Gh-987: Upgrade dependencies (#995)

* Update selenium to the latest version * Add missing plugin version This was defaulting to a very old beta version * Exclude Log4j dependencies * Adjust plugin property changed in Gaffer * Remove plugin versions which are now managed centrally * Replace usage of CloseableIterable and WrappedCloseableIterable with Iterable * Replace findbugs with spotbugs * Updated Gaffer version to 2.0.0-alpha-0.2 (#996) * Updated Gaffer version to 2.0.0-alpha-0.2 * Added new koryphe function to gafferpy Co-authored-by: Gaffer <github-actions@github.com> * Replace tomcat7-maven-plugin with cargo-maven3-plugin, upgrade to Tomcat 9 * Fix Selenium tests to be able to run again Co-authored-by: t92549 <80890692+t92549@users.noreply.github.com> Co-authored-by: Gaffer <github-actions@github.com>
gchq · May 3, 2022 · 6687617 · 6687617
1 parent 278791f
commit 6687617
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diff --git a/NOTICES b/NOTICES
@@ -20,7 +20,7 @@ Gaffer tools is built using maven. This process will automatically pull in depen
  projects below.
 
 
-Gaffer (uk.gov.gchq.gaffer:gaffer2:2.0.0-alpha-0.1):
+Gaffer (uk.gov.gchq.gaffer:gaffer2:2.0.0-alpha-0.2):
 
 - Apache License, Version 2.0
 

diff --git a/cd/setup_ui_system_tests.sh b/cd/setup_ui_system_tests.sh
@@ -3,7 +3,7 @@
 set -e
 
 mvn install -P quick,road-traffic-demo -B -pl ui &
-curl -OL https://github.com/mozilla/geckodriver/releases/download/v0.23.0/geckodriver-v0.23.0-linux64.tar.gz
-tar -xf geckodriver-v0.23.0-linux64.tar.gz
+curl -OL https://github.com/mozilla/geckodriver/releases/download/v0.31.0/geckodriver-v0.31.0-linux64.tar.gz
+tar -xf geckodriver-v0.31.0-linux64.tar.gz
 mv geckodriver ui/
 sleep 1m
diff --git a/mini-accumulo-cluster/pom.xml b/mini-accumulo-cluster/pom.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!--
-  ~ Copyright 2016-2019 Crown Copyright
+  ~ Copyright 2016-2022 Crown Copyright
   ~
   ~ Licensed under the Apache License, Version 2.0 (the "License");
   ~ you may not use this file except in compliance with the License.
@@ -40,16 +40,49 @@
             <groupId>org.apache.accumulo</groupId>
             <artifactId>accumulo-minicluster</artifactId>
             <version>${accumulo.version}</version>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.accumulo</groupId>
             <artifactId>accumulo-core</artifactId>
             <version>${accumulo.version}</version>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-hdfs</artifactId>
             <version>${hadoop.version}</version>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
     </dependencies>
 
@@ -58,6 +91,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-assembly-plugin</artifactId>
+                <version>3.3.0</version>
                 <configuration>
                     <skipAssembly>${skip.jar-with-dependencies}</skipAssembly>
                 </configuration>

diff --git a/performance-testing/performance-testing-accumulo-store/pom.xml b/performance-testing/performance-testing-accumulo-store/pom.xml
@@ -32,12 +32,34 @@
             <artifactId>accumulo-minicluster</artifactId>
             <version>${accumulo.version}</version>
             <scope>test</scope>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-hdfs</artifactId>
             <version>${hadoop.version}</version>
             <scope>test</scope>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>uk.gov.gchq.gaffer</groupId>

diff --git a/...ov/gchq/gaffer/accumulostore/performancetesting/ingest/BytesWritableElementGenerator.java b/...ov/gchq/gaffer/accumulostore/performancetesting/ingest/BytesWritableElementGenerator.java
@@ -17,7 +17,6 @@
 
 import org.apache.hadoop.io.BytesWritable;
 
-import uk.gov.gchq.gaffer.commonutil.iterable.WrappedCloseableIterable;
 import uk.gov.gchq.gaffer.data.element.Element;
 import uk.gov.gchq.gaffer.data.generator.ElementGenerator;
 import uk.gov.gchq.gaffer.exception.SerialisationException;
@@ -46,6 +45,6 @@ public Iterable<? extends Element> apply(final Iterable<? extends BytesWritable>
                     }
                 });
         final Iterable<Element> elementIterable = elementStream::iterator;
-        return new WrappedCloseableIterable<>(elementIterable::iterator);
+        return elementIterable::iterator;
     }
 }
diff --git a/performance-testing/performance-testing-aws/pom.xml b/performance-testing/performance-testing-aws/pom.xml
@@ -32,6 +32,17 @@
             <groupId>org.apache.accumulo</groupId>
             <artifactId>accumulo-server-base</artifactId>
             <version>${accumulo.version}</version>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
 
