Merge pull request #187 from NASA-Openscapes/harmony-transform

README.md

@@ -96,4 +96,3 @@ At our 2nd hackday we had a brief overview of cookbook progress since we'd last
 
 -   [Cookbook GitHub Issues](https://github.com/NASA-Openscapes/earthdata-cloud-cookbook/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc) - began organizing ideas in Issues
 
-## 

how-tos/subset.qmd

@@ -1,10 +1,124 @@
 ---
 title: How do I subset data granules?
+execute:
+  eval: false
 ---
 
-How do I subset a data granule using Harmony?  
-How do I subset an OPeNDAP granule in the cloud?  
-How do I subset a data granule using xarray?  
+## How do I subset a data granule using Harmony?
+
+::: {.panel-tabset group="language"}
+
+## Python
+
+Install the [harmony-py]("https://github.com/nasa/harmony-py") package:
+
+```{bash}
+# Install harmony-py
+pip install -U harmony-py
+```
+
+Import packages: 
+
+```{python}
+import datetime as dt
+
+from harmony import BBox, Client, Collection, Request, LinkType
+
+import s3fs
+import xarray as xr
+```
+
+### Set up Harmony client and authentication
+
+We will authenticate the following Harmony request using a netrc file. See the [appendix]("https://nasa-openscapes.github.io/earthdata-cloud-cookbook/appendix/authentication.html") for more information on [Earthdata Login]("https://urs.earthdata.nasa.gov/") and netrc setup. This basic line below to create a Harmony Client assumes that we have a .netrc available.
+
+```{python}
+harmony_client = Client()
+```
+### Create and submit Harmony request
+
+We are interested in the [GHRSST Level 4 MUR Global Foundation Sea Surface Temperature Analysis dataset](https://doi.org/10.5067/GHGMR-4FJ04). We are subsetting over the Pacific Ocean to the west of Mexico during 1:00 - 2:00 on 10 March 2021. The dataset is organized into daily files, so while we are specifying a single hour in our request, this will return that full day's worth of data. 
+
+```{python}
+dataset_short_name = 'MUR-JPL-L4-GLOB-v4.1'
+
+request = Request(
+  collection=Collection(id=dataset_short_name),
+  spatial=BBox(-125.469,15.820,-99.453,35.859),
+  temporal={
+    'start': dt.datetime(2021, 3, 10, 1),
+    'stop': dt.datetime(2021, 3, 10, 2)
+  }
+)
+
+job_id = harmony_client.submit(request)
+
+harmony_client.wait_for_processing(job_id)
+```
+### Open and read the subsetted file in `xarray`
+
+Harmony data outputs can be accessed within the cloud using the s3 URLs and AWS credentials provided in the Harmony job response. Using `aws_credentials` we can retrieve the credentials needed to access the Harmony s3 staging bucket and its contents. We then use the AWS `s3fs` package to create a file system that can then be read by xarray.
+
+```{python}
+results = harmony_client.result_urls(job_id, link_type=LinkType.s3)
+urls = list(results)
+url = urls[0]
+
+creds = harmony_client.aws_credentials()
+
+s3_fs = s3fs.S3FileSystem(
+    key=creds['aws_access_key_id'],
+    secret=creds['aws_secret_access_key'],
+    token=creds['aws_session_token'],
+    client_kwargs={'region_name':'us-west-2'},
+)
+
+f = s3_fs.open(url, mode='rb')
+ds = xr.open_dataset(f)
+ds
+```
+### Plot data
+
+Use the xarray built in plotting function to create a simple plot along the x and y dimensions of the dataset:
+
+```{python}
+ds.analysed_sst.plot() ;
+```
+
+## R
+
+R code coming soon!
+
+```{r}
+# Coming soon!
+```
+
+## Matlab
+
+Matlab code coming soon!
+
+```{bash}
+#| echo: true
+# Coming soon!
+```
+
+## Command Line
+
+With `wget` and `curl`:
+
+```{bash}
+# Coming soon!
+```
+
+
+
+:::
+
+## How do I subset an OPeNDAP granule in the cloud?
+
+
+## How do I subset a data granule using xarray?
+
 
 ## How do I download a subset of NetCDF-4?
 *this might be a deprecated idea*