Upgrade dependencies (#67)

Author: labkey-adam

CHANGELOG.md

@@ -5,6 +5,12 @@
 * [Issue 49238](https://www.labkey.org/home/Developer/issues/issues-details.view?issueId=49238): Fix so all command responses correctly decode as UTF-8.
 * Add MoveRowsCommand to query
   * Earliest compatible LabKey Server version: 24.1.0
+* Remove deprecated `GetDomainCommand`; use `GetDomainDetailsCommand` instead.
+* Remove deprecated method `RowsResponse.getRequiredVersion()`.
+* Deprecate `GetUsersCommand` methods `getIncludeDeactivated()` and `setIncludeDeactivated()`; use `getIncludeInactive()`
+  and `setIncludeInactive()` instead.
+* Update Commons Logging, Gradle, Gradle Plugins, HttpClient, and HttpCore versions
+* Remove Hamcrest references (unused)
 
 ## version 6.0.0
 *Released*: 1 December 2023

build.gradle

@@ -82,17 +82,6 @@ dependencies {
     implementation "commons-codec:commons-codec:${commonsCodecVersion}"
 }
 
-configurations.all
-        { Configuration config ->
-            resolutionStrategy {
-                // force versions so we can remain consistent with what comes through transitively
-                // in :server:modules:platform:api via jackson
-                force "org.hamcrest:hamcrest-core:${hamcrestVersion}"
-                force "org.hamcrest:hamcrest-library:${hamcrestVersion}"
-                force "junit:junit:${junitVersion}"
-            }
-        }
-
 jar {
     sourceCompatibility = project.sourceCompatibility
     targetCompatibility = project.targetCompatibility

gradle.properties

@@ -7,20 +7,19 @@ artifactory_contextUrl=https://labkey.jfrog.io/artifactory
 sourceCompatibility=17
 targetCompatibility=17
 
-gradlePluginsVersion=1.43.1
+gradlePluginsVersion=2.0.0
 
 commonsCodecVersion=1.16.0
-commonsLoggingVersion=1.2
+commonsLoggingVersion=1.3.0
 
-hamcrestVersion=1.3
-
-httpclient5Version=5.2.1
-httpcore5Version=5.2.3
+httpclient5Version=5.3
+httpcore5Version=5.2.4
 
 jsonObjectVersion=20231013
 
 junitVersion=4.13.2
 
+# Obsolete? Switch to com.opencsv:opencsv 5.9? Or maybe just get rid of MS2SearchClient (only user)?
 opencsvVersion=2.3
 
 #If iterating on the java client api and deploying it to a non-LabKey directory, uncomment and set this property (or set at command line),

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradlew

@@ -145,15 +145,15 @@ if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
     case $MAX_FD in #(
       max*)
         # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         MAX_FD=$( ulimit -H -n ) ||
             warn "Could not query maximum file descriptor limit"
     esac
     case $MAX_FD in  #(
       '' | soft) :;; #(
       *)
         # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-        # shellcheck disable=SC3045
+        # shellcheck disable=SC2039,SC3045
         ulimit -n "$MAX_FD" ||
             warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
@@ -202,11 +202,11 @@ fi
 # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
-# Collect all arguments for the java command;
-#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
-#     shell script including quotes and variable substitutions, so put them in
-#     double quotes to make sure that they get re-expanded; and
-#   * put everything else in single quotes, so that it's not re-expanded.
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \

src/org/labkey/remoteapi/Connection.java

@@ -391,12 +391,6 @@ public Connection stopImpersonating() throws IOException, CommandException
         return this;
     }
 
