minor updates to listing datasets

sensors/06-list-datasets-by-plot.md → sensors/06-list-datasets-by-plot.Rmd

@@ -7,25 +7,26 @@ from the workbench or Globus.
 ## Getting started
 
 After installing terrautils, you should be able to import the *product* module.
-```
+```{python}
 from terrautils.products import get_sensor_list, unique_sensor_names
 from terrautils.products import get_file_listing, extract_file_paths
 ```
 
-The get\_sensor\_list and get\_file\_listing both require connection, url,
+The `get_sensor_list` and `get_file_listing` functions both require connection, url,
 and key parameters. *Connection* can be 'None', the *url* (called host in the
 code) should be something like https://terraref.ncsa.illinois.edu/clowder/.
 The *key* is a unique access key for the Clowder api.
 
 ## Getting the sensor list
+
 The first thing to get is the sensor name. This can be retreived using the
-get\_sensor\_list function. This function returns the full record which may
+`get_sensor_list` function. This function returns the full record which may
 be useful in some cases but primarily includes sensor names that include
-a plot id number. The utility function unique_sensor_names accpets the 
+a plot id number. The utility function `unique_sensor_names` accpets the 
 sensor list and provides a list of names suitable for use in the 
-get_file_listing function.
+`get_file_listing` function.
 
-```
+```{python}
 sensors = get_sensor_list(None, url, key)
 names = unique_sensor_names(sensors)
 ```
@@ -36,16 +37,16 @@ geostreams API. The currently available sensors are:
 * IR Surface Temperature
 * Thermal IR GeoTIFFs Datasets
 * flirIrCamera Datasets
-* (EL) sensor\_weather\_station
+* (EL) sensor_weather_station
 * Irrigation Observations
 * Canopy Cover
 * Energy Farm Observations SE
-* (EL) sensor\_par
+* (EL) sensor_par
 * scanner3DTop Datasets
 * Weather Observations
 * Energy Farm Observations NE
 * RGB GeoTIFFs Datasets
-* (EL) sensor\_co2
+* (EL) sensor_co2
 * stereoTop Datasets
 * Energy Farm Observations CEN
 
@@ -55,28 +56,30 @@ The geostreams API can be used to get a list of datasets that overlap a
 specific plot boundary and, optionally, limited by a time range. Iterating 
 over the datasets allows the paths to all the files to be extracted.
 
-```
+```{python}
 sensor = 'Thermal IR GeoTIFFs Datasets'
 sitename = 'MAC Field Scanner Season 1 Field Plot 101 W'
 datasets = get_file_listing(None, url, key, sensor, sitename)
 files = extract_file_paths(datasets)
 ```
 
 Datasets can be further filtered using the *since* and *until* parameters
-of get\_file\_listing with a date string.
+of `get_file_listing` with a date string.
 
-```
+```{python}
 dataset = get_file_listing(None, url, key, sensor, sitename, 
         since='2016-06-01', until='2016-06-10')
 ```
 
 
 # Alternative method
+
 The following method demonstrates the same approach using the Clowder API. This
 approach is useful for understanding the data layout and when the Python
 terrautils package is not available.
 
 ## Finding plot ID
+
 ```
 SENSOR_NAME = "MAC Field Scanner Season 1 Field Plot 101 W"
 GET https://terraref.ncsa.illinois.edu/clowder/api/geostreams/sensors?sensor_name={SENSOR_NAME}
@@ -85,7 +88,9 @@ GET https://terraref.ncsa.illinois.edu/clowder/api/geostreams/sensors?sensor_nam
 This returns a JSON object with an 'id' parameter. You can use this ID parameter to specify the right data stream.
 
 ## Finding stream ID within a plot
+
 The names are formatted as "<Sensor Group> Datasets (<Sensor ID>)".
+
 ```
 SENSOR_ID = 3355
 STREAM_NAME = "Thermal IR GeoTIFFs Datasets ({SENSOR_ID})"
@@ -95,13 +100,15 @@ GET https://terraref.ncsa.illinois.edu/clowder/api/geostreams/streams?stream_nam
 This returns a JSON object with an 'id' parameter. You can use this ID parameter to get the right datapoints.
 
 ## Listing Clowder file IDs for that plot & sensor stream
+
 ```
 STREAM_ID = "11586"
 GET https://terraref.ncsa.illinois.edu/clowder/api/geostreams/datapoints?stream_id={STREAM_ID}
 ```
 
 This returns a list of datapoint JSON objects, each with a 'properties' parameter that looks like:
-```
+
+```{python}
 properties: {
     dataset_name: "Thermal IR GeoTIFFs - 2016-05-09__12-07-57-990",
     source_dataset: "https://terraref.ncsa.illinois.edu/clowder/datasets/59fc9e7d4f0c3383c73d2905"
@@ -111,19 +118,23 @@ properties: {
 The source_dataset URL can be used to view the dataset in Clowder.
 
 You can also filter the datapoints by date:
+
 ```
 GET https://terraref.ncsa.illinois.edu/clowder/api/geostreams/datapoints?stream_id={STREAM_ID}&since=2017-01-02&until=2017-06-10
 ```
 
 ## Getting ROGER file path from dataset
+
 Given a source dataset URL, we can call the API to get the files and their paths.
+
 ```
 SOURCE_DATASET = "https://terraref.ncsa.illinois.edu/clowder/datasets/59fc9e7d4f0c3383c73d2905"
 # Add /api after /clowder, and add /files at the end of the URL
 GET "https://terraref.ncsa.illinois.edu/clowder/api/datasets/59fc9e7d4f0c3383c73d2905/files"
 ```
 
 This returns a list of files in the dataset and their paths if available:
+
 ```
 [
     {