shacl + ui v0.1

reqtool/ReqmanAngular11/src/app/components/boilerplate-list/boilerplate-list.component.html

@@ -25,6 +25,7 @@
         <ul  *ngFor="let inf of infer;" fxLayout fxLayoutGap="15px" class="navigation-items">
             <div>
           <input class="btn btn-info" 
+                [disabled] = "exporting"
                 type="button" 
                 value="Inferencing"
                 (click)="updateInfer(inf.id)"/>
@@ -34,6 +35,9 @@
       
     </div>
 </div>
+<div [hidden] = "!showSpinner">
+<mat-progress-bar mode="indeterminate"></mat-progress-bar>  
+</div>
 <div class="mat-elevation-z8">
 <table mat-table [dataSource]="newdataSource" class="mat-elevation-z8">
   <!-- Position Column -->
@@ -45,12 +49,13 @@
   <!-- Name Column -->
   <ng-container matColumnDef="prefix_data">
     <th mat-header-cell *matHeaderCellDef> Prefix </th>
-    <td mat-cell *matCellDef="let element"> {{element.prefix_data}} </td>
+    <td mat-cell *matCellDef="let element">{{element.prefix_data}} </td>
   </ng-container>
   <!-- Name Column -->
   <ng-container matColumnDef="title_data">
     <th mat-header-cell *matHeaderCellDef> Title </th>
-    <td mat-cell *matCellDef="let element"> {{element.title_data}} </td>
+    <td mat-cell *matCellDef="let element"  matTooltip={{get_metrics(element.title_data)}}>{{element.title_data}} <span *ngIf="get_metrics(element.title_data).length > 0" matBadge={{get_metrics(element.title_data).length}}  matBadgeColor="warn" matBadgeSize="small" position="above">&nbsp;&nbsp; </span>
+    </td>
   </ng-container>
 
   <ng-container matColumnDef="main_data">

reqtool/ReqmanAngular11/src/app/components/boilerplate-list/boilerplate-list.component.ts

@@ -35,7 +35,12 @@ export class BoilerplateListComponent implements OnInit {
   thenewdataSource:BoilerplateData[] = [{}];
   newdataSource = new MatTableDataSource(this.thenewdataSource);
   infer:InferenceResults[] = [{}];
+  //when inference button is pressed
+  showSpinner = false;
+  exporting = false;
 
+  num = 1
+  
   @ViewChild(MatPaginator) paginator= this.newdataSource.paginator;
 
 
@@ -50,7 +55,7 @@ export class BoilerplateListComponent implements OnInit {
   ngOnInit(): void {
     this.retrieveBoilerplates();
     this.retrieve();
-    this.getInfer()
+    this.getInfer();
   }
 
   retrieveBoilerplates(): void {
@@ -135,13 +140,21 @@ export class BoilerplateListComponent implements OnInit {
   }
 
   updateInfer(id: any): void {
+    this.showSpinner = !this.showSpinner;
+    this.exporting = !this.exporting
     this.boilerplateService.inferUpdate(this.route.snapshot.params.gb, id, this.currentInfer)
     .subscribe(
       data => {
-        console.log(data);
+        this.currentInfer = data[0];
+        //this.infer = data;
+        this.showSpinner = !this.showSpinner;
+        this.exporting = !this.exporting;
+        location.reload();
       },
       error => {
         console.log(error);
+        this.showSpinner = !this.showSpinner;
+        this.exporting = !this.exporting
       });
   }
 
@@ -150,4 +163,14 @@ export class BoilerplateListComponent implements OnInit {
     this.newdataSource.filter = filterValue.trim().toLowerCase();
   }
 
+  get_metrics(i:any): any {
+    if (this.currentInfer?.inference_data){
+      const obj = JSON.parse(this.currentInfer['inference_data'].replace(/'/g,"\""))
+      if (obj[i]){
+        return obj[i]
+      }
+    }
+  return 0
+  }
+
 }

reqtool/ReqmanAngular11/src/app/models/boilerplate.model.ts

@@ -25,7 +25,7 @@ export class GroupBoilerplate {
 export class InferenceResults {
     id?:any;
     infer_group_of_boilerplate?: any;
-    inference_data?: string;
+    inference_data?: any;
 }
 
 export class Sections {

reqtool/reqman/api/reqman/apps/reqtool/rest_api/services/inference.py

+import os, subprocess, shutil
 from rdflib import Graph, BNode
 from rdflib.namespace import RDFS
 from rdflib import ConjunctiveGraph, URIRef, RDFS, RDF, Namespace
@@ -15,12 +16,15 @@ def getclassofmain(main):
 
