Merge remote-tracking branch 'Unidata/main' into metno

metno · Jan 1, 2025 · 06cc19b · 06cc19b
2 parents 777a1a7 + 2c471cc
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diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -15,7 +15,7 @@
 # users just like we do for commit author emails.
 # docs/*  [email protected]
 
-* @haileyajohnson
+* @lesserwhirls
 
 #####################
 # top level modules #
@@ -26,16 +26,16 @@
 # classpath / not module specific matches #
 ###########################################
 
-**/thredds/server/radarServer2/** @dopplershift
+**/thredds/server/radarServer2/** @dopplershift @lesserwhirls
 
-**/opendap/** @DennisHeimbigner
-**/dap4/** @DennisHeimbigner
+**/opendap/** @DennisHeimbigner @lesserwhirls
+**/dap4/** @DennisHeimbigner @lesserwhirls
 
 ######################
 # general file types #
 ######################
 
-*.py @dopplershift
+*.py @dopplershift @lesserwhirls
 
 ####################
 # individual files #

diff --git a/.github/workflows/deps.yml b/.github/workflows/deps.yml
@@ -6,10 +6,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK 11
-        uses: actions/setup-java@v2
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '17'
       - name: Build with Gradle (refresh dependencies)
         run: ./gradlew clean classes testClasses assemble --refresh-dependencies
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -10,22 +10,25 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Setup Java 11
-        uses: actions/setup-java@v2
+      - name: Setup Java 17
+        uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '17'
       - name: Cache Gradle packages
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-          restore-keys: ${{ runner.os }}-gradle
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
       - name: Build docs using Gradle
         run: './gradlew :docs:build'
       - name: Upload a preview of the rendered html
         if: success()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: documentation_${{ github.sha }}
           path: docs/build/site
diff --git a/.github/workflows/style.yml b/.github/workflows/style.yml
@@ -6,16 +6,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK 11
-        uses: actions/setup-java@v2
+      - name: Set up JDK 17
+        uses: actions/setup-java@v4
         with:
-          distribution: 'adopt'
-          java-version: '11'
+          distribution: 'temurin'
+          java-version: '17'
       - name: Cache Gradle packages
-        uses: actions/cache@v1
+        uses: actions/cache@v4
         with:
-          path: ~/.gradle/caches
-          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
-          restore-keys: ${{ runner.os }}-gradle
+          path: |
+            ~/.gradle/caches
+            ~/.gradle/wrapper
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
       - name: Code Style Check with Gradle and Spotless
         run: ./gradlew clean spotlessCheck
diff --git a/.github/workflows/tds.yml b/.github/workflows/tds.yml
@@ -6,10 +6,9 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        java-version: [ 11 ]
-        java-vendor: [ 'zulu', 'temurin' ]
-        # test against tomcat 8.5.x and tomcat 9.x
-        servletcontainer: [ 'tomcat85', 'tomcat9' ]
+        java-version: [ 17 ]
+        java-vendor: [ 'temurin' ]
+        servletcontainer: [ 'tomcat10' ]
     steps:
       - uses: actions/checkout@v4
       - name: Build and test with Gradle (${{ matrix.java-vendor }} ${{ matrix.java-version }})
@@ -21,7 +20,7 @@ jobs:
           test-command: '-Dtds.content.root.path=$CONTENT_DIR -Dtds.test.gretty.container=${{ matrix.servletcontainer }} --info --stacktrace testAll'
         env:
           CONTENT_DIR: ${{ github.workspace }}/tds/src/test/content
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         if: failure()
         with:
           name: tds_JUnit_Results_${{ github.sha }}_AdoptOpenJDK-HS-${{ matrix.java }}-${{ matrix.servletcontainer }}

diff --git a/README.md b/README.md
@@ -26,9 +26,12 @@ respond to the confirmation email. Mailing list archives are available at:
 
 * https://www.unidata.ucar.edu/mailing_lists/archives/thredds/
 
-We appreciate feedback from users of this package. Please send comments,
-suggestions, and bug reports to <[email protected]>.
+We appreciate feedback from users of this package.
+Open a GitHub issue or discussion if you have comments,
+suggestions, or bug reports.
 Please identify the version of the package.
+For security or server set up issues that cannot be addressed on GitHub,
+you may send your question with the relevant details to <[email protected]>.
 
