Package implementation and test fixes

namedgraph · namedgraph · commit e3eaf64334b0 · 2025-12-01T15:51:38.000+01:00
diff --git a/http-tests/admin/packages/install-package-400.sh b/http-tests/admin/packages/install-package-400.sh
@@ -12,5 +12,5 @@ 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" \
-  "$ADMIN_BASE_URL"packages/install \
+  "${ADMIN_BASE_URL}packages/install" \
 | grep -q "$STATUS_BAD_REQUEST"
diff --git a/http-tests/admin/packages/install-package-403.sh b/http-tests/admin/packages/install-package-403.sh
@@ -7,10 +7,10 @@ purge_cache "$END_USER_VARNISH_SERVICE"
 purge_cache "$ADMIN_VARNISH_SERVICE"
 purge_cache "$FRONTEND_VARNISH_SERVICE"
 
-# Unauthorized access (without certificate) should return 401 Unauthorized
+# Unauthorized access (without certificate) should return 403 Forbidden
 curl -k -w "%{http_code}\n" -o /dev/null -s \
   -X POST \
   -H "Content-Type: application/x-www-form-urlencoded" \
   --data-urlencode "package-uri=https://packages.linkeddatahub.com/skos/#this" \
-  "$ADMIN_BASE_URL"packages/install \
-| grep -q "$STATUS_UNAUTHORIZED"
+  "${ADMIN_BASE_URL}packages/install" \
+| grep -q "$STATUS_FORBIDDEN"
diff --git a/http-tests/admin/packages/install-package-404.sh b/http-tests/admin/packages/install-package-404.sh
@@ -14,5 +14,5 @@ curl -k -w "%{http_code}\n" -o /dev/null -s \
   -X POST \
   -H "Content-Type: application/x-www-form-urlencoded" \
   --data-urlencode "package-uri=https://packages.linkeddatahub.com/nonexistent/#package" \
-  "$ADMIN_BASE_URL"packages/install \
+  "${ADMIN_BASE_URL}packages/install" \
 | grep -q "$STATUS_NOT_FOUND"
diff --git a/http-tests/admin/packages/install-package.sh b/http-tests/admin/packages/install-package.sh
@@ -16,21 +16,13 @@ curl -k -w "%{http_code}\n" -o /dev/null -f -s \
   -X POST \
   -H "Content-Type: application/x-www-form-urlencoded" \
   --data-urlencode "package-uri=$package_uri" \
-  "$ADMIN_BASE_URL"packages/install \
+  "${ADMIN_BASE_URL}packages/install" \
 | grep -q "$STATUS_SEE_OTHER"
 
-# verify package stylesheet was installed to filesystem
-# path should be: /static/com/linkeddatahub/packages/skos/layout.xsl
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  test -f /usr/local/tomcat/webapps/ROOT/static/com/linkeddatahub/packages/skos/layout.xsl
+# verify package stylesheet was installed (should return 200)
+curl -k -f -s -o /dev/null \
+  "$END_USER_BASE_URL"static/com/linkeddatahub/packages/skos/layout.xsl
 
 # verify master stylesheet was regenerated and includes package import
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  grep -q "com/linkeddatahub/packages/skos/layout.xsl" \
-  /usr/local/tomcat/webapps/ROOT/static/localhost/layout.xsl
+curl -k -s "${END_USER_BASE_URL}static/localhost/layout.xsl" \
+  | grep -q "com/linkeddatahub/packages/skos/layout.xsl"
diff --git a/http-tests/admin/packages/install-uninstall-package.sh b/http-tests/admin/packages/install-uninstall-package.sh
@@ -10,13 +10,6 @@ purge_cache "$FRONTEND_VARNISH_SERVICE"
 # test package URI (SKOS package)
 package_uri="https://packages.linkeddatahub.com/skos/#this"
 
