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cmungallcmungall
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Merge pull request #44 from INCATools/adding-sources
adding reacto
2 parents f76f5b8 + 2cf58a4 commit bc331cb

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Lines changed: 92 additions & 93 deletions

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‎Dockerfile‎

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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:20.04
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FROM obolibrary/odkfull
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LABEL maintainer="cjmungall@lbl.gov" \
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name="semanticsql" \
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version="0.0.1"
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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 pyproject.toml /tools/
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COPY ./utils/create-semsql-db.sh /tools/
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##COPY utils/* /tools/
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WORKDIR /semsql
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# Install packages
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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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openjdk-8-jdk \
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maven \
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python3-pip \
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python3-dev \
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subversion \
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make \
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automake \
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gcc \
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g++ \
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unzip \
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rsync \
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curl \
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wget \
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jq \
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openssl \
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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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libfreetype6-dev \
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libpng-dev \
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pkg-config \
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xlsx2csv &&\
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cd /usr/local/bin \
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&& ln -s /usr/bin/python3 python \
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&& pip3 install --upgrade pip setuptools \
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&& pip3 install -r /tools/requirements.txt
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#&& npm install -g obographviz \
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#&& chmod +x /tools/node_modules
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RUN pip install semsql
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#COPY ./node_modules/obographviz /tools/node_modules/obographviz/
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#ENV PATH "/tools/node_modules/obographviz/bin/:$PATH"
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COPY *Makefile .
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COPY reports/obo.tsv ./reports/
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###### ROBOT ######
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ENV ROBOT v1.8.3
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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 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/robot && \
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chmod +x /tools/robot.jar
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# Avoid repeated downloads of script dependencies by mounting the local coursier cache:
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# docker run -v $HOME/.coursier/cache/v1:/tools/.coursier-cache ...
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ENV COURSIER_CACHE "/tools/.coursier-cache"
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###### JENA ######
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ENV JENA 4.4.0
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RUN wget http://archive.apache.org/dist/jena/binaries/apache-jena-$JENA.tar.gz -O- | tar xzC /tools
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ENV PATH "/tools/apache-jena-$JENA/bin:$PATH"
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###### relation-graph ######
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ENV RGVERSION=2.2.0
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ENV PATH "/tools/relation-graph/bin:$PATH"
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# LAYERSIZE ~200MB
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RUN wget -nv https://github.com/balhoff/relation-graph/releases/download/v$RGVERSION/relation-graph-cli-$RGVERSION.tgz \
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&& tar -zxvf relation-graph-cli-$RGVERSION.tgz \
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&& mv relation-graph-cli-$RGVERSION /tools/relation-graph \
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&& chmod +x /tools/relation-graph
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### TODO REVIEW THIS. As we speak, jq is official still stalled at 1.5, but for the walk function, we
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### Need 1.6 - once 1.6 is offcial, the following RUN can be removed.
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# LAYERSIZE: ~4MB
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RUN wget https://github.com/stedolan/jq/releases/download/jq-1.6/jq-linux64 -O /tools/jq && chmod +x /tools/jq
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COPY semsql /tools/semsql/
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COPY db /tools/db
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ENV LC_ALL=C.UTF-8
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ENV LANG=C.UTF-8
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ENV PATH "/usr/bin/:$PATH"
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#CMD python3 -m semsql.subgraph -d db/envo.db ocean% -m label -f viz
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#CMD sqlite db/envo.db
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CMD /bin/bash
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CMD [ "make -k all RUN=" ]

‎Makefile‎

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OBO = http://purl.obolibrary.org/obo
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RUN = poetry run
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VERSION = $(shell git tag | tail -1)
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SRC_DIR = src/semsql/linkml
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BUILDER_DIR = src/semsql/builder
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DDL_DIR = $(BUILDER_DIR)/sql_schema
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# Prefixes
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# ---
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# TODO: sync with bioregistry
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# NOTE: this is now managed in build folder
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# NOTE: move this to build folder
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build_prefixes: $(PREFIX_DIR)/prefixes.csv
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@@ -137,16 +138,34 @@ db/phenio.owl:
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db/bero.owl:
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curl -L -s https://github.com/berkeleybop/bero/releases/download/2022-05-26/bero.owl > $@.tmp && mv $@.tmp $@
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db/reacto.owl:
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curl -L -s http://purl.obolibrary.org/obo/go/extensions/reacto.owl > $@.tmp && mv $@.tmp $@
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db/go-lego.owl:
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curl -L -s http://purl.obolibrary.org/obo/go/extensions/go-lego.owl > $@.tmp && mv $@.tmp $@
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db/bao.owl:
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robot merge -I http://www.bioassayontology.org/bao/bao_complete.owl -o $@
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# https://github.com/ontodev/rdftab.rs/issues/21
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db/biopax.owl:
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robot convert -I http://www.biopax.org/release/biopax-level3.owl -o $@
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# https://github.com/enanomapper/ontologies/issues/323
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db/enanomapper.owl:
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robot merge -I https://raw.githubusercontent.com/enanomapper/ontologies/master/enanomapper.owl -o $@
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db/efo.owl: STAMP
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robot merge -I http://www.ebi.ac.uk/efo/efo.owl -o $@
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db/reactome-Homo-sapiens.owl: download/reactome-biopax.zip db/biopax.owl
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unzip -p $< Homo_sapiens.owl > $@.tmp &&\
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robot merge -i $@.tmp -i db/biopax.owl -o $@
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download/reactome-biopax.zip:
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curl -L -s https://reactome.org/download/current/biopax.zip > $@
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#fma.owl:#
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# http://purl.org/sig/ont/fma.owl
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s3-deploy:
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aws s3 sync stage s3://bbop-sqlite --acl public-read && \
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aws s3 sync stage s3://bbop-sqlite/releases/$(DATE) --acl public-read
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################################################
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#### Commands for building the Docker image ####
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################################################
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IM=linkml/semantic-sql
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docker-build-no-cache:
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@docker build --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 -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 build -t $(DEV):$(VERSION) . \
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&& docker tag $(DEV):$(VERSION) $(DEV):latest
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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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docker-run:
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@docker run -v $(PWD):/work -w /work -ti $(IM):$(VERSION)
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test-docker-run:
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cd docker-test && docker run -v `pwd`/db:/semsql/db -w /semsql -ti $(IM):$(VERSION) make -k all RUN=

