No description, website, or topics provided.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
kurator-tdwg17-yw-docker
kurator_FileBranchingTaxonLookup
queries
rules
views
workspace_8b7dda80-634e-11e8-9f66-4a0002b0edf0
LICENSE
README.md
clean.sh
make.sh
settings.sh
yw.properties
yw_make.properties
yw_wf.properties

README.md

kurator-TDWG17-YW

Demonstration of revealing data lineage/provenance from biodiversity data curation activities at different levels of granularity on a YesWorkflow marked-up Kurator workflow for TDWG 2017

Run from Dockerfile

Docker image for kurator-TDWG17-YW demo.

  1. First, clone this project via git:

    https://github.com/kurator-org/kurator-TDWG17-YW

  2. Next, with docker installed on your local machine, build the kurator-tdwg17-yw-docker container as root via the provided build.sh script:

    cd kurator-tdwg17-yw-docker 
    sudo ./build.sh
    
  3. Once build has succeeded, run the kurator-tdwg17-yw-docker container via the run.sh script:

    sudo ./run.sh

    The working directory will be kurator-validation.

  4. Lastly, run the Kurator workflow as well as yesworkflow and associated xsb scripts to generate prospective and hybrid (retrospective) graphs and queries:

    source settings.sh
    sh clean.sh
    source settings.sh
    sh make.sh
    

    The data files in results folder is mounted and thus visualized from ~/Downloads/results/ on your host machine.

Run without Dockerfile

Prerequisites

  • Install kurator-validation

    • Checkout kurator-validation

      git clone https://github.com/kurator-org/kurator-validation.git

    • Build kurator-validation

        mvn package -DskipTests
        mkdir  kurator-validation/yw_jar
    
    • You may need to checkout and build (mvn install) various other kurator projects, including kurator-akka, and ffdq-api.
  • Install YesWorkflow jar (in kurator-validation/yw_jar).

  • Install XSB

    Download XSB from https://sourceforge.net/projects/xsb/files/xsb/3.8%20Three-Buck%20Chuck/XSB38.tar.gz/download and install it.

  • Copy .sh files and queries into kurator-validation/

    cd kurator-TDWG17-YW
    cp *.sh ../kurator-validation
    cp -R rules/ ../kurator-validation
    cp -R queries/ ../kurator-validation
    
  • Set the path to the xsb binary in settings.sh

    e.g. export XSB="~/Downloads/xsb-src/XSB/config/i386-apple-darwin17.4.0/bin/xsb"

  • Set up the prerequisites for a kurator workflow run (install jython, jython pip install unicodecsv, chardet)

To run

  • Run the Kurator workflow as well as yesworkflow and associated xsb scripts to generate prospective and hybrid (retrospective) graphs and queries:
    source settings.sh
    sh clean.sh
    source settings.sh
    sh make.sh
  • In particular, to run kurator-validation on the marked-up workflow to generate a logfile for analysis:
    java -jar target/kurator-validation-1.0.2-jar-with-dependencies.jar -f packages/kurator_FileBranchingTaxonLookup/workflows/file_branching_taxon_lookup.yaml -p inputfile=packages/kurator_FileBranchingTaxonLookup/data/kurator_sample_data_v2.txt -l ALL > ./packages/kurator_FileBranchingTaxonLookup/workflows/results/runlog.log 2>&1