \nThis will likely output either :code:`x11` or :code:`wayland`.\nIf you are using Wayland, launch the app with environment variable \n:code:`GDK_BACKEND=x11` set, e.g. via\n\n.. code:: bash\n\n GDK_BACKEND=x11 dtool-gui\n\n\nUse\n---\n\nSearching\n^^^^^^^^^\n\nThe app searches the index of a dtool-lookup-server. How exactly the index is searched depends on the implementation of the search plugin on the server side.\nIn the case of the reference search plugin, the `dtool-lookup-server-search-plugin-mongo`_, a word in the search field will search for exactly that word within all string fields stored in the underlying database.\nThis, of course, includes the content of the `README.yml` file attached to a dataset, but also matches against contents of the manifest (such as file names of the packaged items) and the basic set of administrative metadata, namely the fields\n\n.. code:: json\n\n {\n \"base_uri\": \"s3://test-bucket\",\n \"created_at\": 1683797360.056,\n \"creator_username\": \"jotelha\",\n \"dtoolcore_version\": \"3.18.2\",\n \"frozen_at\": 1683797362.855,\n \"name\": \"test_dataset_2\",\n \"number_of_items\": 1,\n \"size_in_bytes\": 19347,\n \"tags\": [],\n \"type\": \"dataset\",\n \"uri\": \"s3://test-bucket/26785c2a-e8f8-46bf-82a1-cec92dbdf28f\",\n \"uuid\": \"26785c2a-e8f8-46bf-82a1-cec92dbdf28f\"\n }\n\nThe `dtool-lookup-server-search-plugin-mongo`_ README offers more information on the exact search mechanism.\n\nIf the `dtool-lookup-server-direct-mongo-plugin`_ is installed on the server side, very specific search queries that make use of operators from the MongoDB language are possible.\nEnclose a MongoDB language query in curly brackets ``{...}`` and all fields in double quotes ``\"...\"`` to use this direct Mongo query functionality.\n\nThe query\n\n.. code:: json\n\n {\n \"creator_username\": {\n \"$in\": [\"anna\", \"bert\"]\n },\n \"readme.description\": {\n \"$regex\": \"toluene\"\n }\n }\n\nsearches for all datasets created by users with the either the local user name \"anna\" or \"bert\" on the machine of dataset creation and with the word \"toluene\" included in the README field \"description\".\nThe regular expression operator can of course formulate more sophisticated criteria than a plain text search on the content of a specific field.\n\nThe `direct query`_ section of the `dtool-lookup-server-direct-mongo-plugin`_ README lists a few\nother query examples.\n\nDevelopment\n-----------\n\nPlease read the `contributing guidelines`_ before diving into the development process.\n\nRequirements\n^^^^^^^^^^^^\n\nThis application requires Gtk_ 3 and GtkSourceView_ 4.\n\nOn Ubuntu (20.04),\n\n.. code:: bash\n\n apt install -y gir1.2-gtksource-4\n\nsuffices to to install these dependencies from the standard system package repositories.\n\nOn recent macOS (>= 10.15) use homebrew, \n\n.. code:: bash\n\n brew install gtksourceview4 gnome-icon-theme\n\nOn earlie macOs, `MacPorts <https://www.macports.org/>`_ allows the installation of `gtksourceview4`\n\n.. code:: bash\n \n sudo port -v selfupdate\n sudo port install xorg-server\n sudo port install gtksourceview4 py-gobject3 py-pip py-numpy py-scipy\n sudo port install adwaita-icon-theme\n\n sudo port select --set python python310\n sudo port select --set pip pip310\n\n mkdir -p ~/venv\n python -m venv --system-site-packages ~/venv/python-3.10\n source ~/venv/python-3.10/bin/activate\n \n pip install --upgrade pip\n pip install wheel\n pip install dtool-lookup-gui dtool-s3 dtool-smb\n\n\nThis has been tested on macOS 10.13.6.\n\nOn Windows, use `mingw64/msys2 <https://www.msys2.org>`_ and refer to the\n`Using GTK from MSYS2 packages <https://www.gtk.org/docs/installations/windows#using-gtk-from-msys2-packages>`_\non the GTK project's pages.\n\nAlso refer to the build workflows `.github/workflows/build-on-[linux|macos|windows].yml` within this repository \nfor understanding the requirements for the different systems.\n\nOn Windows WSL, install\n\n apt install gcc cmake python3-dev libcairo2-dev gir1.2-gtksource-4 libgirepository1.0-dev\n\nto allow a development installation of the GUI as described below.