-# ensure package is not installed initially
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  test ! -f /usr/local/tomcat/webapps/ROOT/static/com/linkeddatahub/packages/skos/layout.xsl || true
-
 # install package
 curl -k -w "%{http_code}\n" -o /dev/null -f -s \
   -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
@@ -26,20 +19,13 @@ curl -k -w "%{http_code}\n" -o /dev/null -f -s \
   "$ADMIN_BASE_URL"packages/install \
 | grep -q "$STATUS_SEE_OTHER"
 
-# verify package was installed
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  test -f /usr/local/tomcat/webapps/ROOT/static/com/linkeddatahub/packages/skos/layout.xsl
+# verify package stylesheet was installed (should return 200)
+curl -k -f -s -o /dev/null \
+  "${END_USER_BASE_URL}static/com/linkeddatahub/packages/skos/layout.xsl"
 
 # verify master stylesheet includes package
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  grep -q "com/linkeddatahub/packages/skos/layout.xsl" \
-  /usr/local/tomcat/webapps/ROOT/static/localhost/layout.xsl
+curl -k -s "$END_USER_BASE_URL"static/localhost/layout.xsl \
+  | grep -q "com/linkeddatahub/packages/skos/layout.xsl"
 
 # uninstall package
 curl -k -w "%{http_code}\n" -o /dev/null -f -s \
@@ -50,16 +36,11 @@ curl -k -w "%{http_code}\n" -o /dev/null -f -s \
   "$ADMIN_BASE_URL"packages/uninstall \
 | grep -q "$STATUS_SEE_OTHER"
 
-# verify package was uninstalled
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  test ! -f /usr/local/tomcat/webapps/ROOT/static/com/linkeddatahub/packages/skos/layout.xsl
+# verify package stylesheet was deleted (should return 404)
+curl -k -w "%{http_code}\n" -o /dev/null -s \
+  "${END_USER_BASE_URL}static/com/linkeddatahub/packages/skos/layout.xsl" \
+| grep -q "$STATUS_NOT_FOUND"
 
 # verify master stylesheet no longer includes package
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  bash -c '! grep -q "com/linkeddatahub/packages/skos/layout.xsl" /usr/local/tomcat/webapps/ROOT/static/localhost/layout.xsl'
+curl -k -s "$END_USER_BASE_URL"static/localhost/layout.xsl \
+  | grep -v -q "com/linkeddatahub/packages/skos/layout.xsl"
diff --git a/http-tests/admin/packages/uninstall-package-400.sh b/http-tests/admin/packages/uninstall-package-400.sh
@@ -12,5 +12,5 @@ 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" \
-  "$ADMIN_BASE_URL"packages/uninstall \
+  "{$ADMIN_BASE_URL}packages/uninstall" \
 | grep -q "$STATUS_BAD_REQUEST"
diff --git a/http-tests/admin/packages/uninstall-package.sh b/http-tests/admin/packages/uninstall-package.sh
@@ -16,35 +16,27 @@ curl -k -w "%{http_code}\n" -o /dev/null -f -s \
   -X POST \
   -H "Content-Type: application/x-www-form-urlencoded" \
   --data-urlencode "package-uri=$package_uri" \
-  "$ADMIN_BASE_URL"packages/install \
+  "${ADMIN_BASE_URL}packages/install" \
 | grep -q "$STATUS_SEE_OTHER"
 
-# verify package stylesheet exists before uninstall
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  test -f /usr/local/tomcat/webapps/ROOT/static/com/linkeddatahub/packages/skos/layout.xsl
+# verify package stylesheet exists before uninstall (should return 200)
+curl -k -f -s -o /dev/null \
+  "${END_USER_BASE_URL}static/com/linkeddatahub/packages/skos/layout.xsl"
 
 # uninstall package via POST to packages/uninstall endpoint
 curl -k -w "%{http_code}\n" -o /dev/null -f -s \
   -E "$OWNER_CERT_FILE":"$OWNER_CERT_PWD" \
   -X POST \
   -H "Content-Type: application/x-www-form-urlencoded" \
   --data-urlencode "package-uri=$package_uri" \
-  "$ADMIN_BASE_URL"packages/uninstall \
+  "${ADMIN_BASE_URL}packages/uninstall" \
 | grep -q "$STATUS_SEE_OTHER"
 