 
 def inferencing(project, boilerlate, prefix, main, suffix):
+    metrics = {}
     listofboil = []
     listofprefix = []
     listofmain = []
     listofsuffix = []
     for i in boilerlate:
             listofboil.append(list(i.values()))
+            #print(list(i.values('title'))[0]['title'])
+            metrics[list(i.values('title'))[0]['title']] = []
     for i in prefix:
             listofprefix.append(list(i.values()))
     for i in main:
@@ -28,14 +32,26 @@ def inferencing(project, boilerlate, prefix, main, suffix):
     for i in suffix:
             listofsuffix.append(list(i.values()))
     #findclassofmain(listofmain)
-    exportboiltottl(project, listofprefix, listofboil, listofmain, listofsuffix)
-    #print(project)
-    #print(listofboil[0][0]['id'])
-    #print(listofprefix[0][0]['id'])
+    ontology_with_new_req = exportboiltottl(project, listofprefix, listofboil, listofmain, listofsuffix)
+    infer_result = shacl(ontology_with_new_req)
+    #find in which metrics the requirements belongs e.g. title:REQ-1 is only an Incomplete req (and Ambiguous req), 
+    # so -> 'REQ-1' : [Incomplete] ('REQ-1' : [Incomplete, Ambiguous])
+    for met in infer_result:
+        for title in metrics:
+            if title in infer_result[met]:
+                metrics[title].append(met)
+    metrics.update(infer_result)
+    return metrics
 
 
 def exportboiltottl(project, prefix, boilerplate, main, suffix):
+    ''' Export boilerplate to ttl file and return the file path'''
     #print(out_list) #A list with the values and the file that is the instance
+    file_name = project.replace('/', '')
+    if (os.path.exists("../../Ontologies/"+file_name+"/") == False):
+        os.mkdir("../../Ontologies/"+file_name)
+    save_path = "../../Ontologies/"+file_name+"/"
+    completeName = os.path.join(save_path, file_name)
     per_instances = URIRef("http://delab.csd.auth.gr/ontologies/2018/RDO-instances#")
     rdo = URIRef("http://delab.csd.auth.gr/ontologies/2018/RDO#")
     rbo = URIRef("http://delab.csd.auth.gr/ontologies/2018/RBO#")
@@ -61,7 +77,8 @@ def exportboiltottl(project, prefix, boilerplate, main, suffix):
                         break
                 g.add((per_instances+(title+"_"+ main[i][0]['main_choices']), rbo+"isRelatedToSubject", URIRef(str(instance_file))+"#"+ str(spliter_1[len(spliter_1) -1])))
             if main[i][0]['verb'] != "":
-                g.add((per_instances+(title+"_"+ main[i][0]['main_choices']), rbo+"isRelatedToAction", lo + main[i][0]['verb']))
+                mainverb = main[i][0]['verb'].split(':')
+                g.add((per_instances+(title+"_"+ main[i][0]['main_choices']), rbo+"isRelatedToAction", lo + mainverb[1].strip()))
             if main[i][0]['flow_function_interface_item_system_state_stateset'] != "":
                 for j in range(0,(len(out_list)-1),2):
                     if out_list[j]==main[i][0]['flow_function_interface_item_system_state_stateset']:
@@ -76,10 +93,40 @@ def exportboiltottl(project, prefix, boilerplate, main, suffix):
         
         #if (boilerplate[i][0]['has_prefix'] == True):
          #   g.add((per_instances+(title+"_"+ main[i][0]['main_choices']), RDF.type, rbo + main[i][0]['main_choices']))
-    g.serialize(destination='../../Ontologies/'+project+'.ttl', format='turtle')
-
+    g.serialize(destination=save_path+file_name+'.ttl', format='turtle')
+    return (save_path+file_name)
     #print(g.serialize(format="turtle").decode("utf-8"))
 
+def shacl(ontotlogy_file):
+    metrics_dict = {}
+    metrics_dict["IncompleteRequirement"] = []
+    metrics_dict["AmbiguousRequirement"] = []
+    file1 = ontotlogy_file + ".ttl"
+    target = ontotlogy_file+"infer.ttl"
+    open(target, 'w').close()
+    shutil.copyfile(file1, target)
+    for i in range(3):
+            print(i+1, 'Cycle of inferencing')
+            result = subprocess.check_output(["./reqman/apps/reqtool/rest_api/services/shacl-1.3.2/bin/shaclinfer.sh", "-datafile", target])
+            file_object = open(target, 'a')
+            res = str(result,'utf-8')
+            file_object.write(res.strip())
+            file_object.close()
+    
+    #need to fiil with all the metrics
+    g = Graph()
+    g.load(target, format="turtle")
+    p = URIRef("http://delab.csd.auth.gr/ontologies/2018/RDO#IncompleteRequirement")
+    for s, p, o in g.triples((None, RDF.type, p)):
+        #metrics_dict["IncompleteRequirement"] = [s]
+        get_title = str(s).split("#")
+        metrics_dict["IncompleteRequirement"].append(get_title[1])
+    p = URIRef("http://delab.csd.auth.gr/ontologies/2018/RDO#AmbiguousRequirement")
+    for s, p, o in g.triples((None, RDF.type, p)):
+        #metrics_dict["IncompleteRequirement"] = [s]
+        get_title = str(s).split("#")
+        metrics_dict["AmbiguousRequirement"].append(get_title[1])
+    return(metrics_dict)
 
