- Nov 27, 2017
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M.D. Driver authored
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M.D. Driver authored
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M.D. Driver authored
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M.D. Driver authored
This is now down on creation of the SSIP molecule to ensure consistency in atomID labelling betwee nthe CmlMolecule and the SSIPs.
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- Nov 26, 2017
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Mark J. Williamson authored
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- Oct 23, 2017
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Mark Williamson authored
Errors seen with: [ERROR] Errors: [ERROR] ChemicalStructureTest.initializationError » Objenesis java.lang.reflect.Invoca... [ERROR] VF2Test.initializationError » Objenesis java.lang.reflect.InvocationTargetExce... [ERROR] PDBReaderTest.initializationError » Objenesis java.lang.reflect.InvocationTarg... Caused by: Caused by: java.lang.IllegalAccessError: class jdk.internal.reflect.ConstructorAccessorImpl loaded by org/powermock/core/classloader/MockClassLoader cannot access jdk/internal/reflect superclass jdk.internal.reflect.MagicAccessorImpl Switching to mockito2, but not as of yet switching to powermock 2.0.0-beta.5 which actually fixes these. Please see: https://github.com/powermock/powermock/issues/783
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Mark Williamson authored
Use: YourClass.class.getResource() not: YourClass.getClass().getResource() Please see: https://javachannel.org/posts/how-to-access-static-resources/
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Mark Williamson authored
Use: YourClass.class.getResource() not: YourClass.getClass().getResource() Please see: https://javachannel.org/posts/how-to-access-static-resources/
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Mark Williamson authored
Issue: ------------------------------------------------------------------------------- Test set: uk.ac.cam.ch.hunter.ssip.cml.io.CMLReaderTest ------------------------------------------------------------------------------- Tests run: 1, Failures: 0, Errors: 1, Skipped: 0, Time elapsed: 0.213 s <<< FAILURE! - in uk.ac.cam.ch.hunter.ssip.cml.io.CMLReaderTest testDemarshal(uk.ac.cam.ch.hunter.ssip.cml.io.CMLReaderTest) Time elapsed: 0.213 s <<< ERROR! java.lang.NoClassDefFoundError: javax/activation/DataSource at uk.ac.cam.ch.hunter.ssip.cml.io.CMLReaderTest.testDemarshal(CMLReaderTest.java:58) Caused by: java.lang.ClassNotFoundException: javax.activation.DataSource at uk.ac.cam.ch.hunter.ssip.cml.io.CMLReaderTest.testDemarshal(CMLReaderTest.java:58) com.sun.activation Background: https://blog.codefx.org/java/java-9-migration-guide/#Dependencies-On-Java-EE-Modules
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Mark Williamson authored
[INFO] Compiling 44 source files to /home/mw529/workspace/ssip/target/test-classes [WARNING] /home/mw529/workspace/ssip/src/test/java/uk/ac/cam/ch/hunter/ssip/footprint/io/ApproximateSurfaceAreaTest.java:[24,33] Double(double) in java.lang.Double has been deprecated [WARNING] /home/mw529/workspace/ssip/src/test/java/uk/ac/cam/ch/hunter/ssip/footprint/io/ApproximateSurfaceAreaTest.java:[25,33] Double(double) in java.lang.Double has been deprecated [WARNING] /home/mw529/workspace/ssip/src/test/java/uk/ac/cam/ch/hunter/ssip/footprint/io/ApproximateSurfaceAreaTest.java:[26,33] Double(double) in java.lang.Double has been deprecated
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Mark Williamson authored
Fixes the following "mvn clean test" error with Java 9: [ERROR] There was an error in the forked process [ERROR] javax/xml/bind/JAXBException [ERROR] org.apache.maven.surefire.booter.SurefireBooterForkException: There was an error in the forked process [ERROR] javax/xml/bind/JAXBException which was being caused by: java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException at java.base/java.lang.Class.getDeclaredMethods0(Native Method) at java.base/java.lang.Class.privateGetDeclaredMethods(Class.java:3139) ... which is due to: https://stackoverflow.com/questions/43574426/how-to-resolve-java-lang-noclassdeffounderror-javax-xml-bind-jaxbexception-in-j which was due to: http://openjdk.java.net/jeps/261
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- Oct 20, 2017
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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M.D. Driver authored
information.
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
The current matching approach is fragile with respect to version number and breaks during a mvn jgitflow:release-start, mvn jgitflow:release-finish cycle. This goes someway towards fixing #29 refs: ===== https://stackoverflow.com/questions/82064/a-regex-for-version-number-parsing https://regex101.com/
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- Oct 19, 2017
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Mark J. Williamson authored
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M.D. Driver authored
copied across.
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Mark Williamson authored
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Mark Williamson authored
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Mark Williamson authored
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M.D. Driver authored
Atom array from the PDBreader, to use the proper atom index so that they match. This corrects Issue #28: NPE in CmlMolecule constructor when run using the command line.
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- Oct 18, 2017
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M.D. Driver authored
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M.D. Driver authored
Conflicts: src/main/java/uk/ac/cam/ch/hunter/ssip/footprint/SSIPList.java
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- Oct 13, 2017
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M.D. Driver authored
Creation of new class to extract this information from the project.properties file. This is then included in the SSSIPMolecule, so the creation version is recorded.
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- Oct 10, 2017
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M.D. Driver authored
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M.D. Driver authored
information about schema locations to the output files. Update to not double encapsulate the SSIP information.
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M.D. Driver authored
attributeFormDefault set to qualified.
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- Sep 24, 2017
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M.D. Driver authored
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