From d450c68bfd18a6d0d1bc22aa4b60ae69a7dda4ab Mon Sep 17 00:00:00 2001 From: Emma Turetsky Date: Fri, 24 May 2024 14:53:54 -0500 Subject: [PATCH] Added another example for PelicanFS --- examples/pelicanfs_example.ipynb | 923 +++++++++++++++++++++++++++++++ 1 file changed, 923 insertions(+) create mode 100644 examples/pelicanfs_example.ipynb diff --git a/examples/pelicanfs_example.ipynb b/examples/pelicanfs_example.ipynb new file mode 100644 index 0000000..95e8bba --- /dev/null +++ b/examples/pelicanfs_example.ipynb @@ -0,0 +1,923 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# PelicanFS Example\n", + "\n", + "An example demonstrating the various ways to use the PelicanFS fsspec with data." + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [], + "source": [ + "# Display output of plots directly in Notebook\n", + "%matplotlib inline\n", + "import warnings\n", + "warnings.filterwarnings(\"ignore\")\n", + "\n", + "import xarray as xr\n", + "import fsspec\n", + "import seaborn as sns\n", + "import re\n", + "import nest_asyncio\n", + "nest_asyncio.apply()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "from pelicanfs.core import PelicanFileSystem, PelicanMap, OSDFFileSystem" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "import dask \n", + "from dask_jobqueue import PBSCluster\n", + "from dask.distributed import Client\n", + "from dask.distributed import performance_report" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using the PelicanFS Direction\n", + "\n", + "The following example instantiates and `PelicanFileSystem` with the OSDF Federation Discovery URL and then lists all the files in the `ncar` namespace below the `rda` folder." + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + 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'type': 'file'},\n", + " {'name': '/ncar/rda/ds712.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds390.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds277.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds769.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds605.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds607.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds111.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds816.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds318.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds067.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds600.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds207.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds240.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds124.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds313.2', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds535.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds520.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds867.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds115.7', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds564.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds541.2', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds726.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds401.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds463.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds728.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds391.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds090.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds285.3', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds701.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds271.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds110.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds067.4', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds256.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds069.5', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds736.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds808.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds698.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds770.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds625.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds510.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds610.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds389.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds383.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds094.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds511.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds627.2', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds728.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds469.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds627.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds082.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds719.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds633.2', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds260.4', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds553.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds277.8', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds289.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds631.4', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds513.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds104.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds582.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds228.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds633.1', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds682.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds999.5', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds353.4', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds630.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds208.0', 'size': None, 'type': 'file'},\n", + " {'name': '/ncar/rda/ds497.0', 'size': None, 'type': 'file'}]" + ] + }, + "execution_count": 9, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pelfs = PelicanFileSystem(\"pelican://osg-htc.org\")\n", + "pelfs.ls('/ncar/rda')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using the Pelican Map\n", + "\n", + "The following example shows loading in a file as a PelicanMap using the previous PelicanFileSytem object (which uses the `odsf` director)" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "file = PelicanMap('/chtc/PUBLIC/eturetsky/ncar-subset/ncar/monthly/cesm2LE-historical-cmip6-FLUT.zarr', pelfs)\n", + "test = xr.open_dataset(file, engine='zarr')\n", + "test" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Using an the OSDF protocol directly\n", + "\n", + "The following example shows how to use the `osdf://` protocol plus the filepath within the namespace to open a dataset" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "test = xr.open_dataset(\"osdf:///chtc/PUBLIC/eturetsky/ncar-subset/ncar/monthly/cesm2LE-historical-cmip6-FLUT.zarr\", engine='zarr')\n", + "test" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Use FSSpec directly\n", + "\n", + "Since PelicanFS is a registered backend with fsspec, it can also be used directly with fsspec with either the `osdf://` or `pelican://` protocols." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "open_test = fsspec.open(\"osdf:///chtc/PUBLIC/eturetsky/ncar-subset/ncar/monthly/cesm2LE-historical-cmip6-FLUT.zarr/.zmetadata\")\n", + "open_test" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.6" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +}