Run HermiT on the command line

[owlcs]

Run HermiT on the command line

[pbouda]

FYI, I was not aware of the FAQ (and not to familiar with Java ...) so I searched a lot until I could build a jar with all dependencies. I cloned this repo and added the following to pom.xml:

<plugin>
        <artifactId>maven-assembly-plugin</artifactId>
        <configuration>
                <archive>
                <manifest>
                        <mainClass>org.semanticweb.HermiT.cli.CommandLine</mainClass>
                </manifest>
                </archive>
                <descriptorRefs>
                <descriptorRef>jar-with-dependencies</descriptorRef>
                </descriptorRefs>
        </configuration>
        <executions>
                <execution>
                <id>make-assembly</id>
                <phase>package</phase>
                <goals>
                        <goal>single</goal>
                </goals>
                </execution>
        </executions>
</plugin>

Then you can build the jar with everything:

mvn clean compile assembly:single

Run the command line:

 java -jar org.semanticweb.hermit-1.4.6.519-SNAPSHOT-jar-with-dependencies.jar YOUR.owl

[ignazio1977]

Sounds to me like this is HermiT 1.3.8, am I right? If so, it's a fairly old build of the library and uses an even older OWLAPI version. It's possible that the best fix is to use a recent HermiT build (e.g., https://search.maven.org/artifact/net.sourceforge.owlapi/org.semanticweb.hermit/1.4.5.456)

The most recent builds include the same command line interface as the old HermiT but I haven't tried it with the -jar option; it might need more classpath setup.

[mikael1234]

Yes, it is version 1.3.8. I downloaded never version from maven.org and it says java -jar org.semanticweb.hermit-1.4.5.519.jar -V no main manifest attribute, in org.semanticweb.hermit-1.4.5.519.jar Sorry I don't have skills in java, is this easily fixed?

…

On 02/04/2020 19.48, Ignazio Palmisano wrote: Sounds to me like this is HermiT 1.3.8, am I right? If so, it's a fairly old build of the library and uses an even older OWLAPI version. It's possible that the best fix is to use a recent HermiT build (e.g., https://search.maven.org/artifact/net.sourceforge.owlapi/org.semanticweb.hermit/1.4.5.456) The most recent builds include the same command line interface as the old HermiT but I haven't tried it with the -jar option; it might need more classpath setup. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <https://github.com/owlcs/owlapi/issues/922#issuecomment-607963009>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEIN4QN5MX7WKETPEEZWAILRKS6XTANCNFSM4L2PYSBQ>.

-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fi Speech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-books Mikael Pesonen System Engineer e-mail: [email protected] Tel. [phone] Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND

[ignazio1977]

It's a matter of command line arguments, nothing should be broken. I'll experiment and let you know.

[ignazio1977]

I can get HermiT to run on the command line but it requires manually downloading some libraries and adding them to the classpath.

So, to explain what's going on: HermiT 1.3.8 was packaged as an uber jar, meaning all the dependencies were included - making it impossible to update a dependency without rebuilding the jar, and making conflicts with other libraries common. However, that was convenient for command line use. Stuck with OWLAPI 3, though, which is where a lot of the issues you've found are rooted.

The builds on this fork only include in HermiT a subset of dependencies - the ones not available as Maven dependencies. This simplifies replacing the OWLAPI version but requires more work to run it from the command line.

Specifically, you need to download:

• the set of jars required for OWLAPI (for convenience there are packed releases here https://github.com/owlcs/releases/blob/master/owlapi/5/owlapi-dependencypack-5.1.9.jar ). Unzip this last jar file: unzip owlapi-dependencypack-5.1.9.jar. This command extracts the contents of the jar file (it contains a lib folder full of jars). Any zip manipulation program will do.

