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[#58] get data from biolink

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jnguyenx committed Apr 7, 2017
1 parent a04dc24 commit 2f228dd2738c0d5f5ba35df207bb3110a7e346d8
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@@ -27,14 +27,20 @@ ENV JAVA_HOME /usr/lib/jvm/java-8-oracle
# Define working directory.
WORKDIR /data
ADD owlsim-services/target/owlsim-services-3.0-SNAPSHOT.jar /data/
ADD configuration-samples/configuration-all.yaml /data/configuration.yaml
#ADD configuration-samples/configuration-all.yaml /data/configuration.yaml
ADD scripts/golr-exporter.py /data/golr-exporter.py
ADD scripts/configuration-generator.py /data/configuration-generator.py
RUN if [ $species = "human" ]; \
RUN apt-get -y update && apt-get install python-pip -y
RUN pip install pyyaml
RUN if [ $species = "all" ]; \
then \
wget https://data.monarchinitiative.org/owl/all-hp.owl -O /data/all.owl; \
cd /data && python golr-exporter.py; \
else \
wget http://ci.monarchinitiative.org/view/dev/job/create-owlsim-files-on-dev/lastSuccessfulBuild/artifact/server/all.owl -O /data/all.owl; \
cd /data && python golr-exporter.py -t $species; \
fi
RUN cd /data && python configuration-generator.py
CMD java -jar /data/owlsim-services-3.0-SNAPSHOT.jar server /data/configuration.yaml
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@@ -76,6 +76,7 @@ To restrict to specific species:
```
docker build --build-arg species=all -t owlsim-all . # default if no args is provided or not matching any species
docker build --build-arg species=human -t owlsim-human
docker build --build-arg species=Hs -t owlsim-human .
docker build --build-arg species=Hs,Mm -t owlsim-multi .
# supported species: Hs,Mm,Dr,Dm,Ce
```
@@ -363,8 +363,8 @@ private void setPropertyValues(OWLOntology ont, OWLNamedIndividual i) {
addPropertyValue(pvm, pid, getShortForm(((OWLNamedIndividual) obj).getIRI()));
}
} else if (false) {
// TODO check this...
} else if (false) {
String pid = getShortForm(((OWLDataProperty) p).getIRI());
OWLLiteral obj = ((OWLDataPropertyAssertionAxiom) paa).getObject();
if (obj instanceof OWLLiteral) {
@@ -33,7 +33,7 @@ public KnowledgeBaseModule(Collection<String> ontologyUris, Collection<String> o
logger.info("Loading curies:");
curies.entrySet().forEach(logger::info);
logger.info("Loading labels:");
//labels.entrySet().forEach(logger::info);
labelTsvs.forEach(logger::info);
//The OwlKnowledgeBase.Loader uses the ELKReasonerFactory and Concurrency.CONCURRENT as defaults.
this.bmKnowledgeBase = OwlKnowledgeBase.loader()
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@@ -43,7 +43,8 @@ def transformAssociation(input, output):
def main():
biolink = "http://localhost:5000/api" #mart/labels/gene/phenotype/NCBITaxon%3A7955
#biolink = "http://localhost:5000/api" #mart/labels/gene/phenotype/NCBITaxon%3A7955
biolink = "https://api.monarchinitiative.org/api"
taxon_map = {
'Hs': 9606,

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