 ## THREDDS Catalogs
 

diff --git a/build.gradle b/build.gradle
@@ -51,9 +51,9 @@ allprojects {
   // Matches Maven's "project.version". Used in MANIFEST.MF for "Implementation-Version".
   // We try to follow semantic versioning, and thus we use <major>.<minor>.<patch>-<prerelease version>
   // <prerelease version> may be SNAPSHOT, alphax, betax, etc.
-  version = '5.5'
+  version = '5.6-SNAPSHOT'
   // Eventually, we'll stop appending "SNAPSHOT" to our versions and just use this.
-  status = 'release'
+  status = 'development'
 }
 
 // Matches Maven's "project.description".
@@ -101,7 +101,7 @@ ext {
 
 tasks.named('wrapper') {
   distributionType = Wrapper.DistributionType.ALL
-  gradleVersion = '6.9.1'
+  gradleVersion = '7.6.4'
 }
 
 gradle.projectsEvaluated {

diff --git a/dap4/d4servlet/build.gradle b/dap4/d4servlet/build.gradle
@@ -8,6 +8,7 @@ dependencies {
   implementation 'edu.ucar:httpservices'
   implementation 'edu.ucar:cdm-core'
 
+  implementation 'org.apache.commons:commons-lang3'
   compileOnly 'jakarta.servlet:jakarta.servlet-api'
   compileOnly 'org.slf4j:slf4j-api'
 }
diff --git a/dap4/d4servlet/src/main/java/dap4/servlet/DapController.java b/dap4/d4servlet/src/main/java/dap4/servlet/DapController.java
@@ -11,9 +11,9 @@
 import dap4.core.dmr.*;
 import dap4.core.util.*;
 import dap4.dap4lib.*;
-import javax.servlet.http.HttpServlet;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServlet;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.*;
 import java.net.MalformedURLException;
 import java.nio.ByteOrder;

diff --git a/dap4/d4servlet/src/main/java/dap4/servlet/DapDSR.java b/dap4/d4servlet/src/main/java/dap4/servlet/DapDSR.java
@@ -9,14 +9,16 @@
 import dap4.dap4lib.DapProtocol;
 import dap4.dap4lib.RequestMode;
 
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringWriter;
 import java.net.MalformedURLException;
 import java.net.URL;
 
+import org.apache.commons.lang3.StringEscapeUtils;
+
 /**
  * Generate the DSR for a dataset.
  * Currently only generates a minimal DSR.
@@ -132,6 +134,8 @@ protected String getTemplate(ResponseFormat format) throws IOException {
   }
 
   protected void substitute(StringBuilder buf, String macro, String value) {
+    value = StringEscapeUtils.escapeHtml4(value);
+
     int from = 0;
     String tag = "${" + macro + "}";
     int taglen = tag.length();

diff --git a/dap4/d4servlet/src/main/java/dap4/servlet/DapRequest.java b/dap4/d4servlet/src/main/java/dap4/servlet/DapRequest.java
@@ -7,8 +7,8 @@
 
 import dap4.core.util.*;
 import dap4.dap4lib.RequestMode;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.net.URISyntaxException;

diff --git a/dap4/d4ts/build.gradle b/dap4/d4ts/build.gradle
@@ -8,12 +8,12 @@ dependencies {
   implementation 'edu.ucar:dap4'
   implementation project(":dap4:d4servlet")
 
-  providedCompile "jakarta.servlet:jakarta.servlet-api:${depVersion.javaxServletApi}"
+  providedCompile "jakarta.servlet:jakarta.servlet-api:${depVersion.jakartaServletApi}"
 
   compileOnly 'org.slf4j:slf4j-api'
 