‎src/semsql/builder/build.Makefile‎

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# Directory containing this Makefile
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# https://stackoverflow.com/questions/18136918/how-to-get-current-relative-directory-of-your-makefile
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THIS_DIR := $(dir $(abspath $(firstword $(MAKEFILE_LIST))))
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PREFIX_DIR = $(THIS_DIR)/prefixes
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# Template sqlite database
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TEMPLATE = .template.db
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--ontology-file $<\
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--output-file $@.ttl.tmp \
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--equivalence-as-subclass true \
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--output-individuals true \
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--output-subclasses true \
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--reflexive-subclasses true && \
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riot --out RDFXML $@.ttl.tmp > $@.owl.tmp && \
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riot --out RDFXML --syntax turtle $@.ttl.tmp > $@.owl.tmp && \
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sqlite3 $@.db.tmp -cmd ".mode csv" ".import $(THIS_DIR)/prefixes/prefixes.csv prefix" && \
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rdftab $@.db.tmp < $@.owl.tmp && \
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sqlite3 $@.db.tmp -cmd '.separator "\t"' -cmd '.header on' "SELECT subject,predicate,object FROM statements " > $@.tmp && \
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mv $@.tmp $@ && \
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rm $@.*.tmp
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.PRECIOUS: %-$(RGSUFFIX).tsv
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# ---
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# Prefixes
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# ---
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build_prefixes: $(PREFIX_DIR)/prefixes.csv
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$(PREFIX_DIR)/obo_prefixes.owl:
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robot convert -I http://purl.obolibrary.org/meta/obo_prefixes.ttl -o $@
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$(PREFIX_DIR)/obo_prefixes.db: $(PREFIX_DIR)/obo_prefixes.owl
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sqlite3 $@ < $(PREFIX_DIR)/prefix_ddl.sql && ./bin/rdftab $@ < $<
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$(PREFIX_DIR)/obo_prefixes.csv: $(PREFIX_DIR)/obo_prefixes.db
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sqlite3 $< -cmd ".separator ','" "SELECT p.value AS prefix, ns.value AS base FROM statements AS p JOIN statements AS ns ON (p.subject=ns.subject) WHERE p.predicate='<http://www.w3.org/ns/shacl#prefix>' AND ns.predicate='<http://www.w3.org/ns/shacl#namespace>'" > $@
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$(PREFIX_DIR)/prefixes.csv: $(PREFIX_DIR)/prefixes_curated.csv $(PREFIX_DIR)/obo_prefixes.csv
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cat $^ > $@
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‎src/semsql/builder/prefixes/prefixes.csv‎

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@@ -23,6 +23,8 @@ CoVIC,https://cvdb.ontodev.com/antibody/
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EXAMPLE,http://purl.obolibrary.org/obo/EXAMPLE_
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ENM,http://purl.enanomapper.org/onto/ENM_
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BAO,http://www.bioassayontology.org/bao#BAO_
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biopax,http://www.biopax.org/release/biopax-level3.owl#
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reactome.biopax,http://www.reactome.org/biopax/81/48887#
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PSO,http://purl.obolibrary.org/obo/PSO_
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CHIRO,http://purl.obolibrary.org/obo/CHIRO_
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PW,http://purl.obolibrary.org/obo/PW_
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BTO,http://purl.obolibrary.org/obo/BTO_
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PLANP,http://purl.obolibrary.org/obo/PLANP_
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CARO,http://purl.obolibrary.org/obo/CARO_
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NPO,http://purl.bioontology.org/ontology/npo#NPO_

‎src/semsql/builder/prefixes/prefixes_curated.csv‎

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@@ -23,3 +23,5 @@ CoVIC,https://cvdb.ontodev.com/antibody/
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EXAMPLE,http://purl.obolibrary.org/obo/EXAMPLE_
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ENM,http://purl.enanomapper.org/onto/ENM_
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BAO,http://www.bioassayontology.org/bao#BAO_
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biopax,http://www.biopax.org/release/biopax-level3.owl#
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reactome.biopax,http://www.reactome.org/biopax/81/48887#

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