[#5] Refactoring - generalizing for the whole ontology header

psiotwo · Mar 14, 2023 · f5521b6 · f5521b6
1 parent da4d518
commit f5521b6
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Showing 14 changed files with 76 additions and 79 deletions.
diff --git a/src/main/java/cz/sio2/obo/OBOFoundryVersionExtractor.java b/src/main/java/cz/sio2/obo/OBOFoundryVersionExtractor.java
@@ -26,19 +26,19 @@
 @Slf4j
 public class OBOFoundryVersionExtractor {
 
-    private static void writeRDF(final String file, final Map<String, Version> map) throws IOException {
+    private static void writeRDF(final String file, final Map<String, OntologyHeader> map) throws IOException {
         try (final OutputStream os = new FileOutputStream(file)) {
             new TurtleReport().write(map, os);
         }
     }
 
-    private static void writeCSV(final String file, final Map<String, Version> map) throws IOException {
+    private static void writeCSV(final String file, final Map<String, OntologyHeader> map) throws IOException {
         try (final OutputStream os = new FileOutputStream(file)) {
             new CSVReport().write(map, os);
         }
     }
 
-    private static void writeHTML(final String file, final Map<String, Version> map) throws IOException {
+    private static void writeHTML(final String file, final Map<String, OntologyHeader> map) throws IOException {
         try (final OutputStream os = new FileOutputStream(file)) {
             new HTMLReport().writeHTML(map, os);
         }
@@ -58,29 +58,29 @@ private static List<String> getOntologyUrls(final String registry) {
         return list;
     }
 
-    private static Map<String, Version> fetchVersions(final List<String> ontologyUrls, final int headerLength) throws MalformedURLException {
+    private static Map<String, OntologyHeader> fetchVersions(final List<String> ontologyUrls, final int headerLength) throws MalformedURLException {
         final VersionFetcher f = new VersionFetcher();
-        final Map<String, Version> map = new HashMap<>();
+        final Map<String, OntologyHeader> map = new HashMap<>();
         for (final String url : ontologyUrls) {
             log.info(url);
-            final Version v = f.fetch(new URL(url), headerLength);
+            final OntologyHeader v = f.fetch(new URL(url), headerLength);
             map.put(url, v);
         }
         return map;
     }
 
     public void extract(final String registryUrl, final String outputFile, final int headerLength) throws IOException {
         final List<String> ontologyUrls = getOntologyUrls(registryUrl);
-        final Map<String, Version> ontologyVersions = fetchVersions(ontologyUrls, headerLength);
+        final Map<String, OntologyHeader> ontologyVersions = fetchVersions(ontologyUrls, headerLength);
         writeRDF(outputFile, ontologyVersions);
     }
 
-    private Map<String, Version> loadVersions(final String inputFile) {
-        final Map<String, Version> map = new HashMap<>();
+    private Map<String, OntologyHeader> loadVersions(final String inputFile) {
+        final Map<String, OntologyHeader> map = new HashMap<>();
         final Model model = ModelFactory.createDefaultModel();
         model.read(inputFile, Lang.TURTLE.toString());
         model.listSubjectsWithProperty(RDF.type, OWL.Ontology).forEach(ontology -> {
-            final Version version = new Version();
+            final OntologyHeader version = new OntologyHeader();
             version.setOwlOntologyIri(ontology.getURI());
             final Statement versionIri = ontology.getProperty(OWL2.versionIRI);
             if ( versionIri != null ) {

diff --git a/src/main/java/cz/sio2/obo/Version.java → ...main/java/cz/sio2/obo/OntologyHeader.java b/src/main/java/cz/sio2/obo/Version.java → ...main/java/cz/sio2/obo/OntologyHeader.java
@@ -11,12 +11,12 @@
 import static cz.sio2.obo.Constants.*;
 
 /**
- * Object that represents the version extracted from the ontology.
+ * Object that represents the ontology header extracted from the ontology.
  */
 @Getter
 @Setter
 @Slf4j
-public class Version {
+public class OntologyHeader {
 
     /**
      * owl:Ontology IRI.
@@ -109,7 +109,7 @@ String extractVersionFromVersionIri() {
     public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
-        Version version = (Version) o;
+        OntologyHeader version = (OntologyHeader) o;
         return Objects.equals(owlOntologyIri, version.owlOntologyIri) && Objects.equals(owlVersionIri, version.owlVersionIri) && Objects.equals(owlVersionInfo, version.owlVersionInfo);
     }
 

diff --git a/src/main/java/cz/sio2/obo/VersionFetcher.java b/src/main/java/cz/sio2/obo/VersionFetcher.java
@@ -1,9 +1,9 @@
 package cz.sio2.obo;
 
