pstlab /
KOaLaR
| Total Complexity | 49 |
| Total Lines | 484 |
| Duplicated Lines | 17.56 % |
| Changes | 2 | ||
| Bugs | 0 | Features | 0 |
Duplicate code is one of the most pungent code smells. A rule that is often used is to re-structure code once it is duplicated in three or more places.
Common duplication problems, and corresponding solutions are:
Complex classes like it.cnr.istc.pst.cognition.semantic.owl.jena.OWLModel often do a lot of different things. To break such a class down, we need to identify a cohesive component within that class. A common approach to find such a component is to look for fields/methods that share the same prefixes, or suffixes.
Once you have determined the fields that belong together, you can apply the Extract Class refactoring. If the component makes sense as a sub-class, Extract Subclass is also a candidate, and is often faster.
| 1 | package it.cnr.istc.pst.cognition.semantic.owl.jena; |
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| 28 | public abstract class OWLModel |
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| 29 | { |
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| 30 | protected final AtomicLong idCounter; |
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| 31 | protected String ontologyFile; |
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| 32 | protected String inferenceRuleFile; |
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| 33 | protected OntModel model; |
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| 34 | protected InfModel infModel; |
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| 35 | |||
| 36 | /** |
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| 37 | * |
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| 38 | * @param ontologyFile |
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| 39 | * @param domainNameSpace |
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| 40 | */ |
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| 41 | protected OWLModel(String ontologyFile, String domainNameSpace) |
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| 42 | { |
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| 43 | // set ID counter |
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| 44 | this.idCounter = new AtomicLong(0); |
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| 45 | // set onto file |
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| 46 | this.ontologyFile = ontologyFile; |
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| 47 | // create the model schema from the onto |
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| 48 | this.model = ModelFactory.createOntologyModel( |
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| 49 | OntModelSpec.RDFS_MEM_TRANS_INF); // create in-memory onto model with RDFS language and transitive rule-based reasoner with RDFS rules |
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| 50 | // use DocumentManager API to specify that onto is replicated locally on disk |
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| 51 | this.model.getDocumentManager().addAltEntry(domainNameSpace, "file:" + this.ontologyFile); |
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| 52 | // read onto file |
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| 53 | this.model.read(domainNameSpace); |
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| 54 | } |
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| 55 | |||
| 56 | /** |
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| 57 | * |
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| 58 | * @param ontologyFile |
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| 59 | * @param inferenceRuleFile |
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| 60 | * @param domainNameSpace |
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| 61 | */ |
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| 62 | protected OWLModel(String ontologyFile, String inferenceRuleFile, String domainNameSpace) |
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| 63 | { |
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| 64 | this(ontologyFile, domainNameSpace); |
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| 65 | // set inference rule file |
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| 66 | this.inferenceRuleFile = inferenceRuleFile; |
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| 67 | // parse the list of inference rules for feature extraction |
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| 68 | List<Rule> rules = Rule.rulesFromURL("file:" + inferenceRuleFile); |
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| 69 | // create a generic rule-based reasoner |
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| 70 | GenericRuleReasoner reasoner = new GenericRuleReasoner(rules); |
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| 71 | // configure reasoner - user forward chaining RETE rule engine |
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| 72 | reasoner.setParameter(ReasonerVocabulary.PROPruleMode, "forwardRETE"); |
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| 73 | // create an inference model on the raw data model |
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| 74 | this.infModel = ModelFactory.createInfModel(reasoner, this.model); |
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| 75 | } |
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| 76 | |||
| 77 | /** |
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| 78 | * |
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| 79 | * @return |
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| 80 | */ |
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| 81 | public String getOntologyFile() { |
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| 82 | return ontologyFile; |
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| 83 | } |
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| 84 | |||
| 85 | /** |
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| 86 | * |
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| 87 | * @return |
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| 88 | */ |
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| 89 | public String getInferenceRuleFile() { |
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| 90 | return inferenceRuleFile; |
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| 91 | } |
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| 92 | |||
| 93 | /** |
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| 94 | * |
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| 95 | * @param model |
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| 96 | * @param domainNameSpace |
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| 97 | */ |
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| 98 | protected void setup(Model model, String domainNameSpace) |
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| 99 | { |
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| 100 | // setup a new model |
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| 101 | this.model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RDFS_INF, model); |
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| 102 | // use DocumentManager API to specify that ontology is replicated locally on disk |
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| 103 | this.model.getDocumentManager().addAltEntry(domainNameSpace, "file:" + this.ontologyFile); |
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| 104 | // read ontology file |
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| 105 | this.model.read(domainNameSpace); |
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| 106 | |||
| 107 | // parse the list of inference rules for feature extraction |
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| 108 | List<Rule> rules = Rule.rulesFromURL("file:" + inferenceRuleFile); |
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| 109 | // create a generic rule-based reasoner |
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| 110 | GenericRuleReasoner reasoner = new GenericRuleReasoner(rules); |
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| 111 | // configure reasoner - user forward chaining RETE rule engine |