-# verify package stylesheet was deleted
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  test ! -f /usr/local/tomcat/webapps/ROOT/static/com/linkeddatahub/packages/skos/layout.xsl
+# verify package stylesheet was deleted (should return 404)
+curl -k -w "%{http_code}\n" -o /dev/null -s \
+  "${END_USER_BASE_URL}static/com/linkeddatahub/packages/skos/layout.xsl" \
+| grep -q "$STATUS_NOT_FOUND"
 
 # verify master stylesheet was regenerated without package import
-docker compose -f "$HTTP_TEST_ROOT/../docker-compose.yml" \
-  -f "$HTTP_TEST_ROOT/docker-compose.http-tests.yml" \
-  --env-file "$HTTP_TEST_ROOT/.env" \
-  exec -T linkeddatahub \
-  bash -c '! grep -q "com/linkeddatahub/packages/skos/layout.xsl" /usr/local/tomcat/webapps/ROOT/static/localhost/layout.xsl'
+curl -k -s "$END_USER_BASE_URL"static/localhost/layout.xsl \
+  | grep -v -q "com/linkeddatahub/packages/skos/layout.xsl"
diff --git a/src/main/java/com/atomgraph/linkeddatahub/resource/admin/pkg/Install.java b/src/main/java/com/atomgraph/linkeddatahub/resource/admin/pkg/Install.java
@@ -16,6 +16,7 @@
  */
 package com.atomgraph.linkeddatahub.resource.admin.pkg;
 
+import com.atomgraph.client.util.DataManager;
 import com.atomgraph.linkeddatahub.apps.model.AdminApplication;
 import com.atomgraph.linkeddatahub.apps.model.EndUserApplication;
 import com.atomgraph.linkeddatahub.client.LinkedDataClient;
@@ -49,6 +50,7 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
+import org.apache.jena.util.FileManager;
 
 /**
  * JAX-RS resource that installs a LinkedDataHub package.
@@ -67,6 +69,7 @@ public class Install
 
     private final com.atomgraph.linkeddatahub.apps.model.Application application;
     private final com.atomgraph.linkeddatahub.Application system;
+    private final DataManager dataManager;
 
     @Context ServletContext servletContext;
 
@@ -75,13 +78,16 @@ public class Install
      *
      * @param application matched application (admin app)
      * @param system system application
+     * @param dataManager data manager
      */
     @Inject
     public Install(com.atomgraph.linkeddatahub.apps.model.Application application,
-                   com.atomgraph.linkeddatahub.Application system)
+                   com.atomgraph.linkeddatahub.Application system,
+                   DataManager dataManager)
     {
         this.application = application;
         this.system = system;
+        this.dataManager = dataManager;
     }
 
     /**
@@ -112,14 +118,13 @@ public Response post(@FormParam("package-uri") String packageURI, @HeaderParam("
 
             if (ontology == null) throw new BadRequestException("Package ontology not found");
 
-            URI ontologyURI = URI.create(ontology.getURI());
             URI stylesheetURI = (stylesheet != null) ? URI.create(stylesheet.getURI()) : null;
 
             String packagePath = UriPath.convert(packageURI);
 
             // 2. Download and install ontology
-            if (log.isDebugEnabled()) log.debug("Downloading package ontology from: {}", ontologyURI);
-            Model ontologyModel = downloadOntology(ontologyURI);
+            if (log.isDebugEnabled()) log.debug("Downloading package ontology from: {}", ontology.getURI());
+            Model ontologyModel = downloadOntology(ontology.getURI());
             installOntology(endUserApp, ontologyModel);
 
             // 3. Download and install stylesheet if present
@@ -164,8 +169,21 @@ private com.atomgraph.linkeddatahub.apps.model.Package getPackage(String package
         {
             if (log.isDebugEnabled()) log.debug("Loading package from: {}", packageURI);
 
