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Merge pull request #408 from INCATools/odk.1.2.27
All changes for ODK 1.2.27 at once
2 parents b8028cd + e02c571 commit 278e812

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‎Changes.md‎

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# v1.2.27 (4 April 2021)
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- revived odklite image with a minimum install (smaller in size than odkfull, with just robot and owltools!)
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- revived robot image with just robot installed
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- Added Jena 3.12.0 to odkfull image
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- Added module configs (see docs)
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- added a complete new documentation system for ontologies using mkdocs (see docs)
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- added OWL2 DL profile checking (see [here](tests/test-robot-validate-profile.yaml) for example)
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- Added sqlite3, dos2unix, and aha to odkfull image
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- Added a `use_custom_import_module` feature (see docs for example)
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- Added ability to add completely customised release artefacts (see Uberon repo for example)
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- Revised update mechanism. Please run the `make update_repo` *multiple times if you encounter problems and to ensure that all changes are picked up*.
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# v1.2.26 (10 February 2021): HOTFIXES
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- Hotfixes:
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- The new mireot module technique was buggy and is therefore removed again. Sorry; we will try again next time. You can still use the `custom` option to implement mireot yourself!

‎Dockerfile‎

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@@ -39,6 +39,7 @@ RUN apt-get update &&\
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aha \
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dos2unix \
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sqlite3 \
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libjson-perl \
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xlsx2csv &&\
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cd /usr/local/bin \
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&& ln -s /usr/bin/python3 python \
@@ -94,6 +95,11 @@ ENV FASTOBO_VALIDATOR v0.4.0
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RUN wget https://dl.bintray.com/fastobo/fastobo-validator/$FASTOBO_VALIDATOR/fastobo_validator-x86_64-linux-musl.tar.gz -O- | tar xzC /tools \
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&& chmod +x /tools/fastobo-validator
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###### JENA ######
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ENV JENA 3.12.0
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RUN wget http://archive.apache.org/dist/jena/binaries/apache-jena-$JENA.tar.gz -O- | tar xzC /tools
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ENV PATH "/tools/apache-jena-$JENA/bin:$PATH"
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##### Ammonite #####
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# LAYERSIZE ~31MB
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RUN (echo "#!/usr/bin/env sh" \
@@ -139,6 +145,12 @@ RUN cd /tools/ && chmod +x /tools/obodash && git clone --depth 1 --branch docker
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# ls -l /tools/
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#RUN chmod +x /tools/droid
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# ######
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# RUN cd /tools/ && git clone --depth 1 https://github.com/cmungall/blipkit.git && cd blipkit &&\
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# ./configure && make && make install && cd /tools/ && rm -rf blipkit
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# ENV PATH "/usr/local/bin:$PATH"
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### 5. Install ODK
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ARG ODK_VERSION=0.0.0
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ENV ODK_VERSION=${ODK_VERSION}
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RUN chmod +x /tools/*.py
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ENV LC_ALL=C.UTF-8
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ENV LANG=C.UTF-8
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RUN echo "PLEASE DONT FORGET TO UPDATE odklite (docker/odklite/Dockerfile) and robot (docker/robot/Dockerfile) images!"
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CMD python /tools/odk.py

