-
Notifications
You must be signed in to change notification settings - Fork 119
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
WIP validate files with skohub shape #14
- Loading branch information
Showing
2 changed files
with
228 additions
and
44 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| #!/bin/bash | ||
| set -euo pipefail | ||
|
|
||
| scripts=$(realpath $(dirname -- "$0")) | ||
| shape=$(realpath "$scripts/../skos.shacl.ttl") | ||
| severity=all | ||
| report= | ||
|
|
||
| usage() { | ||
| echo "$0 [OPTION]... FILE" | ||
| echo "Validate SKOS file (Turtle syntax). No return message means everything is fine." | ||
| echo | ||
| echo "Options:" | ||
| echo " -s FILE shape file (default: $shape)" | ||
| echo " -l LEVEL severity violation|warning|all (default: $severity)" | ||
| echo " -o FILE keep full validation report in this file" | ||
| echo " -r show raw validation report and exit" | ||
| echo " -h show this help message" | ||
| exit $1 | ||
| } | ||
|
|
||
| die() { | ||
| echo "$*" >&2 | ||
| exit 1 | ||
| } | ||
|
|
||
| cleanup() { | ||
| echo "Cleaning up" | ||
| #rm -f -- $testfile | ||
| #rm -f -- $result | ||
| docker container stop validate-skos-fuseki > /dev/null | ||
| } | ||
|
|
||
| trap cleanup 0 2 3 15 | ||
|
|
||
| while getopts s:l:o:rh flag | ||
| do | ||
| case "${flag}" in | ||
| s) shape=${OPTARG};; | ||
| l) severity=${OPTARG};; | ||
| o) result=${OPTARG};; | ||
| r) report=1;; | ||
| h) usage 0;; | ||
| *) usage 1;; | ||
| esac | ||
| done | ||
| shift $(($OPTIND - 1)) | ||
|
|
||
| [ -z "${1:-}" ] && usage 1 | ||
|
|
||
| file=$(realpath "$1") | ||
| [ -f "$file" ] || die "File not found: $file" | ||
| # create temporary testfile and make sure it gets deleted | ||
| testfile=$(mktemp /tmp/validate-script.XXXXXX) | ||
|
|
||
|
|
||
| shape=$(realpath "$shape") | ||
| [ -f "$shape" ] || die "File not found: $shape" | ||
| # add the skos definitions to the file if the shape is "skos.shacl.ttl" | ||
| if [ "$(basename $shape)" = "skos.shacl.ttl" ]; then | ||
| cat $file $(realpath skosClassAndPropertyDefinitions.ttl) > $testfile | ||
| else | ||
| cat $file > $testfile | ||
| fi | ||
|
|
||
| grep -vE '^\s*(#.*)?$' "$file" >/dev/null || die "File contains no RDF statements: $testfile" | ||
|
|
||
| if [[ $severity == "warning" ]]; then | ||
| SEVERITY_FILE="./scripts/checkForWarning.rq" | ||
| elif [[ $severity == "all" ]]; then | ||
| SEVERITY_FILE="./scripts/checkForBoth.rq" | ||
| elif [[ $severity == "violation" ]]; then | ||
| SEVERITY_FILE="./scripts/checkForViolation.rq" | ||
| else | ||
| die "Unknown severity: $severity" | ||
| fi | ||
|
|
||
| # create temporary file (will be deleted in cleanup function) | ||
| if [[ -z "${result:-}" ]]; then | ||
| result=$(mktemp /tmp/validate-script.XXXXXX) | ||
| else | ||
| result=$(realpath "$result") | ||
| fi | ||
|
|
||
| # Check if the container is running | ||
| if docker ps | grep -q "validate-skos-fuseki"; then | ||
| docker stop validate-skos-fuseki | ||
| sleep 1 | ||
| fi | ||
|
|
||
| # wait till fuseki is up | ||
| max_attempts=5 | ||
| delay=3 | ||
| attempt=1 | ||
|
|
||
| echo "Starting validation container" | ||
|
|
||
| while [ $attempt -le $max_attempts ]; do | ||
| # start fuseki | ||
| docker run -d --rm --name validate-skos-fuseki -p 0:3030 -v /fuseki/config_inference.ttl:/fuseki/config_inference.ttl skohub/jena-fuseki:latest /jena-fuseki/fuseki-server --config /fuseki/config_inference.ttl > /dev/null | ||
| port=$(docker port validate-skos-fuseki 3030/tcp | head -1 | awk -F: '{print $2}') | ||
| sleep $delay | ||
| curl "http://localhost:$port/$/ping" > /dev/null && break | ||
| attempt=$((attempt + 1)) | ||
| done | ||
|
|
||
| if [ $attempt -gt $max_attempts ]; then | ||
| echo "The command has failed after $max_attempts attempts." | ||
| exit 1 | ||
| fi | ||
|
|
||
| # upload file | ||
| curl --request POST \ | ||
| --url "http://localhost:$port/dataset/data?graph=default" \ | ||
| --header 'Content-Type: text/turtle' \ | ||
| --data-binary @$testfile > /dev/null | ||
|
|
||
| # validate w/ shacl | ||
| curl --request POST \ | ||
| --url "http://localhost:$port/dataset/shacl?graph=default" \ | ||
| --header 'Content-Type: text/turtle' \ | ||
| --data-binary @$shape > "$result" | ||
|
|
||
| echo "Checking validation result" | ||
| ls -la / | ||
|
|
||
| if [[ "$report" -eq 1 ]]; then | ||
| cat "$result" | ||
| else | ||
| # changed to v flag for mounting | ||
| validationResult="$(docker run --rm -v ./checkForViolation.rq:/rdf/checkForViolation.rq -v $result:/rdf/result.ttl skohub/jena:4.6.1 arq --data /rdf/result.ttl --query /rdf/checkForViolation.rq)" | ||
|
|
||
| lines=$(echo "$validationResult" | wc -l ) | ||
|
|
||
| # Correct validation has 4 lines of output | ||
| [[ ${lines} -eq 4 ]] || die "$validationResult" | ||
|
|
||
| fi |