 def findclassofmain(listofmain):
     classlist = []

reqtool/reqman/api/reqman/apps/reqtool/rest_api/services/shacl-1.3.2/README.md

+# TopBraid SHACL API
+
+**An open source implementation of the W3C Shapes Constraint Language (SHACL) based on Apache Jena.**
+
+Contact: Holger Knublauch (holger@topquadrant.com)
+
+Can be used to perform SHACL constraint checking and rule inferencing in any Jena-based Java application.
+This API also serves as a reference implementation of the SHACL spec.
+
+Coverage:
+* [SHACL Core and SHACL-SPARQL validation](https://www.w3.org/TR/shacl/)
+* [SHACL Advanced Features (Rules etc)](https://www.w3.org/TR/shacl-af/)
+* [SHACL JavaScript Extensions](https://www.w3.org/TR/shacl-js/)
+* [SHACL Compact Syntax](https://w3c.github.io/shacl/shacl-compact-syntax/)
+
+See [SHACL-JS](https://github.com/TopQuadrant/shacl-js) for a pure JavaScript implementation.
+
+The same code is used in the TopBraid products (currently aligned with the TopBraid 6.3 release).
+
+Feedback and questions should become GitHub issues or sent to TopBraid Users mailing list:
+https://groups.google.com/forum/#!forum/topbraid-users
+Please prefix your messages with [SHACL API]
+
+To get started, look at the class ValidationUtil in
+the package org.topbraid.shacl.validation.
+There is also an [Example Test Case](../master/src/test/java/org/topbraid/shacl/ValidationExample.java)
+
+## Application dependency
+
+Releases are available in the central maven repository:
+
+```
+<dependency>
+  <groupId>org.topbraid</groupId>
+  <artifactId>shacl</artifactId>
+  <version>*VER*</version>
+</dependency>
+```
+## Command Line Usage
+
+Download the latest release from:
+
+`https://repo1.maven.org/maven2/org/topbraid/shacl/`
+
+The binary distribution is:
+
+`https://repo1.maven.org/maven2/org/topbraid/shacl/*VER*/shacl-*VER*-bin.zip`.
+
+Two command line utilities are included: validate (performs constraint validation) and infer (performs SHACL rule inferencing).
+
+To use them, set up your environment similar to https://jena.apache.org/documentation/tools/ (note that the SHACL download includes Jena).
+
+For example, on Windows:
+
+```
+SET SHACLROOT=C:\Users\Holger\Desktop\shacl-1.0.0-bin
+SET PATH=%PATH%;%SHACLROOT%\bin
+```
+
+As another example, for Linux, add to .bashrc these lines:
+
+```
+# for shacl
+export SHACLROOT=/home/holger/shacl/shacl-1.0.0-bin/shacl-1.0.0/bin
+export PATH=$SHACLROOT:$PATH 
+```
+
+Both tools take the following parameters, for example:
+
+`shaclvalidate.bat -datafile myfile.ttl -shapesfile myshapes.ttl`
+
+where `-shapesfile` is optional and falls back to using the data graph as shapes graph.
+
+Currently only Turtle (.ttl) files and SHACL Compact Syntax (.shaclc) files are supported.
+
+The tools print the validation report or the inferences graph to the output screen.

reqtool/reqman/api/reqman/apps/reqtool/rest_api/services/shacl-1.3.2/log4j.properties

+log4j.rootLogger=INFO, stdlog
+
+log4j.appender.stdlog=org.apache.log4j.ConsoleAppender
+log4j.appender.stdlog.target=System.err
+log4j.appender.stdlog.layout=org.apache.log4j.PatternLayout
+log4j.appender.stdlog.layout.ConversionPattern=%d{HH:mm:ss} %-5p %-20c{1} :: %m%n
+
+## Everything else in Jena
+log4j.logger.org.apache.jena=INFO
+
+## Execution logging
+log4j.logger.org.apache.jena.arq.info=INFO
+log4j.logger.org.apache.jena.arq.exec=INFO

reqtool/reqman/api/reqman/apps/reqtool/rest_api/views/requirements_views.py

@@ -255,10 +255,10 @@ class InferDetailsAPIView(RetrieveUpdateDestroyAPIView):
             prefixdata.append(self.getprefixdata(id.boilerplate_data_id.id))
             maindata.append(self.getmaindata(id.boilerplate_data_id.id))
             suffixdata.append(self.getsuffixdata(id.boilerplate_data_id.id))
-        inference.inferencing(project_title, boildata, prefixdata, maindata, suffixdata)
+        metrics = inference.inferencing(project_title, boildata, prefixdata, maindata, suffixdata)
         #print(prefix[0].boilerplate_data_id.id)
         #inference.inferencing(prefix)
-        instance.update(inference_data = "aaaoooaaa" )
+        instance.update(inference_data = metrics)
         #sprefix = self.simple_prefix(instance["prefix"])
         serializer.save()