-  runtime 'org.apache.logging.log4j:log4j-slf4j-impl'
-  runtime 'org.apache.logging.log4j:log4j-web'
+  runtimeOnly 'org.apache.logging.log4j:log4j-slf4j-impl'
+  runtimeOnly 'org.apache.logging.log4j:log4j-jakarta-web'
 
   compileOnly 'org.slf4j:slf4j-api'
 }

diff --git a/dap4/d4ts/src/main/java/dap4/d4ts/D4TSServlet.java b/dap4/d4ts/src/main/java/dap4/d4ts/D4TSServlet.java
@@ -12,9 +12,9 @@
 import dap4.dap4lib.DapLog;
 import dap4.servlet.*;
 
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;

diff --git a/dap4/d4ts/src/main/java/dap4/d4ts/FrontPage.java b/dap4/d4ts/src/main/java/dap4/d4ts/FrontPage.java
@@ -11,8 +11,8 @@
 import dap4.dap4lib.DapLog;
 import dap4.servlet.DapRequest;
 
-import javax.servlet.ServletContext;
-import javax.servlet.http.HttpServletResponse;
+import jakarta.servlet.ServletContext;
+import jakarta.servlet.http.HttpServletResponse;
 import java.io.*;
 import java.net.MalformedURLException;
 import java.net.URL;

diff --git a/dap4/d4ts/src/main/java/dap4/d4ts/HttpHeadFilter.java b/dap4/d4ts/src/main/java/dap4/d4ts/HttpHeadFilter.java
@@ -12,11 +12,11 @@
  */
 package dap4.d4ts;
 
-import javax.servlet.*;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletRequestWrapper;
-import javax.servlet.http.HttpServletResponse;
-import javax.servlet.http.HttpServletResponseWrapper;
+import jakarta.servlet.*;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequestWrapper;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.servlet.http.HttpServletResponseWrapper;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;

diff --git a/dap4/d4ts/src/main/webapp/WEB-INF/templates/dap4.dsr.html.template b/dap4/d4ts/src/main/webapp/WEB-INF/templates/dap4.dsr.html.template
@@ -7,7 +7,7 @@ See LICENSE file for more info.
 -->
 <head>
 <meta http-equiv="Content-Type" content="text/html">
-<meta> name="title" content="Dataset Services Response">
+<meta name="title" content="Dataset Services Response">
 <style>
 table.t1, td.t1, th.t1 {border: 1px solid}
 td.t1, th.t1 {padding:4px}

diff --git a/docs/adminguide/src/site/_config.yml b/docs/adminguide/src/site/_config.yml
@@ -2,7 +2,7 @@
 theme: unidata-jekyll-theme
 
 # this will appear in an HTML meta tag, sidebar, and perhaps elsewhere
-docset_version: 5.5
+docset_version: 5.6
 
 # this appears on the top navigation bar next to the home button
 topnav_title: THREDDS Data Server (TDS)

diff --git a/docs/adminguide/src/site/_data/sidebars/admin_sidebar.yml b/docs/adminguide/src/site/_data/sidebars/admin_sidebar.yml
@@ -1,7 +1,7 @@
 entries:
 - title: Sidebar
   product: Administrator's Guide
-  version: 5.5
+  version: 5.6
   folders:
   - title:
     output: pdf

diff --git a/docs/adminguide/src/site/pages/installation_upgrade/JVMSettings.md b/docs/adminguide/src/site/pages/installation_upgrade/JVMSettings.md
@@ -41,7 +41,8 @@ export JAVA_HOME="/usr/local/jdk"
 # THIS IS CRITICAL and there is NO DEFAULT - 
 # the TDS will not start without this.
 #
-CONTENT_ROOT=-Dtds.content.root.path=/data/content
+CONTENT_ROOT=/data/content
+CONTENT_ROOT_OPT=-Dtds.content.root.path=$CONTENT_ROOT
 
