add more configuration options to THREDDS catalog

CHANGES.md

@@ -15,7 +15,29 @@
 [Unreleased](https://github.com/bird-house/birdhouse-deploy/tree/master) (latest)
 ------------------------------------------------------------------------------------------------------------------
 
-[//]: # (list changes here, using '-' for each new entry, remove this when items are added)
+## Changes
+
+- THREDDS: add more options to configure catalog.xml
+  - Currently the default THREDDS configuration creates two default datasets, the Service Data dataset and the 
+    Main dataset. The Service Data dataset is used internally and hosts WPS outputs. The Main dataset is the
+    place where users can access data served by THREDDS. Both of these are configured to serve files with the following 
+    extensions: .nc .ncml .txt .md .rst .csv
+
+  - In order to allow the THREDDS server to serve files with additional extensions, this introduces two new
+    variables: 
+    - `THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS`: this allows users to specify additional [filter 
+        elements](https://docs.unidata.ucar.edu/tds/current/userguide/tds_dataset_scan_ref.html#including-only-desired-files) to the Service Data dataset. This is especially useful if a WPS 
+        outputs files with an extension other than the default (eg: .h5) to the `wps_outputs/` directory.
+    - `THREDDS_DATASET_DATASETSCAN_BODY`: this allows users to specify the whole body of the main dataset's 
+       [`<datasetScan>`](https://docs.unidata.ucar.edu/tds/current/userguide/tds_dataset_scan_ref.html) element.
+       This allows users to fully customize how this dataset serves files.
+
+  - We limit the configuration options for the Service Data dataset more than the main dataset because the Service
+    Data dataset requires a basic configuration in order to properly serve WPS outputs. Making significant changes
+    to this configuration could have unexpected negative impacts on WPS usage.
+
+  - The defaults for these new variables are fully backwards compatible. Without changing these variables, the THREDDS
+    server should behave exactly the same as before. 
 
 [2.5.3](https://github.com/bird-house/birdhouse-deploy/tree/2.5.3) (2024-09-11)
 ------------------------------------------------------------------------------------------------------------------

birdhouse/components/thredds/catalog.xml.template

@@ -27,24 +27,14 @@
         <include wildcard="*.md" />
         <include wildcard="*.rst" />
         <include wildcard="*.csv" />
+        ${THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS}
       </filter>
 
     </datasetScan>
 
     <datasetScan name="${THREDDS_DATASET_LOCATION_NAME}" ID="${THREDDS_DATASET_URL_PATH}" path="${THREDDS_DATASET_URL_PATH}" location="${THREDDS_DATASET_LOCATION_ON_CONTAINER}">
 
-      <metadata inherited="true">
-        <serviceName>all</serviceName>
-      </metadata>
-
-      <filter>
-        <include wildcard="*.nc" />
-        <include wildcard="*.ncml" />
-        <include wildcard="*.txt" />
-        <include wildcard="*.md" />
-        <include wildcard="*.rst" />
-        <include wildcard="*.csv" />
-      </filter>
+      ${THREDDS_DATASET_DATASETSCAN_BODY}
 
     </datasetScan>
 

birdhouse/components/thredds/default.env

@@ -17,7 +17,22 @@ export THREDDS_SERVICE_DATA_LOCATION_NAME='Birdhouse'
 export THREDDS_DATASET_URL_PATH='datasets'
 export THREDDS_SERVICE_DATA_URL_PATH='birdhouse'
 
+export THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS=''
 
+export THREDDS_DATASET_DATASETSCAN_BODY='
+      <metadata inherited="true">
+        <serviceName>all</serviceName>
+      </metadata>
+
+      <filter>
+        <include wildcard="*.nc" />
+        <include wildcard="*.ncml" />
+        <include wildcard="*.txt" />
+        <include wildcard="*.md" />
+        <include wildcard="*.rst" />
+        <include wildcard="*.csv" />
+      </filter>
+'
 
 # add any new variables not already in 'VARS' or 'OPTIONAL_VARS' that must be replaced in templates here
 VARS="
@@ -28,6 +43,7 @@ VARS="
   \$THREDDS_DATASET_LOCATION_NAME
   \$THREDDS_DATASET_URL_PATH
   \$THREDDS_DATASET_LOCATION_ON_CONTAINER
+  \$THREDDS_DATASET_DATASETSCAN_BODY
 "
 
 OPTIONAL_VARS="
@@ -39,6 +55,7 @@ OPTIONAL_VARS="
   \$THREDDS_IMAGE
   \$THREDDS_IMAGE_URI
   \$THREDDS_ADDITIONAL_CATALOG
+  \$THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS
 "
 
 export DELAYED_EVAL="

birdhouse/env.local.example

@@ -476,6 +476,40 @@ export THREDDS_ADDITIONAL_CATALOG=""
 #    </datasetScan>
 #"
 
+# Additional file filters to add for the Service Data THREDDS dataset. By default, the Service Data dataset will only
+# serve files with the following extensions: .nc .ncml .txt .md .rst .csv
+# If you need this dataset to serve other files you should update the THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS to add
+# additional file filters.
+# This may be useful to set if a WPS outputs files to the wps_outputs/ directory (hosted under the Service Data dataset) 
+# in a file format other than one of the defaults.
+# See the example below which would also enable serving .png and .h5 files.
+#export THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS="
+#    <include wildcard="*.png" />
+#    <include wildcard="*.h5" />
+#"
+
+# Set this variable to customize the body of the <datasetScan> XML element for the main THREDDS dataset. This is typically
+# the dataset where you would store most of the data served by THREDDS (additional datasets can be configured by setting the
+# THREDDS_ADDITIONAL_CATALOG variable).
+# By default, the main dataset will only serve files with the following extensions: .nc .ncml .txt .md .rst .csv and will use
+# the THREDDS service named "all" (see components/thredds/catalog.xml.template). However this can be customized if desired.
+# See the example below which would change the configuration to also serve .h5 and .json files instead of .md and .rst files.
+# See the THREDDS documentation for the <datasetScan> element for all configuration options.
+#export THREDDS_DATASET_DATASETSCAN_BODY='
+#      <metadata inherited="true">
+#        <serviceName>all</serviceName>
+#      </metadata>
+#
+#      <filter>
+#        <include wildcard="*.nc" />
+#        <include wildcard="*.ncml" />
+#        <include wildcard="*.txt" />
+#        <include wildcard="*.h5" />
+#        <include wildcard="*.json" />
+#        <include wildcard="*.csv" />
+#      </filter>
+#'
+
 # Allow using Github as external AuthN/AuthZ provider with Magpie
 #   To setup Github as login, goto <https://github.com/settings/developers> under section [OAuth Apps]
 #   and create a new Magpie application with configurations: