Develop

.github/workflows/http-tests.yml

@@ -49,7 +49,7 @@ jobs:
         run: ./run.sh "$PWD/ssl/owner/cert.pem" "${{ secrets.HTTP_TEST_OWNER_CERT_PASSWORD }}" "$PWD/ssl/secretary/cert.pem" "${{ secrets.HTTP_TEST_SECRETARY_CERT_PASSWORD }}"
         shell: bash
         working-directory: http-tests
-      - name: Stop Docker containers
-        run: docker compose --env-file ./http-tests/.env down
+      - name: Stop Docker containers and remove volumes
+        run: docker compose --env-file ./http-tests/.env down -v
       - name: Remove Docker containers
         run: docker compose --env-file ./http-tests/.env rm -f

CHANGELOG.md

@@ -1,3 +1,17 @@
+## [5.2.0] - 2026-01-14
+### Added
+- Application settings form with modal UI for editing dataspace configuration
+- Settings endpoint (`/settings`) with `GET` and `PATCH` support for dataspace settings
+- HTTP tests for the settings endpoint
+- LinkedDataHub packages system with install/uninstall functionality
+
+### Changed
+- Core library refactored Graph Store Protocol implementation - split into `GraphStoreBase` (common functionality), `DirectGraphStoreImpl` (direct graph identification), and `GraphStoreImpl` (indirect graph identification with query parameters)
+- Incorporated AtomGraph Server code directly into LinkedDataHub codebase
+- System configuration dataset now uses named graphs instead of default graph
+- Web-Client dependency version bump
+- CLI scripts improved for better parameter handling
+
 ## [5.1.0] - 2025-12-12
 ### Added
 - ORCID OpenID Connect login support with JWT token verification

CLAUDE.md

@@ -112,4 +112,26 @@ export PATH="$(find bin -type d -exec realpath {} \; | tr '\n' ':')$PATH"
 - XSLT stylesheets are processed during build to inline XML entities
 - Saxon-JS SEF files are generated during Maven package phase for client-side XSLT
 - WebID certificates are required for authenticated API access
-- The system expects Jena CLI tools to be available (`JENA_HOME` environment variable)
+- The system expects Jena CLI tools to be available (`JENA_HOME` environment variable)
+
+## Debugging Test Failures
+
+When HTTP tests fail:
+1. NEVER speculate about failures - always add debug output first
+2. Add echo statements showing:
+    - The actual values being tested
+    - The expected values
+    - HTTP response codes and bodies where relevant
+3. Run the test to see actual output
+4. Only then diagnose and fix
+
+Example debug pattern:
+```bash
+result=$(curl ...)
+expected="..."
+echo "DEBUG: Expected: $expected"
+echo "DEBUG: Got: $result"
+if [ "$result" != "$expected" ]; then
+echo "DEBUG: Mismatch!"
+exit 1
+fi

README.md

@@ -187,7 +187,7 @@ The options are described in more detail in the [configuration documentation](ht
 
   If you need to start fresh and wipe the existing setup (e.g. after configuring a new base URI), you can do that using
   ```shell
-  sudo rm -rf data uploads && docker-compose down -v
+  sudo rm -rf fuseki uploads ssl datasets && docker-compose down -v
   ```
 
 _:warning: This will **remove the persisted data and files** as well as Docker volumes._
@@ -266,7 +266,6 @@ See the [Web-Algebra repository](https://github.com/AtomGraph/Web-Algebra) for s
 
 LinkedDataHub includes an HTTP [test suite](https://github.com/AtomGraph/LinkedDataHub/tree/master/http-tests). The server implementation is also covered by the [Processor test suite](https://github.com/AtomGraph/Processor/tree/master/http-tests).
 