 # Set java prefs related variables (used by the wms service)
 JAVA_PREFS_ROOTS="-Djava.util.prefs.systemRoot=$CONTENT_ROOT/thredds/javaUtilPrefs \
@@ -57,7 +58,7 @@ HEADLESS="-Djava.awt.headless=true"
 #
 # Standard setup.
 #
-JAVA_OPTS="$CONTENT_ROOT $NORMAL $HEAP_DUMP $HEADLESS $JAVA_PREFS_ROOTS"
+JAVA_OPTS="$CONTENT_ROOT_OPT $NORMAL $HEAP_DUMP $HEADLESS $JAVA_PREFS_ROOTS"
 
 export JAVA_OPTS
 ~~~

diff --git a/docs/adminguide/src/site/pages/overview/TDSVetted.md b/docs/adminguide/src/site/pages/overview/TDSVetted.md
@@ -37,7 +37,10 @@ When identified, any security-related issues are addressed immediately and fixed
 ### Providing Feedback
 
 We appreciate feedback from users of the TDS!
-Send comments, suggestions, and bug reports to <{{site.feedback_email}}>. 
+Open a GitHub issue or discussion [here](https://github.com/Unidata/tds) if you have comments,
+suggestions, or bug reports.
 Please identify the version of the package.
+For server set up issues that cannot be addressed on GitHub,
+you may send your question with the relevant details to <[email protected]>.
 
 To report a potential security-related issue or bug, contact: <[email protected]>
diff --git a/docs/adminguide/src/site/pages/tds_tutorial/tds_configuration/AddingNcss.md b/docs/adminguide/src/site/pages/tds_tutorial/tds_configuration/AddingNcss.md
@@ -32,21 +32,28 @@ Details on other configuration options for NCSS are available in the [`threddsCo
 
 ## Serving Datasets With NCSS
 
-In your configuration catalogs, you must define the service like this:
+In your configuration catalogs, you must define the service based on the type of data being served.
+For Feature Type `GRID`, use:
 
 ~~~xml
-<service name="subsetServer" serviceType="NetcdfSubset" base="/thredds/ncss/" />
+<service name="ncssGrid" serviceType="NetcdfSubset" base="/thredds/ncss/grid/" />
+~~~
+
+For Feature Types `POINT` or `STATION`, use:
+
+~~~xml
+<service name="ncssPoint" serviceType="NetcdfSubset" base="/thredds/ncss/point/" />
 ~~~
 
 Then as usual, add the service to any datasets that you want served, e.g.:
 
 ~~~xml
 <dataset name="datasetName" ID="datasetID" urlPath="/my/urlPath"> 
-   <serviceName>subsetServer</serviceName> 
+   <serviceName>ncssGrid</serviceName> 
 </dataset> 
 ~~~
 
-Note that the name of the service (`subsetServer` in this example) is arbitrary, but the `serviceType` and base must be _exactly_ as shown.
+Note that the name of the service (`ncssGrid` in this example) is arbitrary, but the `serviceType` and base must be _exactly_ as shown.
 
 ## Restrictions On What Files Can Be Served
 

diff --git a/docs/adminguide/src/site/pages/tds_tutorial/tds_configuration/ConfigCatalog.md b/docs/adminguide/src/site/pages/tds_tutorial/tds_configuration/ConfigCatalog.md
@@ -111,13 +111,13 @@ Therefore, it is required that service base URLs must [exactly match the values
 
 * NetCDF Subset Service (Grid Data)
    ~~~xml
-   <service name="ncss" serviceType="NetcdfSubset" base="/thredds/ncss/grid/" />
+   <service name="ncssGrid" serviceType="NetcdfSubset" base="/thredds/ncss/grid/" />
    ~~~
 
 * NetCDF Subset Service (Point Data)
 
    ~~~xml
-   <service name="ncss" serviceType="NetcdfSubset" base="/thredds/ncss/point/" />
+   <service name="ncssPoint" serviceType="NetcdfSubset" base="/thredds/ncss/point/" />
    ~~~
 
 * WCS