@@ -50,6 +50,15 @@ public RDFService(@Value("${sparql.endpoint}") String rdfService) {
5050 this .rdfService = rdfService ;
5151 }
5252
53+ /**
54+ * Add to ontologies in the triple store
55+ * @param model The model to be stored
56+ */
57+ public void addToOntologies (Model model ) {
58+ DatasetAccessor accessor = DatasetAccessorFactory .createHTTP (rdfService );
59+ accessor .putModel ("ontologies" , model );
60+ }
61+
5362 /**
5463 * Store a model with triples in the triple store
5564 * @param graphName The name of the graph to store the model in
@@ -75,39 +84,77 @@ public boolean graphExists(String graphName) {
7584 }
7685 }
7786
87+ /**
88+ * Check if a property of the ontology exists within the triple store
89+ * @param ontUri The URI of the property
90+ * @return Whether the graph exists
91+ */
92+ public boolean ontPropertyExists (String ontUri ) {
93+ ParameterizedSparqlString graphQuery = new ParameterizedSparqlString ();
94+ graphQuery .setCommandText ("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>" +
95+ "ASK WHERE { GRAPH ?graphName { ?ont rdfs:label ?label } }" );
96+ graphQuery .setIri ("ont" , ontUri );
97+ graphQuery .setIri ("graphName" , rdfService + "ontologies" );
98+ Query query = QueryFactory .create (graphQuery .toString ());
99+ try (QueryExecution qexec = QueryExecutionFactory .createServiceRequest (rdfService , query )) {
100+ return qexec .execAsk ();
101+ }
102+ }
103+
78104 /**
79105 * Get the label and doc strings for a workflow resource
80- * @param graphName The graph containing the model
81106 * @param workflowURI The URI of the workflow
82107 * @return Result set with label and doc strings
83108 */
84- public ResultSet getLabelAndDoc (String graphName , String workflowURI ) {
109+ public ResultSet getLabelAndDoc (String workflowURI ) {
85110 ParameterizedSparqlString labelQuery = new ParameterizedSparqlString ();
86111 labelQuery .setCommandText (queryCtx +
87112 "SELECT ?label ?doc\n " +
88113 "WHERE {\n " +
89- " GRAPH ?graphName {" +
114+ " GRAPH ?wf {" +
90115 " OPTIONAL { ?wf sld:label|rdfs:label ?label }\n " +
91116 " OPTIONAL { ?wf sld:doc|rdfs:comment ?doc }\n " +
92117 " }" +
93118 "}" );
94119 labelQuery .setIri ("wf" , workflowURI );
95- labelQuery .setIri ("graphName" , rdfService + graphName );
96120 return runQuery (labelQuery );
97121 }
98122
123+ /**
124+ * Get the label for an ontology URL
125+ * TODO: can be merged with getLabelAndDoc when cwltool namespace bug is resolved
126+ * @param ontologyURI The format URI for the ontology
127+ * @return Result set with label and doc strings
128+ */
129+ public String getOntLabel (String ontologyURI ) {
130+ ParameterizedSparqlString labelQuery = new ParameterizedSparqlString ();
131+ labelQuery .setCommandText ("PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>" +
132+ "SELECT ?label\n " +
133+ "WHERE {\n " +
134+ " GRAPH ?graphName {\n " +
135+ " ?ont rdfs:label ?label\n " +
136+ " }\n " +
137+ "}\n " );
138+ labelQuery .setIri ("ont" , ontologyURI );
139+ labelQuery .setIri ("graphName" , rdfService + "ontologies" );
140+ ResultSet result = runQuery (labelQuery );
141+ if (result .hasNext ()) {
142+ return result .next ().get ("label" ).toString ();
143+ }
144+ return null ;
145+ }
146+
99147 /**
100148 * Get the inputs for the workflow in the model
101- * @param graphName The graph containing the model
102149 * @param workflowURI URI of the workflow
103150 * @return The result set of inputs
104151 */
105- public ResultSet getInputs (String graphName , String workflowURI ) {
152+ public ResultSet getInputs (String workflowURI ) {
106153 ParameterizedSparqlString inputsQuery = new ParameterizedSparqlString ();
107154 inputsQuery .setCommandText (queryCtx +
108155 "SELECT ?name ?type ?format ?label ?doc\n " +
109156 "WHERE {\n " +
110- " GRAPH ?graphName {" +
157+ " GRAPH ?wf {" +
111158 " ?wf rdf:type cwl:Workflow .\n " +
112159 " ?wf cwl:inputs ?name .\n " +
113160 " OPTIONAL { ?name sld:type ?type }\n " +
@@ -117,22 +164,20 @@ public ResultSet getInputs(String graphName, String workflowURI) {
117164 " }" +
118165 "}" );
119166 inputsQuery .setIri ("wf" , workflowURI );
120- inputsQuery .setIri ("graphName" , rdfService + graphName );
121167 return runQuery (inputsQuery );
122168 }
123169
124170 /**
125171 * Get the outputs for the workflow in the model
126- * @param graphName The graph containing the model
127172 * @param workflowURI URI of the workflow
128173 * @return The result set of outputs
129174 */
130- public ResultSet getOutputs (String graphName , String workflowURI ) {
175+ public ResultSet getOutputs (String workflowURI ) {
131176 ParameterizedSparqlString outputsQuery = new ParameterizedSparqlString ();
132177 outputsQuery .setCommandText (queryCtx +
133178 "SELECT ?name ?type ?format ?label ?doc\n " +
134179 "WHERE {\n " +
135- " GRAPH ?graphName {" +
180+ " GRAPH ?wf {" +
136181 " ?wf rdf:type cwl:Workflow .\n " +
137182 " ?wf cwl:outputs ?name .\n " +
138183 " OPTIONAL { ?name sld:type ?type }\n " +
@@ -142,17 +187,15 @@ public ResultSet getOutputs(String graphName, String workflowURI) {
142187 " }" +
143188 "}" );
144189 outputsQuery .setIri ("wf" , workflowURI );
145- outputsQuery .setIri ("graphName" , rdfService + graphName );
146190 return runQuery (outputsQuery );
147191 }
148192
149193 /**
150194 * Get the steps for the workflow in the model
151- * @param graphName The graph containing the model
152195 * @param workflowURI URI of the workflow
153196 * @return The result set of steps
154197 */
155- public ResultSet getSteps (String graphName , String workflowURI ) {
198+ public ResultSet getSteps (String workflowURI ) {
156199 ParameterizedSparqlString stepQuery = new ParameterizedSparqlString ();
157200 stepQuery .setCommandText (queryCtx +
158201 "SELECT ?step ?run ?runtype ?label ?doc ?stepinput ?default ?src\n " +
@@ -170,74 +213,67 @@ public ResultSet getSteps(String graphName, String workflowURI) {
170213 " }" +
171214 "}" );
172215 stepQuery .setIri ("wf" , workflowURI );
173- stepQuery .setIri ("graphName" , rdfService + graphName );
174216 return runQuery (stepQuery );
175217 }
176218
177219 /**
178220 * Get links between steps for the workflow in the model
179- * @param graphName The graph containing the model
180221 * @param workflowURI URI of the workflow
181222 * @return The result set of step links
182223 */
183- public ResultSet getStepLinks (String graphName , String workflowURI ) {
224+ public ResultSet getStepLinks (String workflowURI ) {
184225 ParameterizedSparqlString linkQuery = new ParameterizedSparqlString ();
185226 linkQuery .setCommandText (queryCtx +
186227 "SELECT ?src ?dest ?default\n " +
187228 "WHERE {\n " +
188- " GRAPH ?graphName {" +
229+ " GRAPH ?wf {" +
189230 " ?wf Workflow:steps ?step .\n " +
190231 " ?step cwl:in ?dest .\n " +
191232 " { ?dest cwl:source ?src } UNION { ?dest cwl:default ?default }\n " +
192233 " }" +
193234 "}" );
194235 linkQuery .setIri ("wf" , workflowURI );
195- linkQuery .setIri ("graphName" , rdfService + graphName );
196236 return runQuery (linkQuery );
197237 }
198238
199239 /**
200240 * Get links between steps and outputs for the workflow in the model
201- * @param graphName The graph containing the model
202241 * @param workflowURI URI of the workflow
203242 * @return The result set of steps
204243 */
205- public ResultSet getOutputLinks (String graphName , String workflowURI ) {
244+ public ResultSet getOutputLinks (String workflowURI ) {
206245 ParameterizedSparqlString linkQuery = new ParameterizedSparqlString ();
207246 linkQuery .setCommandText (queryCtx +
208247 "SELECT ?src ?dest\n " +
209248 "WHERE {\n " +
210- " GRAPH ?graphName {" +
249+ " GRAPH ?wf {" +
211250 " ?wf rdf:type cwl:Workflow .\n " +
212251 " ?wf cwl:outputs ?dest .\n " +
213252 " ?dest cwl:outputSource ?src\n " +
214253 " }" +
215254 "}" );
216255 linkQuery .setIri ("wf" , workflowURI );
217- linkQuery .setIri ("graphName" , rdfService + graphName );
218256 return runQuery (linkQuery );
219257 }
220258
221259 /**
222260 * Gets the docker requirement and pull link for a workflow
223- * @param graphName The graph containing the model
224261 * @param workflowURI URI of the workflow
225262 * @return Result set of docker hint and pull link
226263 */
227- public ResultSet getDockerLink (String graphName , String workflowURI ) {
264+ public ResultSet getDockerLink (String workflowURI ) {
228265 ParameterizedSparqlString dockerQuery = new ParameterizedSparqlString ();
229266 dockerQuery .setCommandText (queryCtx +
230267 "SELECT ?docker ?pull\n " +
231268 "WHERE {\n " +
232- " GRAPH ?graphName {" +
269+ " GRAPH ?wf {" +
233270 " ?wf rdf:type cwl:Workflow .\n " +
234271 " { ?wf cwl:requirements ?docker } UNION { ?wf cwl:hints ?docker} .\n " +
235272 " ?docker rdf:type cwl:DockerRequirement\n " +
236273 " OPTIONAL { ?docker DockerRequirement:dockerPull ?pull }\n " +
237274 " }" +
238275 "}" );
239276 dockerQuery .setIri ("wf" , workflowURI );
240- dockerQuery .setIri ("graphName" , rdfService + graphName );
241277 return runQuery (dockerQuery );
242278 }
243279
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