         <!--

diff --git a/performance-testing/performance-testing-core/pom.xml b/performance-testing/performance-testing-core/pom.xml
@@ -27,12 +27,34 @@
             <artifactId>accumulo-minicluster</artifactId>
             <version>${accumulo.version}</version>
             <scope>test</scope>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-hdfs</artifactId>
             <version>${hadoop.version}</version>
             <scope>test</scope>
+            <exclusions>
+                <!-- Conflicts with Reload4j -->
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>log4j</groupId>
+                    <artifactId>log4j</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>uk.gov.gchq.gaffer</groupId>

diff --git a/...nce-testing-core/src/main/java/uk/gov/gchq/gaffer/performancetesting/query/QueryTest.java b/...nce-testing-core/src/main/java/uk/gov/gchq/gaffer/performancetesting/query/QueryTest.java
@@ -18,7 +18,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import uk.gov.gchq.gaffer.commonutil.iterable.CloseableIterable;
 import uk.gov.gchq.gaffer.data.element.Element;
 import uk.gov.gchq.gaffer.graph.Graph;
 import uk.gov.gchq.gaffer.graph.GraphConfig;
@@ -114,7 +113,7 @@ private void queryBatch(final Supplier<? extends ElementSeed> elementSeedSupplie
         final long startTime = System.currentTimeMillis();
         final long numResults;
         try {
-            final CloseableIterable<? extends Element> results = graph.execute(getElements, new User());
+            final Iterable<? extends Element> results = graph.execute(getElements, new User());
             numResults = StreamSupport.stream(results.spliterator(), false).count();
         } catch (final OperationException e) {
             LOGGER.error("OperationException thrown after " + (System.currentTimeMillis() - startTime) / 1000.0

diff --git a/pom.xml b/pom.xml
@@ -21,7 +21,7 @@
     <parent>
         <groupId>uk.gov.gchq.gaffer</groupId>
         <artifactId>gaffer2</artifactId>
-        <version>2.0.0-alpha-0.1</version>
+        <version>2.0.0-alpha-0.2</version>
     </parent>
 
     <artifactId>gaffer-tools</artifactId>
@@ -36,7 +36,7 @@
     </modules>
 
     <properties>
-        <gaffer.version>2.0.0-alpha-0.1</gaffer.version>
+        <gaffer.version>2.0.0-alpha-0.2</gaffer.version>
         <scm.url>
             https://github.com/gchq/gaffer-tools
         </scm.url>
@@ -153,7 +153,8 @@
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-failsafe-plugin</artifactId>
-                        <version>${failsafe.version}</version>
+                        <!-- Older Failsafe required for Selenium -->
+                        <version>2.22.2</version>
                         <executions>
                             <execution>
                                 <id>system-test</id>
@@ -188,8 +189,8 @@
                         </executions>
                     </plugin>
                     <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>findbugs-maven-plugin</artifactId>
+                        <groupId>com.github.spotbugs</groupId>
+                        <artifactId>spotbugs-maven-plugin</artifactId>
                         <executions>
                             <execution>
                                 <id>analyze-compile</id>

diff --git a/python-shell/src/__init__.py b/python-shell/src/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "2.0.0-alpha-0.1"
+__version__ = "2.0.0-alpha-0.2"
 
 __title__ = "gafferpy"
 __description__ = "Gaffer Python Shell"

diff --git a/python-shell/src/gafferpy/__init__.py b/python-shell/src/gafferpy/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "2.0.0-alpha-0.1"
+__version__ = "2.0.0-alpha-0.2"
 
 __title__ = "gafferpy"
 __description__ = "Gaffer Python Shell"

diff --git a/python-shell/src/gafferpy/gaffer_functions.py b/python-shell/src/gafferpy/gaffer_functions.py
@@ -1090,11 +1090,16 @@ def to_json(self):
 class ToSet(AbstractFunction):
     CLASS = 'uk.gov.gchq.koryphe.impl.function.ToSet'
 
-    def __init__(self):
+    def __init__(self, implementation=None):
         super().__init__(_class_name=self.CLASS)
+        self.implementation = implementation
 
     def to_json(self):
-        return super().to_json()
+        function_json = super().to_json()
+        if (self.implementation is not None):
+            function_json["implementation"] = self.implementation
+
+        return function_json
 
 
 class ToArray(AbstractFunction):
@@ -1338,6 +1343,14 @@ def to_json(self):
 
         return function_json
 
+class ToDouble(AbstractFunction):
+    CLASS = "uk.gov.gchq.koryphe.impl.function.ToDouble"
+
+    def __init__(self):
+        super().__init__(_class_name=self.CLASS)
+
+    def to_json(self):
+        return super().to_json()
 
 class FirstValid(AbstractFunction):
     CLASS = "uk.gov.gchq.koryphe.impl.function.FirstValid"

diff --git a/python-shell/src/test/test_connector.py b/python-shell/src/test/test_connector.py
@@ -129,7 +129,7 @@ def test_is_operation_supported(self):
           "exampleJson": {
             "class": "uk.gov.gchq.gaffer.operation.impl.get.GetAllElements"
           },
-          "outputClassName": "uk.gov.gchq.gaffer.commonutil.iterable.CloseableIterable<uk.gov.gchq.gaffer.data.element.Element>"
+          "outputClassName": "java.lang.Iterable<uk.gov.gchq.gaffer.data.element.Element>"
         }
             '''
 

diff --git a/python-shell/src/test/test_connector_requests.py b/python-shell/src/test/test_connector_requests.py
@@ -129,7 +129,7 @@ def test_is_operation_supported(self):
           "exampleJson": {
             "class": "uk.gov.gchq.gaffer.operation.impl.get.GetAllElements"
           },
-          "outputClassName": "uk.gov.gchq.gaffer.commonutil.iterable.CloseableIterable<uk.gov.gchq.gaffer.data.element.Element>"
+          "outputClassName": "java.lang.Iterable<uk.gov.gchq.gaffer.data.element.Element>"
         }
             '''