-            LinkedDataClient ldc = LinkedDataClient.create(getSystem().getClient(), getSystem().getMediaTypes());
-            Model model = ldc.getModel(packageURI);
+            final Model model;
+            
+            // check if we have the model in the cache first and if yes, return it from there instead making an HTTP request
+            if (((FileManager)getDataManager()).hasCachedModel(packageURI) ||
+                    (getDataManager().isResolvingMapped() && getDataManager().isMapped(packageURI))) // read mapped URIs (such as system ontologies) from a file
+            {
+                if (log.isDebugEnabled()) log.debug("hasCachedModel({}): {}", packageURI, ((FileManager)getDataManager()).hasCachedModel(packageURI));
+                if (log.isDebugEnabled()) log.debug("isMapped({}): {}", packageURI, getDataManager().isMapped(packageURI));
+                model = getDataManager().loadModel(packageURI);
+            }
+            else
+            {
+                LinkedDataClient ldc = LinkedDataClient.create(getSystem().getClient(), getSystem().getMediaTypes());
+                model = ldc.getModel(packageURI);
+            }
 
             return model.getResource(packageURI).as(com.atomgraph.linkeddatahub.apps.model.Package.class);
         }
@@ -185,12 +203,23 @@ private com.atomgraph.linkeddatahub.apps.model.Package getPackage(String package
     /**
      * Downloads RDF from a URI using LinkedDataClient.
      */
-    private Model downloadOntology(URI uri) throws IOException
+    private Model downloadOntology(String uri) throws IOException
     {
-        if (log.isDebugEnabled()) log.debug("Downloading RDF from: {}", uri);
+        if (log.isDebugEnabled()) log.debug("Downloading ontology from: {}", uri);
 
-        LinkedDataClient ldc = LinkedDataClient.create(getSystem().getClient(), getSystem().getMediaTypes());
-        return ldc.getModel(uri.toString());
+        // check if we have the model in the cache first and if yes, return it from there instead making an HTTP request
+        if (((FileManager)getDataManager()).hasCachedModel(uri) ||
+                (getDataManager().isResolvingMapped() && getDataManager().isMapped(uri))) // read mapped URIs (such as system ontologies) from a file
+        {
+            if (log.isDebugEnabled()) log.debug("hasCachedModel({}): {}", uri, ((FileManager)getDataManager()).hasCachedModel(uri));
+            if (log.isDebugEnabled()) log.debug("isMapped({}): {}", uri, getDataManager().isMapped(uri));
+            return getDataManager().loadModel(uri);
+        }
+        else
+        {
+            LinkedDataClient ldc = LinkedDataClient.create(getSystem().getClient(), getSystem().getMediaTypes());
+            return ldc.getModel(uri);
+        }
     }
 
     /**
@@ -206,9 +235,7 @@ private String downloadStylesheet(URI uri) throws IOException
         try (Response response = target.request("text/xsl", "text/*;q=0.8").get())
         {
             if (!response.getStatusInfo().getFamily().equals(Response.Status.Family.SUCCESSFUL))
-            {
                 throw new IOException("Failed to download XSLT from " + uri + ": " + response.getStatus());
-            }
 
             return response.readEntity(String.class);
         }
@@ -320,4 +347,14 @@ public ServletContext getServletContext()
         return servletContext;
     }
 
