Fix for missing bin/ zips in package.

Uncommented commons-collections exclusion. collections4 is not a drop-in replacement and some required (by 3rd party) classes are not present.
apache · Aug 16, 2024 · b9c8ceb · b9c8ceb
1 parent b3977a8
commit b9c8ceb
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Showing 2 changed files with 25 additions and 6 deletions.
diff --git a/ctakes-distribution/src/main/assembly/bin.xml b/ctakes-distribution/src/main/assembly/bin.xml
@@ -139,6 +139,18 @@
 	</dependencySets>
 
 	<fileSets>
+		<fileSet>
+			<directory>src/main/bin</directory>
+			<outputDirectory>bin</outputDirectory>
+			<fileMode>755</fileMode>
+			<directoryMode>755</directoryMode>
+		</fileSet>
+		<fileSet>
+			<directory>src/main/config</directory>
+			<outputDirectory>config</outputDirectory>
+			<fileMode>644</fileMode>
+			<directoryMode>755</directoryMode>
+		</fileSet>
 		<fileSet>
 			<directory>../ctakes-assertion/src/user/resources</directory>
 			<outputDirectory>resources</outputDirectory>

diff --git a/pom.xml b/pom.xml
@@ -100,6 +100,7 @@
         <cleartk.version>3.0.0</cleartk.version>
         <commons-beanutils.version>1.9.4</commons-beanutils.version>
         <commons-cli.version>1.2</commons-cli.version>
+        <commons-collections.version>3.2.2</commons-collections.version>
         <commons-collections4.version>4.4</commons-collections4.version>
         <commons-dbcp.version>1.4</commons-dbcp.version>
         <commons-el.version>1.0</commons-el.version>
@@ -781,6 +782,11 @@
                 <artifactId>commons-collections4</artifactId>
                 <version>${commons-collections4.version}</version>
             </dependency>
+            <dependency>
+                <groupId>commons-collections</groupId>
+                <artifactId>commons-collections</artifactId>
+                <version>${commons-collections.version}</version>
+            </dependency>
             <dependency>
                 <groupId>commons-io</groupId>
                 <artifactId>commons-io</artifactId>
@@ -790,12 +796,13 @@
                 <groupId>commons-beanutils</groupId>
                 <artifactId>commons-beanutils</artifactId>
                 <version>${commons-beanutils.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>commons-collections</groupId>
-                        <artifactId>commons-collections</artifactId>
-                    </exclusion>
-                </exclusions>
+<!--                There is a vulnerability in commons-collections, but we can't exclude it.  -->
+<!--                <exclusions>-->
+<!--                    <exclusion>-->
+<!--                        <groupId>commons-collections</groupId>-->
+<!--                        <artifactId>commons-collections</artifactId>-->
+<!--                    </exclusion>-->
+<!--                </exclusions>-->
             </dependency>
             <dependency>
                 <groupId>commons-dbcp</groupId>