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| 112 | reasoner.setParameter(ReasonerVocabulary.PROPruleMode, "forwardRETE"); |
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| 113 | // create an inference model on the raw data model |
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| 114 | this.infModel = ModelFactory.createInfModel(reasoner, this.model); |
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| 115 | } |
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| 116 | |||
| 117 | |||
| 118 | /** |
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| 119 | * |
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| 120 | * @param classURI |
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| 121 | * @return |
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| 122 | */ |
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| 123 | public List<Resource> getIndividuals(String classURI) |
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| 124 | { |
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| 125 | // list of found individuals |
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| 126 | List<Resource> list = new ArrayList<Resource>(); |
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| 127 | // get resource class |
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| 128 | Resource c = this.getResource(classURI); |
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| 129 | if (c != null) { |
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| 130 | // iterate over individuals |
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| 131 | Iterator<Individual> it = this.model.listIndividuals(c); |
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| 132 | while (it.hasNext()) { |
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| 133 | list.add(it.next()); |
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| 134 | } |
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| 135 | } |
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| 136 | |||
| 137 | // get the list |
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| 138 | return list; |
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| 139 | } |
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| 140 | |||
| 141 | |||
| 142 | /** |
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| 143 | * |
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| 144 | * @return |
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| 145 | */ |
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| 146 | public void rebind() { |
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| 147 | // re-bind the inference model to the underlying data model |
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| 148 | this.infModel.rebind(); |
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| 149 | } |
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| 150 | |||
| 151 | /** |
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| 152 | * |
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| 153 | * @return |
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| 154 | */ |
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| 155 | public boolean validate() { |
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| 156 | // re-bind the inference model to the underlying dat model |
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| 157 | this.infModel.rebind(); |
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| 158 | // validate the inference model of the knowledge base |
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| 159 | ValidityReport report = this.infModel.validate(); |
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| 160 | // check if the model is valid |
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| 161 | return report.isValid(); |
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| 162 | } |
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| 163 | |||
| 164 | /** |
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| 165 | * |
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| 166 | * @return |
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| 167 | */ |
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| 168 | public Iterator<Statement> iterator() { |
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| 169 | // get an iterator over the statements of the model |
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| 170 | return this.infModel.listStatements(); |
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| 171 | } |
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| 172 | |||
| 173 | /** |
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| 174 | * |
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| 175 | * @return |
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| 176 | */ |
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| 177 | protected Model getModel(String domainNameSpace) |
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| 178 | { |
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| 179 | // create a new model |
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| 180 | OntModel model = ModelFactory.createOntologyModel(OntModelSpec.OWL_DL_MEM_RDFS_INF, this.model); |
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|
Comprehensibility
introduced
by
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| 181 | // use DocumentManager API to specify that ontology is replicated locally on disk |
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| 182 | model.getDocumentManager().addAltEntry(domainNameSpace, "file:" + this.ontologyFile); |
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| 183 | // read ontology file |
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| 184 | model.read(domainNameSpace); |
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| 185 | |||
| 186 | // add inferred statements |
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| 187 | Iterator<Statement> it = this.infModel.getDeductionsModel().listStatements(); |
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| 188 | while (it.hasNext()) { |
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| 189 | // add inferred statement |
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| 190 | model.add(it.next()); |
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| 191 | } |
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| 192 | |||
| 193 | // get model |
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| 194 | return model; |
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| 195 | } |
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| 196 | |||
| 197 | /** |
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| 198 | * |
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| 199 | * @param classURI |
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| 200 | * @return |
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| 201 | * @throws Exception |
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| 202 | */ |
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| 203 | public Resource createIndividual(String classURI) |
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| 204 | throws Exception |
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| 205 | { |
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| 206 | // check whether a resource with "classURI" actually exists |
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| 207 | Resource res = this.infModel.getResource(classURI); |
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| 208 | if (res == null) { |
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| 209 | throw new Exception("No resource found with URI= \"" + classURI + "\" in the knowledge-base"); |
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| 210 | } |
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| 211 | |||
| 212 | // create an individual of the class |
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| 213 | Resource resource = this.infModel.createResource(res.getLocalName().toLowerCase() + "_" + this.idCounter.getAndIncrement(), res); |