+    /**
+     * Returns RDF data manager.
+     * 
+     * @return RDF data manager
+     */
+    public DataManager getDataManager()
+    {
+        return dataManager;
+    }
+    
 }
diff --git a/src/main/resources/com/linkeddatahub/packages/skos/layout.xsl b/src/main/resources/com/linkeddatahub/packages/skos/layout.xsl
@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE xsl:stylesheet [
+    <!ENTITY ldh    "https://w3id.org/atomgraph/linkeddatahub#">
+    <!ENTITY ac     "https://w3id.org/atomgraph/client#">
+    <!ENTITY rdf    "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+    <!ENTITY rdfs   "http://www.w3.org/2000/01/rdf-schema#">
+    <!ENTITY xsd    "http://www.w3.org/2001/XMLSchema#">
+    <!ENTITY skos   "http://www.w3.org/2004/02/skos/core#">
+    <!ENTITY srx    "http://www.w3.org/2005/sparql-results#">
+    <!ENTITY foaf   "http://xmlns.com/foaf/0.1/">
+]>
+<xsl:stylesheet version="2.0"
+xmlns="http://www.w3.org/1999/xhtml"
+xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+xmlns:xhtml="http://www.w3.org/1999/xhtml"
+xmlns:xs="http://www.w3.org/2001/XMLSchema"
+xmlns:ldh="&ldh;"
+xmlns:ac="&ac;"
+xmlns:rdf="&rdf;"
+xmlns:rdfs="&rdfs;"
+xmlns:xsd="&xsd;"
+xmlns:skos="&skos;"
+xmlns:srx="&srx;"
+xmlns:foaf="&foaf;"
+xmlns:bs2="http://graphity.org/xsl/bootstrap/2.3.2"
+exclude-result-prefixes="#all">
+
+    <xsl:param name="ldh:base" as="xs:anyURI" static="yes"/>
+
+    <xsl:import _href="{resolve-uri('static/com/atomgraph/linkeddatahub/xsl/bootstrap/2.3.2/layout.xsl', $ldh:base)}"/>
+
+    <xsl:param name="foaf:Agent" as="document-node()?"/>
+
+    <xsl:template match="rdf:RDF | srx:sparql" mode="xhtml:Style">
+        <xsl:param name="load-wymeditor" select="exists($foaf:Agent//@rdf:about)" as="xs:boolean"/>
+        <xsl:param name="load-yasqe" select="true()" as="xs:boolean"/>
+
+        <xsl:apply-imports/>
+
+        <!-- inject custom Bootstrap theme that overrides the default one -->
+        <link href="{resolve-uri('static/com/linkeddatahub/demo/skos/css/bootstrap.css', $ac:contextUri)}" rel="stylesheet" type="text/css"/>
+        <!-- re-apply LinkedDataHub's Bootstrap customizations -->
+        <link href="{resolve-uri('static/com/atomgraph/linkeddatahub/css/bootstrap.css', $ac:contextUri)}" rel="stylesheet" type="text/css"/>
+
+        <xsl:if test="$load-wymeditor">
+            <link href="{resolve-uri('static/com/atomgraph/linkeddatahub/js/wymeditor/skins/default/skin.css', $ac:contextUri)}" rel="stylesheet" type="text/css"/>
+        </xsl:if>
+        <xsl:if test="$load-yasqe">
+            <link href="{resolve-uri('static/css/yasqe.css', $ac:contextUri)}" rel="stylesheet" type="text/css"/>
+        </xsl:if>
+    </xsl:template>
+
+    <xsl:template match="rdf:RDF" mode="xhtml:Style">
+        <xsl:next-match/>
+
+        <link href="{resolve-uri('static/com/linkeddatahub/demo/skos/css/bootstrap.css', $ac:contextUri)}" rel="stylesheet" type="text/css"/>
+    </xsl:template>
+
+    <xsl:template match="skos:narrower | skos:broader | skos:related | skos:member" mode="bs2:PropertyList"/>
+    
+</xsl:stylesheet>
diff --git a/src/main/resources/com/linkeddatahub/packages/skos/ns.ttl b/src/main/resources/com/linkeddatahub/packages/skos/ns.ttl
diff --git a/src/main/resources/com/linkeddatahub/packages/skos/package.ttl b/src/main/resources/com/linkeddatahub/packages/skos/package.ttl
diff --git a/src/main/resources/location-mapping.ttl b/src/main/resources/location-mapping.ttl
diff --git a/src/main/resources/prefix-mapping.ttl b/src/main/resources/prefix-mapping.ttl
