Merge remote-tracking branch 'origin/master'

SODALITE-EU · Sep 12, 2021 · adccd1d · adccd1d
2 parents 542dac6 + 33cc3f7
commit adccd1d
Show file tree

Hide file tree

Showing 9 changed files with 42 additions and 23 deletions.
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -38,7 +38,7 @@ pipeline {
       steps {
         sh  """ #!/bin/bash
                 cd tosca
-                mvn clean install
+                mvn  clean install -Ddefault.min.distinct.threshold=104857600
             """
       }
     }

diff --git a/tosca/api/src/main/resources/sparql/suspiciousComment.sparql b/tosca/api/src/main/resources/sparql/suspiciousComment.sparql
@@ -1,5 +1,6 @@
-select distinct ?resource ?comment
+select distinct ?resource ?comment ?classifier
 where {
-   	?resource rdfs:comment ?comment .
+	?resource rdfs:comment|dcterms:description ?comment;
+	DUL:classifies ?classifier
    	FILTER (regex(lcase(str(?comment)), "(bug|hack|later|todo|later2)","i")).
-	}
+}
diff --git a/tosca/core/src/main/java/nl/jads/tosca/DefectPredictorKBApi.java b/tosca/core/src/main/java/nl/jads/tosca/DefectPredictorKBApi.java
@@ -357,7 +357,10 @@ public List<Comment> suspiciousComment(RepositoryConnection connection) throws I
         while (result.hasNext()) {
             BindingSet bindingSet = result.next();
             IRI p1 = (IRI) bindingSet.getBinding("resource").getValue();
-            comments.add(new Comment(p1, bindingSet.getValue("comment").stringValue()));
+            IRI classifier = (IRI) bindingSet.getBinding("classifier").getValue();
+            Comment c = new Comment(classifier, bindingSet.getValue("comment").stringValue());
+            c.setClassifiedBy(p1);
+            comments.add(c);
         }
         result.close();
         return comments;
@@ -457,9 +460,10 @@ public void fillContext(BugRecord bugRecord, Feature property, RepositoryConnect
         String query = PREFIXES + sparql;
         IRI var;
         if (property instanceof Comment) {
-            var = ((Comment) property).getIri();
+        	//var = ((Comment) property).getIri();
+            var = ((Comment) property).getClassifiedBy();
         } else {
-            var = property.getClassifiedBy();
+        var = property.getClassifiedBy();
         }
         TupleQueryResult result = QueryUtil.evaluateSelectQuery(connection,
                 query, new SimpleBinding("var", var));

diff --git a/tosca/core/src/main/resources/sparql/invalidIPAddressBinding.sparql b/tosca/core/src/main/resources/sparql/invalidIPAddressBinding.sparql
@@ -1,6 +1,17 @@
 select distinct ?var ?resource
 where {
-   	?var DUL:hasParameter ?p .
-	?p DUL:classifies tosca:default .
-	?p tosca:hasDataValue "0.0.0.0".
-	}
+	?var DUL:classifies ?resource.
+
+	optional {
+		?var DUL:hasParameter ?p .
+		?p DUL:classifies tosca:default .
+		?p tosca:hasDataValue ?value .
+		VALUES ?value {"0.0.0.0" "0.0.0.0/0"}.
+	}
+
+	optional {
+		?var (DUL:hasParameter)*/tosca:hasDataValue ?value.
+		VALUES ?value {"0.0.0.0" "0.0.0.0/0"}.
+	}
+	FILTER (bound(?value)).
+}
diff --git a/tosca/core/src/main/resources/sparql/invalidPortRange.sparql b/tosca/core/src/main/resources/sparql/invalidPortRange.sparql
@@ -1,15 +1,15 @@
 select distinct ?var ?resource
 where {
     ?var DUL:classifies ?resource.
-    FILTER (regex(str(?resource), "port(.+?)|(.+?)?port","i")).
+    FILTER (regex(str(?resource), "port(.+?)|(.+?)?port|(.+?)?ports","i")).
     optional {
         ?var DUL:hasParameter ?p .
 	    ?p DUL:classifies tosca:default .
 	    ?p tosca:hasDataValue ?value.
 	}.
     optional {
-        ?var tosca:hasDataValue ?value.
+        ?var (tosca:hasDataValue|(tosca:hasObjectValue/tosca:hasDataValue)) ?value.
 	}.
     FILTER (bound(?value)).
     FILTER( ?value < 0 || ?value > 65535 )
-}
+}
diff --git a/tosca/core/src/main/resources/sparql/suspiciousComment.sparql b/tosca/core/src/main/resources/sparql/suspiciousComment.sparql
@@ -1,5 +1,6 @@
-select distinct ?resource ?comment
+select distinct ?resource ?comment ?classifier
 where {
-   	?resource rdfs:comment ?comment .
+	?resource rdfs:comment|dcterms:description ?comment;
+	DUL:classifies ?classifier
    	FILTER (regex(lcase(str(?comment)), "(bug|hack|later|todo|later2)","i")).
-	}
+}
diff --git a/tosca/core/src/test/resources/hpc-clinical-uc-onto-buggy/clinical_tier1.ttl b/tosca/core/src/test/resources/hpc-clinical-uc-onto-buggy/clinical_tier1.ttl
@@ -72,7 +72,7 @@ clinical1:Property_1
 clinical1:Property_2
     rdf:type         tosca:Property ;
     dcterms:description
-                     "Job script template with j2 extension, such that Ansible can process it with the template module" ;
+                     "later Job script template with j2 extension, such that Ansible can process it with the template module" ;
     DUL:classifies   clinical1:script_template ;
     DUL:hasParameter clinical1:SodaliteParameter_P1_2 ;
 .
@@ -664,7 +664,7 @@ clinical1:my.nodes.hpc.wm.torque
     rdf:type        owl:Class ;
     rdfs:subClassOf tosca:tosca.nodes.Compute ;
     soda:hasContext clinical1:SodaliteDescription_1 ;
-    rdfs:comment    "addresses bug: https://bugs.launchpad.net/keystone/+bug/1472285"^^rdfs:Literal
+    dcterms:description "addresses bug: https://bugs.launchpad.net/keystone/+bug/1472285"^^rdfs:Literal
 .
 