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| 214 | // get created individual |
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| 215 | return resource; |
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| 216 | } |
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| 217 | |||
| 218 | /** |
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| 219 | * |
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| 220 | * @param referenceURI |
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| 221 | * @param propertyURI |
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| 222 | * @param targetURI |
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| 223 | * @throws Exception |
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| 224 | */ |
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| 225 | public void assertProperty(String referenceURI, String propertyURI, String targetURI) |
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| 226 | throws Exception |
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| 227 | { |
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| 228 | // check whether a resource with "referenceURI" actually exists |
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| 229 | Resource reference = this.infModel.getResource(referenceURI); |
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| 230 | if (reference == null) { |
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| 231 | throw new Exception("Resource with URI=\"" + referenceURI + "\" not found in the knowledge-base"); |
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| 232 | } |
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| 233 | |||
| 234 | // get target |
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| 235 | Resource target = this.infModel.getResource(targetURI); |
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| 236 | if (target == null) { |
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| 237 | throw new Exception("Resource with URI=\"" + targetURI + "\" not found in the knowledge-base"); |
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| 238 | } |
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| 239 | |||
| 240 | // check whether a resource with "propertyURI" actually exists |
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| 241 | Property property = this.infModel.getProperty(propertyURI); |
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| 242 | if (property == null) { |
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| 243 | throw new Exception("Property with URI=\"" + propertyURI + "\" not found in the knowledge-base"); |
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| 244 | } |
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| 245 | |||
| 246 | // add statement to the knowledge base |
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| 247 | this.infModel.add(reference, property, target); |
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| 248 | } |
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| 249 | |||
| 250 | /** |
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| 251 | * |
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| 252 | * @param referenceURI |
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| 253 | * @param propertyURI |
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| 254 | * @param value |
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| 255 | * @throws Exception |
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| 256 | */ |
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| 257 | View Code Duplication | public void assertDataProperty(String referenceURI, String propertyURI, long value) |
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| 258 | throws Exception |
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| 259 | { |
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| 260 | // check whether a resource with "referenceURI" actually exists |
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| 261 | Resource reference = this.infModel.getResource(referenceURI); |
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| 262 | if (reference == null) { |
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| 263 | throw new Exception("Resource with URI=\"" + referenceURI + "\" not found in the knowledge-base"); |
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| 264 | } |
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| 265 | |||
| 266 | // check whether a resource with "propertyURI" actually exists |
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| 267 | Property property = this.infModel.getProperty(propertyURI); |
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| 268 | if (property == null) { |
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| 269 | throw new Exception("Property with URI=\"" + propertyURI + "\" not found in the knowledge-base"); |
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| 270 | } |
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| 271 | |||
| 272 | // add literal and related property |
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| 273 | this.infModel.addLiteral(reference, property, value); |
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| 274 | } |
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| 275 | |||
| 276 | /** |
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| 277 | * |
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| 278 | * @param referenceURI |
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| 279 | * @param propertyURI |
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| 280 | * @param value |
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| 281 | * @throws Exception |
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| 282 | */ |
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| 283 | View Code Duplication | public void assertDataProperty(String referenceURI, String propertyURI, String value) |
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| 284 | throws Exception |
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| 285 | { |
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| 286 | // check whether a resource with "referenceURI" actually exists |
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| 287 | Resource reference = this.infModel.getResource(referenceURI); |
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| 288 | if (reference == null) { |
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| 289 | throw new Exception("Resource with URI=\"" + referenceURI + "\" not found in the knowledge-base"); |
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| 290 | } |
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| 291 | |||
| 292 | // check whether a resource with "propertyURI" actually exists |
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| 293 | Property property = this.infModel.getProperty(propertyURI); |
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| 294 | if (property == null) { |
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| 295 | throw new Exception("Property with URI=\"" + propertyURI + "\" not found in the knowledge-base"); |
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| 296 | } |
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| 297 | |||
| 298 | // add literal and related property |
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| 299 | this.infModel.add(reference, property, value); |
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| 300 | } |
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| 301 | |||
| 302 | /** |
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| 303 | * |
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| 304 | * @param referenceURI |
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| 305 | * @param propertyURI |
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| 306 | * @param value |
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| 307 | * @throws Exception |
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| 308 | */ |
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| 309 | View Code Duplication | public void assertDataProperty(String referenceURI, String propertyURI, double value) |
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| 310 | throws Exception |