Also the following libraries (for convenience I've put them in the same lib folder as the OWLAPI files; also moved the HermiT jar in there)

• java-getopt jar from Maven Central (I used version 1.0.13 https://search.maven.org/artifact/gnu.getopt/java-getopt/1.0.13/jar)
• trove4j library https://search.maven.org/artifact/net.sf.trove4j/trove4j/3.0.3/jar
• SLF4J https://search.maven.org/artifact/org.slf4j/slf4j-api/1.7.22/jar
• SLF4J implementation https://search.maven.org/artifact/org.slf4j/slf4j-simple/1.7.22/jar

The folder looks like this:

• org.semanticweb.hermit-1.4.5.519.jar
• lib folder, contains all OWLAPI jars and dependencies, trove, slf4j, getopt

In this folder, this command line will run HermiT:

java -cp org.semanticweb.hermit-1.4.5.519.jar:lib/* org.semanticweb.HermiT.cli.CommandLine -V

(If you're on Windows, use ; to separate the entries in the classpath parameter instead of :)

[ignazio1977]

Actually, this process is needlessly complex. I'll write a pom file for creating HermiT builds that work with the same command line as the original.

[ignazio1977]

I've documented the solution here https://github.com/owlcs/hermit-reasoner/wiki/HermiT-FAQ

[mikael1234]

-V works now, but when doing entailment check, there is this error

Exception in thread "main" java.lang.NoClassDefFoundError: org/slf4j/LoggerFactory
at org.semanticweb.owlapi.utilities.Injector.(Injector.java:43)
at org.semanticweb.owlapi.apibinding.OWLManager.(OWLManager.java:101)
at org.semanticweb.HermiT.cli.CommandLine.main(CommandLine.java:360)
Caused by: java.lang.ClassNotFoundException: org.slf4j.LoggerFactory
at java.net.URLClassLoader.findClass(URLClassLoader.java:382)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 3 more

So maybe still need some LoggerFactory jar? Thanks for the help!

[ignazio1977]

Odd, the file is included in the jar.

[ignazio1977]

There were bugs on the command line tool - some options were badly set up. Not sure if that was the problem you've seen, I could not replicate the error. 'm updating the fine in the releases project.

[mikael1234]

I'm running this kind of command, if this helps: java -cp org.semanticweb.hermit-1.4.5.519.jar:java-getopt-1.0.13.jar:lib/* org.semanticweb.HermiT.cli.CommandLine --premise=file://xxx --conclusion=file://yyy --checkEntailment

…

On 08/04/2020 0.25, Ignazio Palmisano wrote: There were bugs on the command line tool - some options were badly set up. Not sure if that was the problem you've seen, I could not replicate the error. 'm updating the fine in the releases project. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEIN4QN5ITUTDYQ4XKWTBI3RLOK4DANCNFSM4L6RTKPA>.

-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fi Speech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-books Mikael Pesonen System Engineer e-mail: [email protected] Tel. [phone] Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND

[ignazio1977]

That's the old build. Use the file in the releases project (name contains -packaged and -SNAPSHOT). You should be able to use the original command line, same as the instructions on the hermit web site.

[mikael1234]

Sorry how do I find it? I searched https://search.maven.org/search?q=hermit and downloaded the newest one dated 18-Feb-2020.

…

On 08/04/2020 13.00, Ignazio Palmisano wrote: That's the old build. Use the file in the releases project (name contains -packaged and -SNAPSHOT). You should be able to use the original command line, same as the instructions on the hermit web site. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEIN4QI4ZKPYG5533OCV3U3RLRDMZANCNFSM4L6RTKPA>.

-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fi Speech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-books Mikael Pesonen System Engineer e-mail: [email protected] Tel. [phone] Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND

[ignazio1977]

It's explained in the link I posted above (last question on the list) https://github.com/owlcs/hermit-reasoner/wiki/HermiT-FAQ

[mikael1234]

Now it's working fine. Thanks for all the help!

…

On 08/04/2020 13.35, Ignazio Palmisano wrote: It's explained in the link I posted above (last question on the list) https://github.com/owlcs/hermit-reasoner/wiki/HermiT-FAQ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEIN4QMQETQ3PBVTBEVT6KLRLRHQ5ANCNFSM4L6RTKPA>.

-- Lingsoft - 30 years of Leading Language Management www.lingsoft.fi Speech Applications - Language Management - Translation - Reader's and Writer's Tools - Text Tools - E-books and M-books Mikael Pesonen System Engineer e-mail: [email protected] Tel. [phone] Time zone: GMT+2 Helsinki Office Eteläranta 10 FI-00130 Helsinki FINLAND Turku Office Kauppiaskatu 5 A FI-20100 Turku FINLAND