 clinical1:my.nodes.hpc.job.torque
@@ -677,4 +677,4 @@ clinical1:my.relationships.jobHostedOn
     rdf:type        owl:Class ;
     rdfs:subClassOf tosca:tosca.relationships.HostedOn ;
     soda:hasContext clinical1:SodaliteDescription_3 ;
-.
+.
diff --git a/tosca/core/src/test/resources/snow/snow_tier1.ttl b/tosca/core/src/test/resources/snow/snow_tier1.ttl
@@ -105,6 +105,7 @@ snowt1:Property_2
     DUL:classifies      snowt1:imageName ;
     DUL:hasParameter    snowt1:SodaliteParameter_19 ;
     DUL:hasParameter    snowt1:SodaliteParameter_20 ;
+dcterms:description    "addresses bug: https://bugs.launchpad.net/keystone/+bug/1472285"^^rdfs:Literal
 .
 
 snowt1:Property_3
@@ -113,6 +114,7 @@ snowt1:Property_3
     DUL:classifies      snowt1:ports ;
     DUL:hasParameter    snowt1:SodaliteParameter_21 ;
     DUL:hasParameter    snowt1:SodaliteParameter_22 ;
+    dcterms:description    "addresses bug: https://bugs.launchpad.net/keystone/+bug/1472285"^^rdfs:Literal
 .
 
 snowt1:Property_4
@@ -687,7 +689,7 @@ snowt1:SodaliteParameter_PS_1
     rdf:type           soda:SodaliteParameter ;
     DUL:classifies     tosca:default ;
     tosca:hasDataValue "admin" ;
-    rdfs:comment       "TODO: Replace hardcoded password with secure vault"^^rdfs:Literal
+    dcterms:description       "TODO: Replace hardcoded password with secure vault"^^rdfs:Literal
 .
 
 snowt1:SodaliteParameter_PS_4
@@ -834,7 +836,7 @@ snowt1:bind_host
     rdf:type        owl:Class ;
     rdfs:subClassOf <https://www.sodalite.eu/ontologies/tosca/tosca.nodes.Compute> ;
     soda:hasContext snowt1:SodaliteDescription_3 ;
-    rdfs:comment    "addresses bug: https://bugs.launchpad.net/keystone/+bug/1472285"^^rdfs:Literal
+    dcterms:description    "addresses bug: https://bugs.launchpad.net/keystone/+bug/1472285"^^rdfs:Literal
 .
 
 snowt1:vm_name

diff --git a/tosca/core/src/test/resources/snow/snow_tier2.ttl b/tosca/core/src/test/resources/snow/snow_tier2.ttl
@@ -189,7 +189,7 @@ snowt1:User_1
 :skyline-extractor
     rdf:type        <https://www.sodalite.eu/ontologies/snow/tier1/sodalite.nodes.DockerizedComponent> ;
     soda:hasContext :SodaliteDescription_6 ;
-    rdfs:comment    "addresses skyline-extractor bug: https://bugs.launchpad.net/keystone/+bug/323345"^^rdfs:Literal
+    dcterms:description    "addresses skyline-extractor bug: https://bugs.launchpad.net/keystone/+bug/323345"^^rdfs:Literal
 .
 
 :vm