-![HTTP-tests](https://github.com/AtomGraph/LinkedDataHub/actions/workflows/http-tests.yml/badge.svg)
 ![HTTP-tests](https://github.com/AtomGraph/LinkedDataHub/actions/workflows/http-tests.yml/badge.svg)
 
 ## Dependencies
@@ -287,8 +286,9 @@ LinkedDataHub includes an HTTP [test suite](https://github.com/AtomGraph/LinkedD
 * [java-jwt](https://github.com/auth0/java-jwt)
 * [ExpiringMap](https://github.com/jhalterman/expiringmap)
 * [CSV2RDF](https://github.com/AtomGraph/CSV2RDF)
-* [Processor](https://github.com/AtomGraph/Processor)
 * [Web-Client](https://github.com/AtomGraph/Web-Client)
+* [Twirl](https://github.com/AtomGraph/Twirl)
+* [jena-shacl](https://mvnrepository.com/artifact/org.apache.jena/jena-shacl)
 
 ### Docker
 

bin/admin/clear-ontology.sh

@@ -1,4 +1,5 @@
 #!/usr/bin/env bash
+set -eo pipefail
 
 print_usage()
 {

bin/admin/packages/install-package.sh

@@ -0,0 +1,104 @@
+#!/usr/bin/env bash
+set -eo pipefail
+
+print_usage()
+{
+    printf "Installs a LinkedDataHub package.\n"
+    printf "\n"
+    printf "Usage:  %s options\n" "$0"
+    printf "\n"
+    printf "Options:\n"
+    printf "  -b, --base BASE_URL                  Base URL of the application\n"
+    printf "  -f, --cert-pem-file CERT_FILE        .pem file with the WebID certificate of the agent\n"
+    printf "  -p, --cert-password CERT_PASSWORD    Password of the WebID certificate\n"
+    printf "  --proxy PROXY_URL                    The host this request will be proxied through (optional)\n"
+    printf "  --package PACKAGE_URI                URI of the package to install (e.g., https://packages.linkeddatahub.com/skos/#this)\n"
+    printf "\n"
+    printf "Example:\n"
+    printf "  %s -b https://localhost:4443/ -f ssl/owner/cert.pem -p Password --package https://packages.linkeddatahub.com/skos/#this\n" "$0"
+}
+
+hash curl 2>/dev/null || { echo >&2 "curl not on \$PATH. Aborting."; exit 1; }
+
+unknown=()
+while [[ $# -gt 0 ]]
+do
+    key="$1"
+
+    case $key in
+        -b|--base)
+        base="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        -f|--cert-pem-file)
+        cert_pem_file="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        -p|--cert-password)
+        cert_password="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        --proxy)
+        proxy="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        --package)
+        package_uri="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        *)    # unknown option
+        unknown+=("$1") # save it in an array for later
+        shift # past argument
+        ;;
+    esac
+done
+set -- "${unknown[@]}" # restore args
+
+if [ -z "$base" ] ; then
+    print_usage
+    exit 1
+fi
+if [ -z "$cert_pem_file" ] ; then
+    print_usage
+    exit 1
+fi
+if [ -z "$cert_password" ] ; then
+    print_usage
+    exit 1
+fi
+if [ -z "$package_uri" ] ; then
+    print_usage
+    exit 1
+fi
+
+# Convert base URL to admin base URL
+admin_uri() {
+    local uri="$1"
+    echo "$uri" | sed 's|://|://admin.|'
+}
+
+admin_base=$(admin_uri "$base")
+target_url="${admin_base}packages/install"
+
+if [ -n "$proxy" ]; then
+    admin_proxy=$(admin_uri "$proxy")
+    # rewrite target hostname to proxy hostname
+    url_host=$(echo "$target_url" | cut -d '/' -f 1,2,3)
+    proxy_host=$(echo "$admin_proxy" | cut -d '/' -f 1,2,3)
+    final_url="${target_url/$url_host/$proxy_host}"
+else
+    final_url="$target_url"
+fi
+
+# POST to packages/install endpoint
+curl -k -f -s -w "%{http_code}\n" -E "$cert_pem_file":"$cert_password" \
+    -X POST \
+    -H "Accept: text/turtle" \
+    -H "Content-Type: application/x-www-form-urlencoded" \
+    --data-urlencode "package-uri=${package_uri}" \
+    "${final_url}"

