From 385daa6c208b6abcf7c1580ebca3df545ffd905d Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 15 Aug 2024 18:59:41 +0200 Subject: [PATCH] updates --- Dockerfile | 30 +++++++++++++----------------- openrefine_export_project.py | 2 +- 2 files changed, 14 insertions(+), 18 deletions(-) diff --git a/Dockerfile b/Dockerfile index 87b610c..18efae5 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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 && \ + 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 #Import data ADD ./get_notebook.py /get_notebook.py diff --git a/openrefine_export_project.py b/openrefine_export_project.py index 5ba5ce3..62db657 100644 --- a/openrefine_export_project.py +++ b/openrefine_export_project.py @@ -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)