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WIP: Several update for the container #2

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30 changes: 13 additions & 17 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -20,32 +20,28 @@ ENV DEBIAN_FRONTEND=noninteractive \
#Vim to modify ass porky
RUN apt-get update && \
apt-get install --no-install-recommends -y \
wget python python-pip \
openjdk-8-jdk vim unzip curl net-tools
wget python3 maven jq \
openjdk-11-jdk vim unzip curl npm

ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64
ENV PATH="/usr/lib/jvm/java-8-openjdk-amd64/bin:${PATH}"
ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64
ENV PATH="/usr/lib/jvm/java-11-openjdk-amd64/bin:${PATH}"

RUN pip install setuptools && \
pip install bioblend galaxy-ie-helpers && \
pip install https://github.com/ValentinChCloud/urllib2_file/archive/master.tar.gz
#RUN pip install setuptools && \
# pip install bioblend galaxy-ie-helpers && \
# pip install https://github.com/ValentinChCloud/urllib2_file/archive/master.tar.gz

# 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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@bgruening bgruening Aug 15, 2024

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A versioned new version of openrefine.

mv OpenRefine-3.8.2 OpenRefine

# make some changes to Openrefine to export data to galaxy history
ADD ./ExportRowsCommand.java OpenRefine/main/src/com/google/refine/commands/project/ExportRowsCommand.java
ADD ./exporters.js OpenRefine/main/webapp/modules/core/scripts/project/exporters.js
ADD ./langs/translation-default.json OpenRefine/main/webapp/modules/core/langs/translation-default.json
ADD ./langs/translation-fr.json OpenRefine/main/webapp/modules/core/langs/translation-fr.json
ADD ./langs/translation-fr.json OpenRefine/main/webapp/modules/core/langs/translation-en.json
#ADD ./ExportRowsCommand.java OpenRefine/main/src/com/google/refine/commands/project/ExportRowsCommand.java
#ADD ./exporters.js OpenRefine/main/webapp/modules/core/scripts/project/exporters.js


RUN /OpenRefine/refine build

#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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@bgruening bgruening Aug 15, 2024

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The new CLI tool to interact with openrefine.


#Import data
ADD ./get_notebook.py /get_notebook.py
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2 changes: 1 addition & 1 deletion openrefine_export_project.py
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Expand Up @@ -11,7 +11,7 @@


if os.path.isfile("fichier_donnee.txt"):
print "sortie erreur"
print("sortie erreur")
os.remove("fichier_donnee.txt")
sys.exit(1)

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