init

.github/PULL_REQUEST_TEMPLATE.md

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+IMPORTANT: Base your PR off the 'dev' branch and target that branch.
+
+Also please note that working on a PR doesn't automatically means that your code will be merged.

.github/workflows/black.yml

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+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
+        with:
+          src: "./any2eln

.gitignore

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+# Created by https://www.toptal.com/developers/gitignore/api/python,vim
+# Edit at https://www.toptal.com/developers/gitignore?templates=python,vim
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+### Vim ###
+# Swap
+[._]*.s[a-v][a-z]
+!*.svg  # comment out if you don't need vector files
+[._]*.sw[a-p]
+[._]s[a-rt-v][a-z]
+[._]ss[a-gi-z]
+[._]sw[a-p]
+
+# Session
+Session.vim
+Sessionx.vim
+
+# Temporary
+.netrwhist
+*~
+# Auto-generated tag files
+tags
+# Persistent undo
+[._]*.un~
+
+# End of https://www.toptal.com/developers/gitignore/api/python,vim
+local.env
+export-*
+# used in dev
+entries.json

CHANGELOG.md

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+# any2eln changelog
+
+## any2eln 0.1.0 - unreleased

DEVDOC.md

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+# Developer documentation
+
+## Run locally
+
+### Install
+
+~~~bash
+git clone https://gitub.com/TheELNConsortium/any2eln
+cd any2eln
+python -m venv venv
+source venv/bin/activate
+poetry install
+~~~
+
+### Usage
+
+~~~bash
+source local.env
+python any2eln
+~~~
+
+### Api doc
+
+https://labfolder.labforward.app/api/v2/docs/development.html
+
+### Using curl
+
+First, login to get a TOKEN
+
+~~~bash
+curl -X POST -H 'Content-Type: application/json' -d '{"user":"[email protected]", "password": "secr3t"}' https://labfolder.labforward.app/api/v2/auth/login
+~~~
+
+and copy token in some env var like T. Then:
+
+~~~bash
+curl -H "Authorization: Bearer $T" "https://labfolder.labforward.app/api/v2/templates/26333?expand=entry"
+~~~

LICENSE

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+MIT License
+
+Copyright (c) 2023 Nicolas CARPI
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+# Description
+
+**any2eln** is a tool to extract data from any Electronic Laboratory Notebook (ELN) software, to a `.eln` archive.
+
+This `.eln` archive can then easily be re-imported in another ELN.
+
+# Supported sources
+
+* [Labfolder](#labfolder-module) (functional)
+* Labguru (coming soon)
+* Scinote (coming soon)
+* Benchling (coming soon)
+
+# Installation
+
+~~~
+git clone https://github.com/TheELNConsortium/any2eln
+cd any2eln
+python -m venv venv
+source venv/bin/activate
+poetry install
+~~~
+
+# Usage
+
+~~~
+python any2eln --help
+~~~
+
+# Labfolder module
+
+## Description
+
+This module allows you to extract all your data from a Labfolder.com account. It goes through all the entries and saves them per author as `.eln` archives. Using this module requires an account on Labfolder.com website.
+
+The `DATA` elements are converted as `.csv` sheet by sheet, when possible, and the full `.json` metadata is also saved alongside.
+
+## Disclaimer
+
+This project is not affiliated with Labfolder software or Labforward GmbH. It simply leverages the [publicly documented API](https://labfolder.labforward.app/api/v2/docs/development.html#notebook-entries) to add a feature: export everything as `.eln`.
+
+## Usage
+
+~~~
+python any2eln --src labfolder
+~~~
+
+The exported data will be saved in the current directory in a folder named `export-Y-m-d-H-M-s`.
+
+For a more verbose output, add ``DEV=1`` to your execution environment.
+
+## Caveats
+
+If there is an error downloading a file for some reason, the error will be logged but the script will continue. Use verbose output (``DEV=1``) to have more information logged.
+
+# License
+
+This piece of software is under [MIT license](./LICENSE).

SECURITY.md

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+See https://www.deltablot.com/security/

any2eln/__main__.py

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+# TheELNConsortium/any2eln
+# © 2024 Nicolas CARPi @ Deltablot
+# License MIT
+import argparse
+
+from any2eln.labfolder.labfolder import Labfolder
+from any2eln.utils.utils import env_or_ask
+
+
+def main():
+    sources = ['labfolder', 'labguru', 'scinote', 'benchling']
+    parser = argparse.ArgumentParser(description='any2eln')
+    parser.add_argument('--src', required=True, help='source service you want to export from', choices=sources)
+    parser.add_argument('--out_dir', required=False, help='output directory', default='.')
+    args = parser.parse_args()
+
+    if (args.src == 'labfolder'):
+        username = env_or_ask('LABFOLDER_USERNAME', 'Your Labfolder username or email: ')
+        password = env_or_ask('LABFOLDER_PASSWORD', 'Your Labfolder password: ')
+        lf = Labfolder(username, password, out_dir=args.out_dir)
+        lf.extract()
+    else:
+        print('Not implemented.')
+
+if __name__ == "__main__":
+    main()