‎Makefile‎

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@@ -38,58 +38,83 @@ schema/project-schema.json:
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./odk/odk.py dump-schema > $@
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# Building docker image
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VERSION = "v1.2.26"
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VERSION = "v1.2.27"
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IM=obolibrary/odkfull
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IMLITE=obolibrary/odklite
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DEV=obolibrary/odkdev
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ROBOT_JAR="https://build.obolibrary.io/job/ontodev/job/robot/job/cmd-metrics/6/artifact/bin/robot.jar"
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ROBOT_JAR_ARGS=
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#--build-arg ROBOT_JAR=$(ROBOT_JAR)
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ROB=obolibrary/robot
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#ROBOT_JAR="https://github.com/monarch-ebi-dev/odk_utils/raw/master/robot_maven_test.jar"
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ROBOT_JAR_ARGS=#--build-arg ROBOT_JAR=$(ROBOT_JAR)
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docker-build-no-cache:
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@docker build --build-arg ODK_VERSION=$(VERSION) $(ROBOT_JAR_ARGS) --no-cache -t $(IM):$(VERSION) . \
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&& docker tag $(IM):$(VERSION) $(IM):latest
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&& docker tag $(IM):$(VERSION) $(IM):latest && docker tag $(IM):$(VERSION) $(DEV):latest && \
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docker build -f docker/odklite/Dockerfile -t $(IMLITE):$(VERSION) . \
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&& docker tag $(IMLITE):$(VERSION) $(IMLITE):latest && cd docker/robot/ && make docker-build
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docker-build:
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@docker build --build-arg ODK_VERSION=$(VERSION) $(ROBOT_JAR_ARGS) -t $(IM):$(VERSION) . \
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&& docker tag $(IM):$(VERSION) $(IM):latest
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docker-build-use-cache-dev:
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&& docker tag $(IM):$(VERSION) $(IM):latest && docker tag $(IM):$(VERSION) $(DEV):latest && \
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docker build -f docker/odklite/Dockerfile -t $(IMLITE):$(VERSION) . \
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&& docker tag $(IMLITE):$(VERSION) $(IMLITE):latest && cd docker/robot/ && make docker-build
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docker-build-dev:
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@docker build --build-arg ODK_VERSION=$(VERSION) -t $(DEV):$(VERSION) . \
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&& docker tag $(DEV):$(VERSION) $(DEV):latest
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docker-run:
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docker run --rm -ti --name odkfull $(IM)
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docker-clean:
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docker kill $(IM) || echo not running ;
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docker rm $(IM) || echo not made
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docker-publish-no-build:
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@docker push $(IM):$(VERSION) \
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&& docker push $(IM):latest
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docker-publish-dev-no-build:
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@docker push $(DEV):$(VERSION) \
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&& docker push $(DEV):latest
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docker-publish: docker-build
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@docker push $(IM):$(VERSION) \
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&& docker push $(IM):latest
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#### TESTING #####
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docker-test: docker-build
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docker-test-full: docker-build
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docker images | grep odkfull &&\
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make test CMD=./seed-via-docker.sh
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docker-test-dev: docker-build-dev
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docker images | grep odkdev &&\
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make test CMD=./seed-via-docker.sh
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docker-test-lite: docker-build
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docker images | grep odklite &&\
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make test CMD=./seed-via-docker.sh
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docker-test: docker-test-full docker-test-dev
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docker-test-no-build:
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docker images | grep odkfull &&\
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make test CMD=./seed-via-docker.sh
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docker-test-dev-no-build:
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docker images | grep odkdev &&\
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make test CMD=./seed-via-docker.sh
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docker-test-lite-no-build:
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docker images | grep odklite &&\
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make test CMD=./seed-via-docker.sh
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#### Publishing #####
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docker-publish-no-build:
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@docker push $(DEV):$(VERSION) \
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&& docker push $(DEV):latest \
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&& docker push $(IMLITE):latest \
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&& docker push $(IMLITE):$(VERSION) \
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&& docker push $(IM):latest \
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&& docker push $(IM):$(VERSION)
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docker-publish: docker-build
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@docker push $(DEV):$(VERSION) \
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&& docker push $(DEV):latest \
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&& docker push $(IMLITE):latest \
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&& docker push $(IMLITE):$(VERSION) \
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&& docker push $(IM):latest \
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&& docker push $(IM):$(VERSION)
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docker-publish-all: docker-publish
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(cd docker/osklite && make publish VERSION=$(VERSION))
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docker-publish-dev-no-build:
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@docker push $(DEV):$(VERSION) \
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&& docker push $(DEV):latest
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clean-tests:
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rm -rf target/*

