https://github.com/jervenbolleman/sapfhir-server

Server/docker image for sapfhir using spring-boot and docker image
https://github.com/jervenbolleman/sapfhir-server

biohackeu20 docker-image rdf sparql spring-boot

Last synced: 19 days ago
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Server/docker image for sapfhir using spring-boot and docker image

• Host: GitHub
• URL: https://github.com/jervenbolleman/sapfhir-server
• Owner: JervenBolleman
• License: agpl-3.0
• Created: 2021-03-10T18:29:57.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-10-29T13:04:50.000Z (about 1 year ago)
• Last Synced: 2024-05-18T07:42:15.500Z (8 months ago)
• Topics: biohackeu20, docker-image, rdf, sparql, spring-boot
• Language: Java
• Homepage:
• Size: 19.5 KB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# SapFhir server

This makes the handlegraph4j-simple available as a [W3C SPARQL API](https://www.w3.org/TR/sparql11-protocol/).

You first need to make a handlegraph4j-simple disk/based buffer image use [sapfhir-cli](https://github.com/JervenBolleman/sapfhir-cli).

```

java -Xmx16G \ # set ram to load GFA into memory as needed

    -jar target/sapfhir-cli-1.0-SNAPSHOT-jar-with-dependencies.jar \

    --gfa ${PATH_TO_GFA_FILE} \

    --byte-buffer ${PATH_TO_STORE_DISK_BASKED_FILE} \

    --convert-to-byte \

    --time \

    "PREFIX vg: SELECT ?path WHERE {?path a vg:Path} LIMIT 1"

```

# Usage

```

docker pull jerven/sapfhir-server

docker run -p 8086:8080 -v $LOCAL_DIR/:/data jerven/sapfhir-server --byteBuffer=/data/1kg_hs37d5.h4js --base=http://example.org/vg/

```

At the moment both the base IRI and byteBuffer location needs to be given.

There is no support yet for loading a GFA into memory directly.

Notice the byteBuffer argument takes a file name in the folder mounted by docker.

The default port is 8080, here remapped to localhost:8086 in the docker host.

Test queries e.g.

```

curl -H 'accept: application/sparql-results+json'  \

  "http://localhost:8086/sparql/"  \

  --data-urlencode "query=SELECT (COUNT(?s) AS ?c) WHERE {?s ?p ?o}"

```

# Build docker image

```

mvn spring-boot:build-image -Dspring-boot.build-image.imageName=jerven/sapfhir-server

docker push jerven/sapfhir-server

```