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| 311 | { |
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| 312 | // check whether a resource with "referenceURI" actually exists |
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| 313 | Resource reference = this.infModel.getResource(referenceURI); |
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| 314 | if (reference == null) { |
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| 315 | throw new Exception("Resource with URI=\"" + referenceURI + "\" not found in the knowledge-base"); |
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| 316 | } |
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| 317 | |||
| 318 | // check whether a resource with "propertyURI" actually exists |
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| 319 | Property property = this.infModel.getProperty(propertyURI); |
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| 320 | if (property == null) { |
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| 321 | throw new Exception("Property with URI=\"" + propertyURI + "\" not found in the knowledge-base"); |
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| 322 | } |
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| 323 | |||
| 324 | // add literal and related property |
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| 325 | this.infModel.addLiteral(reference, property, value); |
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| 326 | } |
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| 327 | |||
| 328 | /** |
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| 329 | * |
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| 330 | * @param referenceURI |
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| 331 | * @param propertyURI |
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| 332 | * @param value |
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| 333 | * @throws Exception |
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| 334 | */ |
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| 335 | View Code Duplication | public void assertDataProperty(String referenceURI, String propertyURI, boolean value) |
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| 336 | throws Exception |
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| 337 | { |
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| 338 | // check whether a resource with "referenceURI" actually exists |
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| 339 | Resource reference = this.infModel.getResource(referenceURI); |
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| 340 | if (reference == null) { |
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| 341 | throw new Exception("Resource with URI=\"" + referenceURI + "\" not found in the knowledge-base"); |
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| 342 | } |
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| 343 | |||
| 344 | // check whether a resource with "propertyURI" actually exists |
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| 345 | Property property = this.infModel.getProperty(propertyURI); |
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| 346 | if (property == null) { |
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| 347 | throw new Exception("Property with URI=\"" + propertyURI + "\" not found in the knowledge-base"); |
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| 348 | } |
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| 349 | |||
| 350 | // add literal and related property |
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| 351 | this.infModel.addLiteral(reference, property, value); |
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| 352 | } |
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| 353 | |||
| 354 | /** |
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| 355 | * |
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| 356 | * @param referenceURI |
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| 357 | * @param propertyURI |
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| 358 | * @param value |
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| 359 | * @throws Exception |
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| 360 | */ |
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| 361 | View Code Duplication | public void assertDataProperty(String referenceURI, String propertyURI, int value) |
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| 362 | throws Exception |
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| 363 | { |
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| 364 | // check whether a resource with "referenceURI" actually exists |
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| 365 | Resource reference = this.infModel.getResource(referenceURI); |
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| 366 | if (reference == null) { |
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| 367 | throw new Exception("Resource with URI=\"" + referenceURI + "\" not found in the knowledge-base"); |
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| 368 | } |
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| 369 | |||
| 370 | // check whether a resource with "propertyURI" actually exists |
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| 371 | Property property = this.infModel.getProperty(propertyURI); |
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| 372 | if (property == null) { |
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| 373 | throw new Exception("Property with URI=\"" + propertyURI + "\" not found in the knowledge-base"); |
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| 374 | } |
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| 375 | |||
| 376 | // add literal and related property |
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| 377 | this.infModel.addLiteral(reference, property, value); |
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| 378 | } |
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| 379 | |||
| 380 | /** |
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| 381 | * |
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| 382 | * @param id |
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| 383 | * @param domainNameSpace |
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| 384 | * @return |
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| 385 | * @throws Exception |
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| 386 | */ |
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| 387 | protected Resource getResourceById(Long id, String domainNameSpace) |
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| 388 | throws Exception |
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| 389 | { |
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| 390 | // get property |
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| 391 | Property property = this.infModel.getProperty(domainNameSpace + "hasId"); |
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| 392 | // check statements |
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| 393 | Iterator<Statement> it = this.infModel.listLiteralStatements(null, property, id); |
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| 394 | if (!it.hasNext()) { |
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| 395 | throw new Exception("Resource with ID " + id + " not found into the knowledge base"); |
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| 396 | } |
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| 397 | |||
| 398 | // get statement |
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| 399 | Statement s = it.next(); |
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| 400 | // get resource |
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| 401 | return s.getSubject(); |
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| 402 | } |
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| 403 | |||
| 404 | /** |
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| 405 | * |
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| 406 | * @param resURI |
