From 23d58acf6ec5f4b718ce53a3716123001d16ea33 Mon Sep 17 00:00:00 2001
From: mishaschwartz <4380924+mishaschwartz@users.noreply.github.com>
Date: Fri, 11 Oct 2024 14:52:07 -0400
Subject: [PATCH] review feedback

---
 CHANGES.md                                    | 18 +++++++--------
 .../components/thredds/catalog.xml.template   | 23 ++++++++-----------
 birdhouse/components/thredds/default.env      | 18 ++++++++++-----
 3 files changed, 30 insertions(+), 29 deletions(-)

diff --git a/CHANGES.md b/CHANGES.md
index 174b71db..03c1ca4b 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -17,27 +17,27 @@
 
 ## 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
+- THREDDS: add more options to configure `catalog.xml`
+  - 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: 
+    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 
+        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 
+    - `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
+  - 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. 
+    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)
 ------------------------------------------------------------------------------------------------------------------
diff --git a/birdhouse/components/thredds/catalog.xml.template b/birdhouse/components/thredds/catalog.xml.template
index 32553173..17e3b257 100644
--- a/birdhouse/components/thredds/catalog.xml.template
+++ b/birdhouse/components/thredds/catalog.xml.template
@@ -4,14 +4,14 @@
          xmlns:xlink="http://www.w3.org/1999/xlink" >
 
     <service name="all" serviceType="Compound" base="" >
-        <service name="http" serviceType="HTTPServer" base="/twitcher/ows/proxy/thredds/fileServer/" />
-        <service name="odap" serviceType="OpenDAP" base="/twitcher/ows/proxy/thredds/dodsC/" />
-        <service name="ncml" serviceType="NCML" base="/twitcher/ows/proxy/thredds/ncml/"/>
-        <service name="uddc" serviceType="UDDC" base="/twitcher/ows/proxy/thredds/uddc/"/>
-        <service name="iso" serviceType="ISO" base="/twitcher/ows/proxy/thredds/iso/"/>
-        <service name="wcs" serviceType="WCS" base="/twitcher/ows/proxy/thredds/wcs/" />
-        <service name="wms" serviceType="WMS" base="/twitcher/ows/proxy/thredds/wms/" />
-        <service name="subsetServer" serviceType="NetcdfSubset" base="/twitcher/ows/proxy/thredds/ncss/" />
+        <service name="http" serviceType="HTTPServer" base="${TWITCHER_PROTECTED_PATH}/thredds/fileServer/" />
+        <service name="odap" serviceType="OpenDAP" base="${TWITCHER_PROTECTED_PATH}/thredds/dodsC/" />
+        <service name="ncml" serviceType="NCML" base="${TWITCHER_PROTECTED_PATH}/thredds/ncml/"/>
+        <service name="uddc" serviceType="UDDC" base="${TWITCHER_PROTECTED_PATH}/thredds/uddc/"/>
+        <service name="iso" serviceType="ISO" base="${TWITCHER_PROTECTED_PATH}/thredds/iso/"/>
+        <service name="wcs" serviceType="WCS" base="${TWITCHER_PROTECTED_PATH}/thredds/wcs/" />
+        <service name="wms" serviceType="WMS" base="${TWITCHER_PROTECTED_PATH}/thredds/wms/" />
+        <service name="subsetServer" serviceType="NetcdfSubset" base="${TWITCHER_PROTECTED_PATH}/thredds/ncss/" />
     </service>
 
     <datasetScan name="${THREDDS_SERVICE_DATA_LOCATION_NAME}" ID="${THREDDS_SERVICE_DATA_URL_PATH}" path="${THREDDS_SERVICE_DATA_URL_PATH}" location="${THREDDS_SERVICE_DATA_LOCATION_ON_CONTAINER}">
@@ -21,12 +21,7 @@
       </metadata>
 
       <filter>
-        <include wildcard="*.nc" />
-        <include wildcard="*.ncml" />
-        <include wildcard="*.txt" />
-        <include wildcard="*.md" />
-        <include wildcard="*.rst" />
-        <include wildcard="*.csv" />
+        ${THREDDS_DEFAULT_FILE_FILTERS}
         ${THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS}
       </filter>
 
diff --git a/birdhouse/components/thredds/default.env b/birdhouse/components/thredds/default.env
index 74450f0f..d3b43e3f 100644
--- a/birdhouse/components/thredds/default.env
+++ b/birdhouse/components/thredds/default.env
@@ -17,6 +17,15 @@ export THREDDS_SERVICE_DATA_LOCATION_NAME='Birdhouse'
 export THREDDS_DATASET_URL_PATH='datasets'
 export THREDDS_SERVICE_DATA_URL_PATH='birdhouse'
 
+export THREDDS_DEFAULT_FILE_FILTERS='
+    <include wildcard="*.nc" />
+    <include wildcard="*.ncml" />
+    <include wildcard="*.txt" />
+    <include wildcard="*.md" />
+    <include wildcard="*.rst" />
+    <include wildcard="*.csv" />
+'
+
 export THREDDS_SERVICE_DATA_EXTRA_FILE_FILTERS=''
 
 export THREDDS_DATASET_DATASETSCAN_BODY='
@@ -25,12 +34,7 @@ export THREDDS_DATASET_DATASETSCAN_BODY='
       </metadata>
 
       <filter>
-        <include wildcard="*.nc" />
-        <include wildcard="*.ncml" />
-        <include wildcard="*.txt" />
-        <include wildcard="*.md" />
-        <include wildcard="*.rst" />
-        <include wildcard="*.csv" />
+        ${THREDDS_DEFAULT_FILE_FILTERS}
       </filter>
 '
 
@@ -44,6 +48,7 @@ VARS="
   \$THREDDS_DATASET_URL_PATH
   \$THREDDS_DATASET_LOCATION_ON_CONTAINER
   \$THREDDS_DATASET_DATASETSCAN_BODY
+  \$THREDDS_DEFAULT_FILE_FILTERS
 "
 
 OPTIONAL_VARS="
@@ -64,4 +69,5 @@ export DELAYED_EVAL="
   THREDDS_SERVICE_DATA_LOCATION_ON_HOST
   THREDDS_IMAGE
   THREDDS_IMAGE_URI
+  THREDDS_DATASET_DATASETSCAN_BODY
 "