bin/admin/packages/uninstall-package.sh

@@ -0,0 +1,104 @@
+#!/usr/bin/env bash
+set -eo pipefail
+
+print_usage()
+{
+    printf "Uninstalls a LinkedDataHub package.\n"
+    printf "\n"
+    printf "Usage:  %s options\n" "$0"
+    printf "\n"
+    printf "Options:\n"
+    printf "  -b, --base BASE_URL                  Base URL of the application\n"
+    printf "  -f, --cert-pem-file CERT_FILE        .pem file with the WebID certificate of the agent\n"
+    printf "  -p, --cert-password CERT_PASSWORD    Password of the WebID certificate\n"
+    printf "  --proxy PROXY_URL                    The host this request will be proxied through (optional)\n"
+    printf "  --package PACKAGE_URI                URI of the package to uninstall (e.g., https://packages.linkeddatahub.com/skos/#this)\n"
+    printf "\n"
+    printf "Example:\n"
+    printf "  %s -b https://localhost:4443/ -f ssl/owner/cert.pem -p Password --package https://packages.linkeddatahub.com/skos/#this\n" "$0"
+}
+
+hash curl 2>/dev/null || { echo >&2 "curl not on \$PATH. Aborting."; exit 1; }
+
+unknown=()
+while [[ $# -gt 0 ]]
+do
+    key="$1"
+
+    case $key in
+        -b|--base)
+        base="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        -f|--cert-pem-file)
+        cert_pem_file="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        -p|--cert-password)
+        cert_password="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        --proxy)
+        proxy="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        --package)
+        package_uri="$2"
+        shift # past argument
+        shift # past value
+        ;;
+        *)    # unknown option
+        unknown+=("$1") # save it in an array for later
+        shift # past argument
+        ;;
+    esac
+done
+set -- "${unknown[@]}" # restore args
+
+if [ -z "$base" ] ; then
+    print_usage
+    exit 1
+fi
+if [ -z "$cert_pem_file" ] ; then
+    print_usage
+    exit 1
+fi
+if [ -z "$cert_password" ] ; then
+    print_usage
+    exit 1
+fi
+if [ -z "$package_uri" ] ; then
+    print_usage
+    exit 1
+fi
+
+# Convert base URL to admin base URL
+admin_uri() {
+    local uri="$1"
+    echo "$uri" | sed 's|://|://admin.|'
+}
+
+admin_base=$(admin_uri "$base")
+target_url="${admin_base}packages/uninstall"
+
+if [ -n "$proxy" ]; then
+    admin_proxy=$(admin_uri "$proxy")
+    # rewrite target hostname to proxy hostname
+    url_host=$(echo "$target_url" | cut -d '/' -f 1,2,3)
+    proxy_host=$(echo "$admin_proxy" | cut -d '/' -f 1,2,3)
+    final_url="${target_url/$url_host/$proxy_host}"
+else
+    final_url="$target_url"
+fi
+
+# POST to packages/uninstall endpoint
+curl -k -f -s -w "%{http_code}\n" -E "$cert_pem_file":"$cert_password" \
+    -X POST \
+    -H "Accept: text/turtle" \
+    -H "Content-Type: application/x-www-form-urlencoded" \
+    --data-urlencode "package-uri=${package_uri}" \
+    "${final_url}"