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| 407 | * @return |
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| 408 | */ |
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| 409 | public Resource getResource(String resURI) { |
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| 410 | return this.infModel.getResource(resURI); |
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| 411 | } |
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| 412 | |||
| 413 | /** |
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| 414 | * |
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| 415 | * @param propertyId |
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| 416 | * @return |
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| 417 | * @throws Exception |
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| 418 | */ |
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| 419 | public List<Statement> getStatements(String propertyId) |
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| 420 | throws Exception { |
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| 421 | // list of statements |
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| 422 | return this.getStatements(null, propertyId, null); |
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| 423 | } |
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| 424 | |||
| 425 | /** |
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| 426 | * |
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| 427 | * @param propertyId |
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| 428 | * @param targetId |
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| 429 | * @return |
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| 430 | * @throws Exception |
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| 431 | */ |
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| 432 | public List<Statement> getStatements(String propertyId, String targetId) |
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| 433 | throws Exception { |
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| 434 | // get statements |
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| 435 | return this.getStatements(null, propertyId, targetId); |
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| 436 | } |
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| 437 | |||
| 438 | /** |
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| 439 | * |
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| 440 | * @param subjectId |
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| 441 | * @param propertyId |
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| 442 | * @param targetId |
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| 443 | * @return |
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| 444 | * @throws Exception |
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| 445 | */ |
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| 446 | public List<Statement> getStatements(String subjectId, String propertyId, String targetId) |
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| 447 | throws Exception |
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| 448 | { |
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| 449 | // list of statements |
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| 450 | List<Statement> list = new ArrayList<Statement>(); |
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| 451 | |||
| 452 | // check resource parameter |
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| 453 | Resource subject = null; |
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| 454 | if (subjectId != null) { |
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| 455 | // get resource |
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| 456 | subject = this.infModel.getResource(subjectId); |
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| 457 | if (subject == null) { |
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| 458 | throw new Exception("Resource with URI=\"" + subjectId + "\" not found in the knowledge-base"); |
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| 459 | } |
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| 460 | } |
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| 461 | |||
| 462 | // check property parameter |
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| 463 | Property prop = null; |
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| 464 | if (propertyId != null) { |
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| 465 | // get property |
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| 466 | prop = this.infModel.getProperty(propertyId); |
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| 467 | if (prop == null) { |
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| 468 | throw new Exception("Property with URI=\"" + propertyId + "\" not found in the knowledge-base"); |
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| 469 | } |
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| 470 | } |
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| 471 | |||
| 472 | // check target parameter |
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| 473 | RDFNode target = null; |
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| 474 | if (targetId != null) { |
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| 475 | // get target |
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| 476 | target = (RDFNode) this.infModel.getResource(targetId); |
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| 477 | if (target == null) { |
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| 478 | throw new Exception("Target with URI=\"" + targetId + "\" not found in the knowledge-base"); |
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| 479 | } |
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| 480 | } |
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| 481 | |||
| 482 | |||
| 483 | // iterate over statements |
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| 484 | Iterator<Statement> it = this.infModel.listStatements(subject, prop, target); |
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| 485 | while (it.hasNext()) { |
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| 486 | // add statement to list |
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| 487 | list.add(it.next()); |
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| 488 | } |
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| 489 | |||
| 490 | |||
| 491 | // get list |
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| 492 | return list; |
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| 493 | } |
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| 494 | |||
| 495 | /** |
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| 496 | * |
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| 497 | * @param propertyId |
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| 498 | * @return |
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| 499 | * @throws Exception |
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| 500 | */ |
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| 501 | public Property getProperty(String propertyId) |
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| 502 | throws Exception |
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| 503 | { |
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| 504 | // get property |
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| 505 | Property prop = this.infModel.getProperty(propertyId); |
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| 506 | if (prop == null) { |
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| 507 | throw new Exception("Property with URI=\"" + propertyId + "\" not found in the knowledge-base"); |
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| 508 | } |
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| 509 | |||
| 510 | // get property |
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| 511 | return prop; |
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| 512 | } |
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| 514 |
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