‎docker/odklite/Dockerfile‎

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FROM openjdk:8-jdk-alpine
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MAINTAINER Chris Mungall <[email protected]>
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RUN apk add --update make
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### From https://stackoverflow.com/questions/51121875/how-to-run-docker-with-python-and-java
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### 1. Get Linux
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FROM ubuntu:18.04
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LABEL maintainer="[email protected]"
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### 2. Get Java, Python and all required system libraries (version control etc)
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ENV JAVA_HOME="/usr"
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WORKDIR /tools
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ENV PATH "/tools/:$PATH"
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COPY requirements.txt.lite /tools/requirements.txt
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COPY odk/make-release-assets.py /tools/
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#ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
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# LAYERSIZE ~1000MB
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RUN apt-get update &&\
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apt-get install -y software-properties-common &&\
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apt-get upgrade -y &&\
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apt-get install -y build-essential \
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git \
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openjdk-8-jre \
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make \
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unzip \
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rsync \
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curl \
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jq \
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openssl
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###### owltools & OORT ######
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# For now we get these from jenkins builds, but these should be obtained
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# by composing existing Dockerfiles, or by obtaining directly from maven
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RUN wget http://build.berkeleybop.org/job/robot/lastSuccessfulBuild/artifact/bin/robot -O /tools/robot
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RUN wget http://build.berkeleybop.org/job/robot/lastSuccessfulBuild/artifact/bin/robot.jar -O /tools/robot.jar
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RUN chmod +x /tools/*
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ENV PATH "/tools/:$PATH"
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ENV OWLTOOLS 2020-04-06
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RUN curl -L https://github.com/owlcollab/owltools/releases/download/$OWLTOOLS/owltools -o /tools/owltools && \
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curl -L https://github.com/owlcollab/owltools/releases/download/$OWLTOOLS/ontology-release-runner -o /tools/ontology-release-runner && \
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curl -L https://github.com/owlcollab/owltools/releases/download/$OWLTOOLS/owltools-oort-all.jar -o /tools/owltools-oort-all.jar && \
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chmod +x /tools/owltools && \
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chmod +x /tools/ontology-release-runner && \
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chmod +x /tools/owltools-oort-all.jar
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###### ROBOT ######
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ENV ROBOT v1.8.1
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ARG ROBOT_JAR=https://github.com/ontodev/robot/releases/download/$ROBOT/robot.jar
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ENV ROBOT_JAR ${ROBOT_JAR}
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# LAYERSIZE ~66MB
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RUN curl -L $ROBOT_JAR -o /tools/robot.jar &&\
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curl -L https://raw.githubusercontent.com/ontodev/robot/$ROBOT/bin/robot -o /tools/robot && \
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chmod +x /tools/robot && \
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chmod +x /tools/robot.jar
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### 5. Install ODK
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ARG ODK_VERSION=0.0.0
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ENV ODK_VERSION=${ODK_VERSION}
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# Setup dosdp tools
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ENV V=0.10.1
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RUN wget -nv https://github.com/INCATools/dosdp-tools/releases/download/v$V/dosdp-tools-$V.tgz
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RUN tar -zxvf dosdp-tools-$V.tgz && mv dosdp-tools-$V /tools/dosdp-tools
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ENV PATH "/tools/dosdp-tools/bin:$PATH"
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### TODO REVIEW THIS. As we speak, jq is official still stalled at 1.5, but for the walk function, we
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### Need 1.6 - once 1.6 is offcial, the following RUN can be removed.
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# LAYERSIZE: ~4MB
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RUN curl -L https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -o /tools/jq && chmod +x /tools/jq
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CMD make -h
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COPY odk/odk.py /tools/
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COPY template/ /tools/templates/
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RUN chmod +x /tools/*.py
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ENV LC_ALL=C.UTF-8
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ENV LANG=C.UTF-8
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RUN echo "Keep me in sync with obolibrary/odkfull!"
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CMD python /tools/odk.py

‎docker/odklite/Makefile‎

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# Building docker image
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VERSION = "v1.1.7"
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VERSION = "v1.2.27"
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IM=obolibrary/odklite
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@docker build -t $(IM):$(VERSION) . \
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&& docker tag $(IM):$(VERSION) $(IM):latest
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run:
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docker run --rm -ti --name odklite $(IM)
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docker-build-no-cache:
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@docker build --build-arg ODK_VERSION=$(VERSION) --no-cache -t $(IM):$(VERSION) . \
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&& docker tag $(IM):$(VERSION) $(IM):latest
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docker-build:
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@docker build --build-arg ODK_VERSION=$(VERSION) -t $(IM):$(VERSION) . \
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&& docker tag $(IM):$(VERSION) $(IM):latest
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publish: build
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@docker push $(IM):$(VERSION) \

‎docker/robot/Dockerfile‎

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FROM openjdk:8-jre-alpine3.9
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MAINTAINER Chris Mungall <[email protected]>
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RUN apk add --no-cache make bash
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FROM openjdk:8-slim
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LABEL maintainer="[email protected]"
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WORKDIR /tools
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ENV ROBOT v1.5.0
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ENV ROBOT v1.8.1
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ARG ROBOT_JAR=https://github.com/ontodev/robot/releases/download/$ROBOT/robot.jar
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ENV ROBOT_JAR ${ROBOT_JAR}
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RUN wget $ROBOT_JAR -O /tools/robot.jar && \
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wget https://raw.githubusercontent.com/ontodev/robot/$ROBOT/bin/robot -O /tools/robot && \
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chmod +x /tools/*
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RUN apt-get update &&\
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apt-get upgrade -y &&\
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apt-get install -y make \
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unzip \
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rsync \
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curl
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RUN curl -L $ROBOT_JAR -o /tools/robot.jar &&\
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curl -L https://raw.githubusercontent.com/ontodev/robot/$ROBOT/bin/robot -o /tools/robot && \
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chmod +x /tools/robot && \
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chmod +x /tools/robot.jar
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ENV PATH "/tools/:$PATH"
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RUN echo "Keep me in sync with obolibrary/odkfull!"
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CMD robot -h

‎docker/robot/Makefile‎

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# Building docker image
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VERSION = "v1.5.0"
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VERSION = "v1.8.1"
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IM=obolibrary/robot
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build:
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docker-build:
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@docker build -t $(IM):$(VERSION) . \
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&& docker tag $(IM):$(VERSION) $(IM):latest
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run:
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docker run --rm -ti --name robot $(IM)
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clean:
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docker kill $(IM) || echo not running ;
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docker rm $(IM) || echo not made

‎docker/testdocker/Dockerfile‎

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