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bd2kccd / causal-cmd

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ausal-cmd output directory handling not creating absolute paths? #21

Closed espinoj closed 6 years ago

espinoj commented 7 years ago

I'm trying to run causal-cmd with an absolute path for --output. E.g.:

java -Xmx1G -jar /home/harryh/causal-cmd-6.1.0-jar-with-dependencies.jar --algorithm FGESc --data /pylon1/bi4s84p/harryh/pam50-basal-continuous.csv --exclude-variables basal-output_zero_variance.txt --output /pylon1/bi4s84p/harryh/basal-output

however, I get an nio exception that looks like it might be looking for a relative path:

java.nio.file.NoSuchFileException: ./pylon1/bi4s84p/harryh/basal-output.txt at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86) at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102) at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107) at sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:214) at java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:434) at java.nio.file.Files.newOutputStream(Files.java:216) at edu.cmu.tetrad.cli.AbstractAlgorithmCli.run(AbstractAlgorithmCli.java:132) at edu.cmu.tetrad.cli.CausalCmdApplication.runAlgorithm(CausalCmdApplication.java:134) at edu.cmu.tetrad.cli.CausalCmdApplication.main(CausalCmdApplication.java:180)

when I run with a relative path - it works fine. e.g.

java -Xmx1G -jar /home/harryh/causal-cmd-6.1.0-jar-with-dependencies.jar --algorithm FGESc --data /pylon1/bi4s84p/harryh/pam50-basal-continuous.csv --exclude-variables basal-output_zero_variance.txt --output basal-output