-    @Deprecated // Will be removed soon. Use stopImpersonating() instead.
-    public Connection stopImpersonate() throws IOException, CommandException
-    {
-        return stopImpersonating();
-    }
-
     CloseableHttpResponse executeRequest(HttpUriRequest request, Integer timeout) throws IOException, AuthenticationException
     {
         // Delegate authentication setup to CredentialsProvider

src/org/labkey/remoteapi/domain/GetDomainCommand.java

@@ -34,8 +34,6 @@
  */
 abstract class RowsResponse extends CommandResponse
 {
-    private final double _requiredVersion;
-
     /**
      * Constructs a new RowsResponse given the specified text and status code.
      * @param text The response text.
@@ -47,22 +45,11 @@ abstract class RowsResponse extends CommandResponse
     RowsResponse(String text, int statusCode, String contentType, JSONObject json, HasRequiredVersion hasRequiredVersion)
     {
         super(text, statusCode, contentType, json);
-        _requiredVersion = hasRequiredVersion.getRequiredVersion();
-        fixupParsedData(_requiredVersion);
+        double requiredVersion = hasRequiredVersion.getRequiredVersion();
+        fixupParsedData(requiredVersion);
         caseInsensitizeRowMaps();
     }
 
-    /**
-     * Returns the API version number required by the source command. This response returns data in a different format
-     * depending on the required version
-     * @return the requested API version number
-     */
-    @Deprecated // Just needed for fixup -- exposing this outside the class seems unnecessary. TODO: Remove this in v6.0.0
-    public double getRequiredVersion()
-    {
-        return _requiredVersion;
-    }
-
     /**
      * Returns the list of rows from the parsed response data. Note that numbers in the map values will be either of
      * type Double or type Long depending on the presence of a decimal point. The most reliable way to work with them
@@ -113,12 +100,12 @@ else if ("int".equalsIgnoreCase(type))
         }
 
         // If no fields to fixup, just return
-        if (dateFields.size() == 0 && floatFields.size() == 0 && intFields.size() == 0)
+        if (dateFields.isEmpty() && floatFields.isEmpty() && intFields.isEmpty())
             return;
 
         // If no rows, just return
         List<Map<String, Object>> rows = getRows();
-        if (null == rows || rows.size() == 0)
+        if (null == rows || rows.isEmpty())
             return;
 
         // The selectRows.api returns dates in a very particular format so that JavaScript can parse them into actual

src/org/labkey/remoteapi/query/RowsResponse.java

@@ -28,7 +28,7 @@ public class GetUsersCommand extends GetCommand<GetUsersResponse>
     private int _groupId = -1;
     private String _name;
     private String _group;
-    private Boolean _includeDeactivated;
+    private boolean _includeInactive = false;
 
     public GetUsersCommand()
     {
@@ -67,32 +67,44 @@ public void setGroup(String group)
         _group = group;
     }
 
-    /** @return the first part of the user name, useful for user name completion */
+    /** @return the first part of the username, useful for username completion */
     public String getName()
     {
         return _name;
     }
 
     /**
-     * @param name The first part of the user name, useful for user name completion. If specified, only users whose
+     * @param name The first part of the username, useful for username completion. If specified, only users whose
      * email address or display name starts with the value supplied will be returned.
      */
     public void setName(String name)
     {
         _name = name;
     }
 
+    @Deprecated(forRemoval = true) // Remove in 7.0.0
+    public Boolean getIncludeDeactivated()
+    {
+        return _includeInactive;
+    }
+
+    @Deprecated(forRemoval = true) // Remove in 7.0.0
+    public void setIncludeDeactivated(Boolean includeInactive)
+    {
+        _includeInactive = (null != includeInactive && includeInactive);
+    }
+
     /**
-     * @return Flag to request Active user accounts only
+     * @return Flag to request inactive users as well
      */
-    public Boolean includeDeactivated()
+    public boolean getIncludeInactive()
     {
-        return _includeDeactivated;
+        return _includeInactive;
     }
 
-    public void setIncludeDeactivated(Boolean active)
+    public void setIncludeInactive(boolean includeInactive)
     {
-        _includeDeactivated = active;
+        _includeInactive = includeInactive;
     }
 
     @Override
@@ -111,9 +123,9 @@ protected Map<String, Object> createParameterMap()
         {
             params.put("name", _name);
         }
-        if (_includeDeactivated != null)
+        if (_includeInactive)
         {
-            params.put("active", !includeDeactivated());
+            params.put("active", false);
         }
         return params;
     }