Bugfix to address log4j security vulnerability - version 4.4.1 (#100)

OPSIN has addressed a security vulnerability (CVE-2021-44228) documented in issue dan2097/opsin#174 - To package this for the RDKit nodes we now use OPSIN 3.0 (beta) build on master commit 6aca244. This includes then naturally also improvements between 2.5 and 3.0 (committed until Dec 11, 2021). Bumped version to from 4.4.0 to 4.4.1.
rdkit · Dec 14, 2021 · 094e4ca · 094e4ca
1 parent c87b7bd
commit 094e4ca
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Showing 15 changed files with 22 additions and 22 deletions.
diff --git a/org.rdkit.knime.bin.linux.x86_64/META-INF/MANIFEST.MF b/org.rdkit.knime.bin.linux.x86_64/META-INF/MANIFEST.MF
@@ -2,8 +2,8 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: RDKit binaries for 64bit Linux
 Bundle-SymbolicName: org.rdkit.knime.bin.linux.x86_64;singleton:=true
-Bundle-Version: 4.4.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.4.0"
+Bundle-Version: 4.4.1.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.4.1"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Eclipse-PlatformFilter: (&(osgi.os=linux)(osgi.arch=x86_64))
 Bundle-Vendor: NIBR
diff --git a/org.rdkit.knime.bin.macosx.x86_64/META-INF/MANIFEST.MF b/org.rdkit.knime.bin.macosx.x86_64/META-INF/MANIFEST.MF
@@ -2,8 +2,8 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: RDKit binaries for 64bit MacOSX
 Bundle-SymbolicName: org.rdkit.knime.bin.macosx.x86_64;singleton:=true
-Bundle-Version: 4.4.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.4.0"
+Bundle-Version: 4.4.1.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.4.1"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Eclipse-PlatformFilter: (&(osgi.os=macosx)(osgi.arch=x86_64))
 Bundle-Vendor: NIBR
diff --git a/org.rdkit.knime.bin.win32.x86_64/META-INF/MANIFEST.MF b/org.rdkit.knime.bin.win32.x86_64/META-INF/MANIFEST.MF
@@ -2,8 +2,8 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: RDKit binaries for 64bit Windows
 Bundle-SymbolicName: org.rdkit.knime.bin.win32.x86_64;singleton:=true
-Bundle-Version: 4.4.0.qualifier
-Fragment-Host: org.rdkit.knime.types;bundle-version="4.4.0"
+Bundle-Version: 4.4.1.qualifier
+Fragment-Host: org.rdkit.knime.types;bundle-version="4.4.1"
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Eclipse-PlatformFilter: (&(osgi.os=win32)(osgi.arch=x86_64))
 Bundle-Vendor: NIBR
diff --git a/org.rdkit.knime.binaries.feature/feature.xml b/org.rdkit.knime.binaries.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.binaries.feature"
       label="RDKit Binaries and Chemistry Type Definitions Feature"
-      version="4.4.0.qualifier"
+      version="4.4.1.qualifier"
       provider-name="NIBR">
 
    <description>

diff --git a/org.rdkit.knime.feature/feature.xml b/org.rdkit.knime.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.feature"
       label="RDKit Nodes Feature"
-      version="4.4.0.qualifier"
+      version="4.4.1.qualifier"
       provider-name="NIBR"
       plugin="org.rdkit.knime.nodes">
 

diff --git a/org.rdkit.knime.nodes/META-INF/MANIFEST.MF b/org.rdkit.knime.nodes/META-INF/MANIFEST.MF
@@ -3,14 +3,14 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Nodes
 Bundle-SymbolicName: org.rdkit.knime.nodes;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.nodes
-Bundle-Version: 4.4.0.qualifier
+Bundle-Version: 4.4.1.qualifier
 Bundle-Vendor: NIBR
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.eclipse.ui;bundle-version="[3.109.0,4.0.0)",
  org.knime.base;bundle-version="[4.2.0,5.0.0)",
  org.knime.chem.types;bundle-version="[4.2.0,5.0.0)",
  org.knime.workbench.repository;bundle-version="[4.2.0,5.0.0)",
- org.rdkit.knime.types;bundle-version="[4.4.0,5.0.0)",
+ org.rdkit.knime.types;bundle-version="[4.4.1,5.0.0)",
  org.knime.ext.svg;bundle-version="[4.2.0,5.0.0)"
 Export-Package: org.rdkit.knime.nodes,
  org.rdkit.knime.nodes.addconformers,
@@ -61,5 +61,5 @@ Export-Package: org.rdkit.knime.nodes,
 Bundle-Activator: org.rdkit.knime.nodes.RDKitNodePlugin
 Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: .,
- lib/opsin-2.5.0-excludingInChI-jar-with-dependencies.jar
+ lib/opsin-core-3.0-excludingInChI-jar-with-dependencies.jar
 Import-Package: org.w3c.dom.events;version="3.0.0"
diff --git a/org.rdkit.knime.nodes/build.properties b/org.rdkit.knime.nodes/build.properties
@@ -4,7 +4,7 @@ output.. = bin/
 bin.includes = META-INF/,\
                .,\
                plugin.xml,\
-               lib/opsin-2.5.0-excludingInChI-jar-with-dependencies.jar,\
+               lib/opsin-core-3.0-excludingInChI-jar-with-dependencies.jar,\
                icons/
-jars.extra.classpath = lib/opsin-2.5.0-excludingInChI-jar-with-dependencies.jar,\
+jars.extra.classpath = lib/opsin-core-3.0-excludingInChI-jar-with-dependencies.jar,\
 					   platform:/plugin/org.rdkit.knime.types/lib/org.RDKit.jar
diff --git a/org.rdkit.knime.nodes/lib/opsin-2.5.0-excludingInChI-jar-with-dependencies.jar b/org.rdkit.knime.nodes/lib/opsin-2.5.0-excludingInChI-jar-with-dependencies.jar
diff --git a/org.rdkit.knime.nodes/lib/opsin-core-3.0-excludingInChI-jar-with-dependencies.jar b/org.rdkit.knime.nodes/lib/opsin-core-3.0-excludingInChI-jar-with-dependencies.jar
diff --git a/org.rdkit.knime.testing.feature/feature.xml b/org.rdkit.knime.testing.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.testing.feature"
       label="RDKit Nodes Tests Feature"
-      version="4.4.0.qualifier"
+      version="4.4.1.qualifier"
       provider-name="NIBR">
 