config/system.trig

@@ -15,40 +15,59 @@
 
 # root admin
 
-<urn:linkeddatahub:apps/admin> a lapp:Application, lapp:AdminApplication ;
-    dct:title "LinkedDataHub admin" ;
-    # ldt:base <https://admin.localhost:4443/> ;
-    ldh:origin <https://admin.localhost:4443> ;
-    ldt:ontology <https://w3id.org/atomgraph/linkeddatahub/admin#> ;
-    ldt:service <urn:linkeddatahub:services/admin> ;
-    ac:stylesheet <static/com/atomgraph/linkeddatahub/xsl/bootstrap/2.3.2/admin/layout.xsl> ;
-    lapp:endUserApplication <urn:linkeddatahub:apps/end-user> ;
-    lapp:frontendProxy <http://varnish-frontend:6060/> .
-
-<urn:linkeddatahub:services/admin> a sd:Service ;
-    dct:title "LinkedDataHub admin service" ;
-    sd:supportedLanguage sd:SPARQL11Query, sd:SPARQL11Update ;
-    sd:endpoint <http://fuseki-admin:3030/ds/> ;
-    a:graphStore <http://fuseki-admin:3030/ds/> ;
-    a:quadStore <http://fuseki-admin:3030/ds/> ;
-    lapp:backendProxy <http://varnish-admin/> .
+<urn:linkeddatahub:apps/admin>
+{
+    <urn:linkeddatahub:apps/admin> a lapp:Application, lapp:AdminApplication ;
+        dct:title "LinkedDataHub admin" ;
+        # ldt:base <https://admin.localhost:4443/> ;
+        lapp:origin <https://admin.localhost:4443> ;
+        ldt:ontology <https://w3id.org/atomgraph/linkeddatahub/admin#> ;
+        ldt:service <urn:linkeddatahub:services/admin> ;
+        ac:stylesheet <static/xsl/admin/layout.xsl> ;
+        lapp:endUserApplication <urn:linkeddatahub:apps/end-user> ;
+        lapp:frontendProxy <http://varnish-frontend:6060/> .
+
+}
+
+<urn:linkeddatahub:services/admin>
+{
+
+    <urn:linkeddatahub:services/admin> a sd:Service ;
+        dct:title "LinkedDataHub admin service" ;
+        sd:supportedLanguage sd:SPARQL11Query, sd:SPARQL11Update ;
+        sd:endpoint <http://fuseki-admin:3030/ds/> ;
+        a:graphStore <http://fuseki-admin:3030/ds/> ;
+        a:quadStore <http://fuseki-admin:3030/ds/> ;
+        lapp:backendProxy <http://varnish-admin/> .
+
+}
 
 # root end-user
 
-<urn:linkeddatahub:apps/end-user> a lapp:Application, lapp:EndUserApplication ;
-    dct:title "LinkedDataHub" ;
-    # ldt:base <https://localhost:4443/> ;
-    ldh:origin <https://localhost:4443> ;
-    ldt:ontology <https://localhost:4443/ns#> ;
-    ldt:service <urn:linkeddatahub:services/end-user> ;
-    lapp:adminApplication <urn:linkeddatahub:apps/admin> ;
-    lapp:frontendProxy <http://varnish-frontend:6060/> ;
-    lapp:public true .
-
-<urn:linkeddatahub:services/end-user> a sd:Service ;
-    dct:title "LinkedDataHub service" ;
-    sd:supportedLanguage sd:SPARQL11Query, sd:SPARQL11Update ;
-    sd:endpoint <http://fuseki-end-user:3030/ds/> ;
-    a:graphStore <http://fuseki-end-user:3030/ds/> ;
-    a:quadStore <http://fuseki-end-user:3030/ds/> ;
-    lapp:backendProxy <http://varnish-end-user/> .
+<urn:linkeddatahub:apps/end-user>
+{
+    <urn:linkeddatahub:apps/end-user> a lapp:Application, lapp:EndUserApplication ;
+        dct:title "LinkedDataHub" ;
+        # ldt:base <https://localhost:4443/> ;
+        lapp:origin <https://localhost:4443> ;
+        ldt:ontology <https://localhost:4443/ns#> ;
+        ldt:service <urn:linkeddatahub:services/end-user> ;
+        ac:stylesheet <static/xsl/layout.xsl> ;
+        lapp:adminApplication <urn:linkeddatahub:apps/admin> ;
+        lapp:frontendProxy <http://varnish-frontend:6060/> ;
+        lapp:public true .
+
+}
+
+<urn:linkeddatahub:services/end-user>
+{
+
+    <urn:linkeddatahub:services/end-user> a sd:Service ;
+        dct:title "LinkedDataHub service" ;
+        sd:supportedLanguage sd:SPARQL11Query, sd:SPARQL11Update ;
+        sd:endpoint <http://fuseki-end-user:3030/ds/> ;
+        a:graphStore <http://fuseki-end-user:3030/ds/> ;
+        a:quadStore <http://fuseki-end-user:3030/ds/> ;
+        lapp:backendProxy <http://varnish-end-user/> .
+
+}