-import cz.sio2.obo.versionextractor.FSVersionExtractor;
-import cz.sio2.obo.versionextractor.RDFXMLVersionExtractor;
-import cz.sio2.obo.versionextractor.VersionExtractor;
-import cz.sio2.obo.versionextractor.XMLVersionExtractor;
+import cz.sio2.obo.extractor.FSExtractor;
+import cz.sio2.obo.extractor.RDFXMLExtractor;
+import cz.sio2.obo.extractor.Extractor;
+import cz.sio2.obo.extractor.XMLExtractor;
 import lombok.extern.slf4j.Slf4j;
 import org.apache.hc.client5.http.classic.HttpClient;
 import org.apache.hc.client5.http.classic.methods.HttpGet;
@@ -28,12 +28,12 @@
 @Slf4j
 public class VersionFetcher {
 
-    final static List<VersionExtractor> extractors = new ArrayList<>();
+    final static List<Extractor> extractors = new ArrayList<>();
 
     static {
-        extractors.add(new RDFXMLVersionExtractor());
-        extractors.add(new FSVersionExtractor());
-        extractors.add(new XMLVersionExtractor());
+        extractors.add(new RDFXMLExtractor());
+        extractors.add(new FSExtractor());
+        extractors.add(new XMLExtractor());
     }
 
     /**
@@ -45,7 +45,7 @@ public class VersionFetcher {
      * @param maxBytes maximal number of bytes to fetch from each side of the document
      * @return Version information from the ontology
      */
-    public Version fetch(final URL url, final int maxBytes) {
+    public OntologyHeader fetch(final URL url, final int maxBytes) {
         final RequestConfig cfg = RequestConfig.custom().setConnectTimeout(Timeout.ofMinutes(1)).build();
         final HttpClientBuilder httpClientBuilder = createBuilder().setDefaultRequestConfig(cfg);
         try (final CloseableHttpClient httpClient = httpClientBuilder.build()) {
@@ -90,9 +90,9 @@ private String extractContentFromResponse(final CloseableHttpResponse response,
         }
     }
 
-    private Version extractVersion(final String content) {
-        final Version version = new Version();
-        for (final VersionExtractor e : extractors) {
+    private OntologyHeader extractVersion(final String content) {
+        final OntologyHeader version = new OntologyHeader();
+        for (final Extractor e : extractors) {
             if (e.extract(content, version)) {
                 return version;
             }

diff --git a/...bo/versionextractor/VersionExtractor.java → ...java/cz/sio2/obo/extractor/Extractor.java b/...bo/versionextractor/VersionExtractor.java → ...java/cz/sio2/obo/extractor/Extractor.java
@@ -1,13 +1,13 @@
-package cz.sio2.obo.versionextractor;
+package cz.sio2.obo.extractor;
 
-import cz.sio2.obo.Version;
+import cz.sio2.obo.OntologyHeader;
 
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import static cz.sio2.obo.Constants.NS_OBO_HTTP;
 
-public abstract class VersionExtractor {
+public abstract class Extractor {
 
     protected abstract Pattern getFormatMatcher();
 
@@ -33,7 +33,7 @@ private String sanitize(final String input) {
         return input.replace("&obo;", NS_OBO_HTTP);
     }
 
-    public boolean extract(final String s, final Version version) {
+    public boolean extract(final String s, final OntologyHeader version) {
         final String singleLine = s.replace('\n', ' ');
         if (!getFormatMatcher().matcher(singleLine).matches()) {
             return false;

diff --git a/.../versionextractor/FSVersionExtractor.java → ...va/cz/sio2/obo/extractor/FSExtractor.java b/.../versionextractor/FSVersionExtractor.java → ...va/cz/sio2/obo/extractor/FSExtractor.java
@@ -1,8 +1,8 @@
-package cz.sio2.obo.versionextractor;
+package cz.sio2.obo.extractor;
 
 import java.util.regex.Pattern;
 
-public class FSVersionExtractor extends VersionExtractor {
+public class FSExtractor extends Extractor {
 
     @Override
     protected Pattern getFormatMatcher() {

diff --git a/...sionextractor/RDFXMLVersionExtractor.java → ...z/sio2/obo/extractor/RDFXMLExtractor.java b/...sionextractor/RDFXMLVersionExtractor.java → ...z/sio2/obo/extractor/RDFXMLExtractor.java
@@ -1,8 +1,8 @@
-package cz.sio2.obo.versionextractor;
+package cz.sio2.obo.extractor;
 
 import java.util.regex.Pattern;
 
-public class RDFXMLVersionExtractor extends VersionExtractor {
+public class RDFXMLExtractor extends Extractor {
 
     @Override
     protected Pattern getFormatMatcher() {

diff --git a/...versionextractor/XMLVersionExtractor.java → ...a/cz/sio2/obo/extractor/XMLExtractor.java b/...versionextractor/XMLVersionExtractor.java → ...a/cz/sio2/obo/extractor/XMLExtractor.java
@@ -1,8 +1,8 @@
-package cz.sio2.obo.versionextractor;
+package cz.sio2.obo.extractor;
 
 import java.util.regex.Pattern;
 
