{ "info": { "author": "Daniel Thonon", "author_email": "d.thonon9@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Environment :: Console", "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)", "Operating System :: POSIX :: Linux", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3 :: Only", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "=============\nClient_API_VN\n=============\n\n.. image:: https://img.shields.io/badge/code%20style-black-000000.svg\n :target: https://github.com/psf/black\n.. image:: https://img.shields.io/pypi/status/Client-API-VN\n :alt: PyPI - Status\n.. image:: https://img.shields.io/pypi/pyversions/Client-API-VN\n :alt: PyPI - Python Version\n.. image:: https://img.shields.io/pypi/l/Client-API-VN\n :alt: PyPI - License\n\nDescription\n===========\n\nPython applications that use Biolovision/VisioNature (VN) API to:\n\n- download data from VN sites and stores it to a Postgresql database.\n- update sightings directly in VN site\n\nApplications are available either as:\n\n- Python modules from PyPI\n- Docker images from Docker Hub\n\nThey are tested under Linux Ubuntu or Debian. Other Linux\ndistributions could work. Windows is not tested at all and will\nprobably not work.\n\nInstallation - Python\n---------------------\n\nThese instructions present the steps required to install the\nPython applications.\n\nCreate a python virtual environment, activate it and update basic tools::\n\n python3 -m venv VN_env\n source VN_env/bin/activate\n python -m pip install --upgrade pip\n\nInstall from PyPI::\n\n pip install Client-API-VN\n\nInstallation - Docker\n---------------------\n\nThese instructions present the steps required to install the\nDocker applications::\n\n docker pull dthonon/client-api-vn\n docker run --name xfer_vn \\\n --mount source=xfer_vn,target=/root \\\n --workdir /root \\\n --tty --interactive \\\n dthonon/client-api-vn bash\n\nThe following steps are the common to both Python and Docker installation.\n\nGetting Started - transfer_vn\n-----------------------------\n\nInitialize the sample YAML file in your HOME directory and edit with\nyour local details. The YAML file is self documented::\n\n transfer_vn --init .evn_your_site.yaml\n editor $HOME/.evn_your_site.yaml\n\nCreate the database and tables::\n\n transfer_vn --db_create --json_tables_create --col_tables_create .evn_your_site.yaml\n\nYou can then download data, as enabled and filtered in the YAML file.\nBeware that, depending on the volume of observations,\nthis can take several hours. We recommend starting with a small taxonomic\ngroup first::\n\n transfer_vn --full .evn_your_site.yaml\n\nAfter this full download, data can be updated. For observations, only new,\nmodified or deleted observations are downloaded. For other controlers, a full\ndownload is always performed. Each controler runs on its own schedule,\ndefined in the YAML configuration file. To create or update, after\nmodifying the configuration file, the schedule::\n\n transfer_vn --schedule .evn_your_site.yaml\n\nOnce this is done, you can update the database with new observations::\n\n transfer_vn --update .evn_your_site.yaml\n\nNote: this script should run hourly or dayly in a cron job.\nIt must run at least every week.\n\nGetting Started - update_vn\n----------------------------\n\nInitialize the sample YAML file in your HOME directory and edit with\nyour local details. The YAML file is self documented::\n\n update_vn --init .evn_your_site.yaml\n editor $HOME/.evn_your_site.yaml\n\n\nPrerequisites\n-------------\n\nFor Linux and Postgresql installation, refer to `Server installation`_\n\n.. _Server installation: _server_install\n\nInstallation requires the following python module::\n\n pip\n\nAll other python dependencies are managed by pip install.\n\nCommand-line options - transfer_vn\n----------------------------------\n\nThe application runs as::\n\n transfer_vn options config\n\nwhere:\n\n- options command line options described below\n- config YAML file, located in $HOME directory, described in sample file\n\n-h, --help Prints help and exits\n--version Print version number\n--verbose Increase output verbosity\n--quiet Reduce output verbosity\n--init Initialize the YAML configuration file\n--db_drop Delete if exists database and roles\n--db_create Create database and roles\n--json_tables_create Create or recreate json tables\n--col_tables_create Create or recreate colums based tables\n--full Perform a full download\n--update Perform an incremental download\n--schedule Create or update the incremental update schedule\n--status Print downloading status (schedule, errors...)\n--count Count observations by site and taxo_group\n--profile Gather and print profiling times\n\nCommand-line options - update_vn\n----------------------------------\n\nThe application runs as::\n\n update_vn options config input\n\nwhere:\n\n- options command line options described below\n- config YAML file, located in $HOME directory, described in sample file\n- input CSV file listing sightings to be updated\n\n-h, --help Prints help and exits\n--version Print version number\n--verbose Increase output verbosity\n--quiet Reduce output verbosity\n--init Initialize the YAML configuration file\n\nCSV input file must contain the followin columns:\n\n- site, as defined in YAML site section\n- id_universal of the sighting to modify\n- path to the attribute to 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