    <description>

diff --git a/org.rdkit.knime.testing/META-INF/MANIFEST.MF b/org.rdkit.knime.testing/META-INF/MANIFEST.MF
@@ -3,10 +3,10 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Nodes Tests
 Bundle-SymbolicName: org.rdkit.knime.testing;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.testing
-Bundle-Version: 4.4.0.qualifier
+Bundle-Version: 4.4.1.qualifier
 Bundle-Vendor: NIBR
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
-Fragment-Host: org.rdkit.knime.nodes;bundle-version="4.4.0"
+Fragment-Host: org.rdkit.knime.nodes;bundle-version="4.4.1"
 Require-Bundle: org.knime.testing;bundle-version="[3.7.0,5.0.0)",
  org.knime.chem.base;bundle-version="[3.6.0,5.0.0)"
 Bundle-ClassPath: rdkit-testing.jar
diff --git a/org.rdkit.knime.types/META-INF/MANIFEST.MF b/org.rdkit.knime.types/META-INF/MANIFEST.MF
@@ -21,7 +21,7 @@ Bundle-ActivationPolicy: lazy
 Bundle-ClassPath: rdkit-chem.jar,
  lib/org.RDKit.jar,
  lib/org.RDKitDoc.jar
-Bundle-Version: 4.4.0.qualifier
+Bundle-Version: 4.4.1.qualifier
 Bundle-Name: RDKit Chemistry Type Definitions
 Bundle-Activator: org.rdkit.knime.RDKitTypesPluginActivator
 Bundle-ManifestVersion: 2

diff --git a/org.rdkit.knime.wizards.feature/feature.xml b/org.rdkit.knime.wizards.feature/feature.xml
@@ -2,7 +2,7 @@
 <feature
       id="org.rdkit.knime.wizards.feature"
       label="RDKit Nodes Creation Wizards Feature"
-      version="4.4.0.qualifier"
+      version="4.4.1.qualifier"
       provider-name="NIBR"
       plugin="org.rdkit.knime.wizards">
 

diff --git a/org.rdkit.knime.wizards.samples/META-INF/MANIFEST.MF b/org.rdkit.knime.wizards.samples/META-INF/MANIFEST.MF
@@ -3,13 +3,13 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Nodes Creation Wizards Samples
 Bundle-SymbolicName: org.rdkit.knime.wizards.samples;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.wizards.samples
-Bundle-Version: 4.4.0.qualifier
+Bundle-Version: 4.4.1.qualifier
 Bundle-Activator: org.rdkit.knime.wizards.samples.Activator
 Bundle-Vendor: NIBR
 Require-Bundle: org.knime.base;bundle-version="[4.3.0,5.0.0)";resolution:=optional,
  org.knime.chem.types;bundle-version="[4.3.0,5.0.0)";resolution:=optional,
- org.rdkit.knime.nodes;bundle-version="[4.4.0,5.0.0)";resolution:=optional,
- org.rdkit.knime.types;bundle-version="[4.4.0,5.0.0)";resolution:=optional,
+ org.rdkit.knime.nodes;bundle-version="[4.4.1,5.0.0)";resolution:=optional,
+ org.rdkit.knime.types;bundle-version="[4.4.1,5.0.0)";resolution:=optional,
  org.eclipse.ui;bundle-version="[3.116.0,4.0.0)";resolution:=optional,
  org.eclipse.core.runtime;bundle-version="[3.17.0,4.0.0)";resolution:=optional
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8

diff --git a/org.rdkit.knime.wizards/META-INF/MANIFEST.MF b/org.rdkit.knime.wizards/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: RDKit Nodes Creation Wizards
 Bundle-SymbolicName: org.rdkit.knime.wizards;singleton:=true
 Automatic-Module-Name: org.rdkit.knime.wizards
-Bundle-Version: 4.4.0.qualifier
+Bundle-Version: 4.4.1.qualifier
 Bundle-Activator: org.rdkit.knime.wizards.RDKitNodesWizardsPlugin
 Bundle-Vendor: NIBR
 Require-Bundle: org.eclipse.core.runtime;bundle-version="[3.7.0,4.0.0)",