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WIP: Several update for the container #2

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bgruening
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  • update openrefine to the latest version
  • tries to rething the handling of pushing back data to Galaxy
    • the current approach was using openrefine python bindings, which are deprecated in favor of a bash-CLI
    • the current approach was relying on python-2

The containers builds and is useable, as far as I can see. But handling data from and back to Galaxy is not working yet.

Pushing this PR out, in case someone wants to work on it.


# Download and "mount" OpenRefine
RUN wget -q -O - --no-check-certificate https://github.com/ValentinChCloud/OpenRefine/archive/master.tar.gz |tar -xz && \
mv OpenRefine-master OpenRefine
RUN wget -q -O - --no-check-certificate https://github.com/OpenRefine/OpenRefine/archive/refs/tags/3.8.2.tar.gz |tar -xz && \
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A versioned new version of openrefine.

#Get python api openrefine
RUN wget -q -O - --no-check-certificate https://github.com/maxogden/refine-python/archive/master.tar.gz | tar -xz && \
mv refine-python-master refine-python
RUN cd /usr/bin/ && wget https://github.com/opencultureconsulting/orcli/raw/main/orcli && chmod +x orcli
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The new CLI tool to interact with openrefine.

@bgruening
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I haven't figured yet out how we can save the provenance information via the API. Any hints welcome.

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