\n\nInstallation\n^^^^^^^^^^^^\n\nFor a locally editable install, clone this repository with\n\n.. code:: console\n\n git clone git+https://github.com/livMatS/dtool-lookup-gui.git\n\nchange into the repository directory,\n\n.. code:: bash\n\n cd dtool-lookup-gui\n\ncreate and activate a clean virtual environment,\n\n.. code:: bash\n\n python -m venv venv\n source venv/bin/activate\n pip install --upgrade pip\n\nand perform an editable install with\n\n.. code:: bash\n\n pip install -e .\n\nAlso run\n\n.. code:: bash\n\n glib-compile-schemas .\n\nfrom within subdirectory ``dtool_lookup_gui``. Otherwise, GUI launch fails with\n\n.. code::\n\n gi.repository.GLib.Error: g-file-error-quark: Failed to open file \u201c/path/to/repository/dtool_lookup_gui/gschemas.compiled\u201d: open() failed: No such file or directory (4)\n\n\nRunning the GUI\n---------------\n\nAfter installation, run the GUI with:\n\n.. code:: bash\n\n dtool-gui\n\nNote that when you run the GUI for the first time, you will need to configure\nthe URL of the lookup and the authentication server as well as provide a\nusername and a password. To do this, click on the \"Burger\" symbol and select\n*Settings*.\n\n\nPinned requirements\n^^^^^^^^^^^^^^^^^^^\n\n``requirements.in`` contains unpinned dependencies. ``requirements.txt`` with pinned versions has been auto-generated with\n\n.. code:: bash\n\n pip install pip-tools\n pip-compile --resolver=backtracking requirements.in > requirements.txt\n\nGTK debugging\n^^^^^^^^^^^^^\n\nAfter\n\n.. code-block:: bash\n\n gsettings set org.gtk.Settings.Debug enable-inspector-keybinding true\n\nuse CTRL-SHIFT-D during execution to display the GTK inspector for interactive debugging.\n\nGUI design\n^^^^^^^^^^\n\nThe GUI uses custom Gtk widgets. To edit the the XML UI definition files with\nGlade_, add the directory ``glade/catalog`` to `Extra Catalog & Template paths`\nwithin Glade's preferences dialog.\n\nRunning unit tests\n^^^^^^^^^^^^^^^^^^\n\nRunning the unit tests requires `pytest` and `pytest-asyncio`. Then, run all tests from repository root with `pytest`.\n\nFunding\n-------\n\nThis development has received funding from the Deutsche Forschungsgemeinschaft within the Cluster of Excellence livMatS_.\n\n.. _contributing guidelines: CONTRIBUTING.md\n\n.. _direct query: https://github.com/livMatS/dtool-lookup-server-direct-mongo-plugin#direct-query\n\n.. _dtool: https://github.com/jic-dtool/dtool\n\n.. _dtool-lookup-server: https://github.com/jic-dtool/dtool-lookup-server\n\n.. _dtool-lookup-server-dependency-graph-plugin: https://github.com/livMatS/dtool-lookup-server-dependency-graph-plugin\n\n.. _dtool-lookup-server-direct-mongo-plugin: https://github.com/livMatS/dtool-lookup-server-direct-mongo-plugin\n\n.. _dtool-lookup-server-search-plugin-mongo: https://github.com/jic-dtool/dtool-lookup-server-search-plugin-mongo\n\n.. _Glade: https://glade.gnome.org/\n\n.. _GTK: https://www.gtk.org/\n\n.. _GtkSourceView: https://wiki.gnome.org/Projects/GtkSourceView\n\n.. _pip: https://pip.pypa.io/en/stable/\n\n.. _Python: https://www.python.org/\n\n.. _setuptools: https://setuptools.readthedocs.io/en/latest/\n\n.. _livMatS: https://www.livmats.uni-freiburg.de/en\n\n.. _latest release: https://github.com/livMatS/dtool-lookup-gui/releases/latest\n\n",
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"license": "# LICENSE\n \n dtool-lookup-gui makes all its materials publicly available under [open source][osi] licenses.\n \n Documents and data are made available under a CC-BY-SA license.\n Software are made available under an MIT license.\n \n ## Documents and data\n \n Documentation and graphics in this repository are licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License][cc-by-sa].\n \n ## Software\n \n Software provided are made available under the [OSI][osi]-approved [MIT license][mit-license].\n \n [cc-by-sa]: https://creativecommons.org/licenses/by-sa/4.0/\n [mit-license]: https://opensource.org/licenses/mit-license.html\n [osi]: https://opensource.org\n ",
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