LinkedDataHub packages (#259)

* Package model and initial implementation

* Removed `PackageManager`

* HTTP unit tests for packages

* Package implementation and test fixes

* Import fix

* Ontology import fixes

* Package installation fixes

* Renamed script

* Removed `/transform` from publicly allowed endpoints

* Package test fixes

* Added getter

* Refactored `XSLTMasterUpdater`

* Refactored `XSLTMasterUpdater`

* Updated SKOS package ontology

* Fixed class filename

* Added SKOS import to the SKOS package ontology

Renamed endpoint classes
Removed VIVO ontology

* Additional install/uninstall tests

* Undo `patch` method changes

* Replaced `LinkedDataClient` with `GraphStoreClient`

Server and Web-Client bumps
`InstallPackage` and `UnistallPackage` use GSP `PATCH` method to add/remove `owl:imports` triple

* Core SNAPSHOT bump

* Updated POM

* `PATCH` update fixes

HTTP test fixes

* Response closure fixes

Use try-with-resources consistently

* Package ontology URI fix

* Test fix

* Varnish ban fix in `ClearOntology`

* HTTP test fixes

Author: namedgraph

bin/admin/model/add-class.sh bin/admin/ontologies/add-class.shbin/admin/model/add-class.sh renamed to bin/admin/ontologies/add-class.sh

@@ -0,0 +1,103 @@
+#!/usr/bin/env bash
+
+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 -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/model/add-construct.sh bin/admin/ontologies/add-construct.shbin/admin/model/add-construct.sh renamed to bin/admin/ontologies/add-construct.sh

@@ -21,7 +21,7 @@
     lapp: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> ;
+    ac:stylesheet <static/xsl/admin/layout.xsl> ;
     lapp:endUserApplication <urn:linkeddatahub:apps/end-user> ;
     lapp:frontendProxy <http://varnish-frontend:6060/> .
 
@@ -41,6 +41,7 @@
     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 .

…n/admin/model/add-property-constraint.sh …in/ontologies/add-property-constraint.shbin/admin/model/add-property-constraint.sh renamed to bin/admin/ontologies/add-property-constraint.sh bin/admin/model/add-property-constraint.sh renamed to bin/admin/ontologies/add-property-constraint.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+initialize_dataset "$END_USER_BASE_URL" "$TMP_END_USER_DATASET" "$END_USER_ENDPOINT_URL"
+initialize_dataset "$ADMIN_BASE_URL" "$TMP_ADMIN_DATASET" "$ADMIN_ENDPOINT_URL"
+purge_cache "$END_USER_VARNISH_SERVICE"
+purge_cache "$ADMIN_VARNISH_SERVICE"
+purge_cache "$FRONTEND_VARNISH_SERVICE"
+
+# Missing package-uri parameter should return 400 Bad Request
+curl -k -w "%{http_code}\n" -o /dev/null -s \
+  -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
+  -X POST \
+  -H "Content-Type: application/x-www-form-urlencoded" \
+  "${ADMIN_BASE_URL}packages/install" \
+| grep -q "$STATUS_BAD_REQUEST"