-public class XMLVersionExtractor extends VersionExtractor {
+public class XMLExtractor extends Extractor {
 
     @Override
     protected Pattern getFormatMatcher() {

diff --git a/src/main/java/cz/sio2/obo/report/CSVReport.java b/src/main/java/cz/sio2/obo/report/CSVReport.java
@@ -1,6 +1,6 @@
 package cz.sio2.obo.report;
 
-import cz.sio2.obo.Version;
+import cz.sio2.obo.OntologyHeader;
 import cz.sio2.obo.VersionType;
 
 import java.io.IOException;
@@ -11,10 +11,10 @@
 
 public class CSVReport {
 
-    public void write(Map<String, Version> map, final OutputStream os) throws IOException {
+    public void write(Map<String, OntologyHeader> map, final OutputStream os) throws IOException {
         try (final Writer writer = new OutputStreamWriter(os)) {
-            for (final Map.Entry<String, Version> entry : map.entrySet()) {
-                final Version v = entry.getValue();
+            for (final Map.Entry<String, OntologyHeader> entry : map.entrySet()) {
+                final OntologyHeader v = entry.getValue();
                 writer.append(v != null ? VersionType.get(v.getOwlOntologyIri()
                                 , v.getOwlVersionIri(), v.getOwlVersionInfo()).name() : VersionType.UNKNOWN.name())
                         .append(',')

diff --git a/src/main/java/cz/sio2/obo/report/HTMLReport.java b/src/main/java/cz/sio2/obo/report/HTMLReport.java
@@ -1,7 +1,7 @@
 package cz.sio2.obo.report;
 
 import cz.sio2.obo.OntologyRecord;
-import cz.sio2.obo.Version;
+import cz.sio2.obo.OntologyHeader;
 import cz.sio2.obo.VersionType;
 import freemarker.template.Configuration;
 import freemarker.template.Template;
@@ -31,7 +31,7 @@ public class HTMLReport {
         cfg.setTemplateExceptionHandler(TemplateExceptionHandler.RETHROW_HANDLER);
     }
 
-    public void writeHTML(Map<String, Version> map, final OutputStream os) throws IOException {
+    public void writeHTML(Map<String, OntologyHeader> map, final OutputStream os) throws IOException {
         try {
             final Map<String, Object> dataModel = new HashMap<>();
             final Set<OntologyRecord> records = new HashSet<>();
@@ -41,9 +41,9 @@ public void writeHTML(Map<String, Version> map, final OutputStream os) throws IO
             final String date = simpleDateFormat.format(new Date());
             dataModel.put("date", date);
 
-            final List<Map.Entry<String, Version>> list = new ArrayList<>(map.entrySet());
+            final List<Map.Entry<String, OntologyHeader>> list = new ArrayList<>(map.entrySet());
 
-            for (Map.Entry<String, Version> entry : list) {
+            for (Map.Entry<String, OntologyHeader> entry : list) {
                 boolean failed = entry.getValue() == null;
                 final OntologyRecord record = new OntologyRecord();
                 record

diff --git a/src/main/java/cz/sio2/obo/report/TurtleReport.java b/src/main/java/cz/sio2/obo/report/TurtleReport.java
@@ -1,6 +1,6 @@
 package cz.sio2.obo.report;
 
-import cz.sio2.obo.Version;
+import cz.sio2.obo.OntologyHeader;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Resource;
@@ -16,18 +16,18 @@
 
 public class TurtleReport {
 
-    public void write(Map<String, Version> map, final OutputStream os) {
+    public void write(Map<String, OntologyHeader> map, final OutputStream os) {
         final Model model = createModel(map);
         RDFDataMgr.write(os, model, Lang.TURTLE);
     }
 
-    private Model createModel(Map<String, Version> map) {
+    private Model createModel(Map<String, OntologyHeader> map) {
         final Model model = ModelFactory.createDefaultModel();
-        for (final Map.Entry<String, Version> entry : map.entrySet()) {
+        for (final Map.Entry<String, OntologyHeader> entry : map.entrySet()) {
             final Resource ontology = ResourceFactory.createResource(entry.getKey());
             model.add(ontology, RDF.type, OWL.Ontology);
 
-            final Version version = entry.getValue();
+            final OntologyHeader version = entry.getValue();
             if ( version != null ) {
                 final String versionIriString = version.getOwlVersionIri();
                 if (versionIriString != null && !versionIriString.isEmpty()) {

diff --git a/src/test/java/cz/sio2/obo/TestVersion.java → .../java/cz/sio2/obo/TestOntologyHeader.java b/src/test/java/cz/sio2/obo/TestVersion.java → .../java/cz/sio2/obo/TestOntologyHeader.java
@@ -4,16 +4,16 @@
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.CsvFileSource;
 
-public class TestVersion {
+public class TestOntologyHeader {
 
     @ParameterizedTest
     @CsvFileSource(resources = "/version-testcases.csv", numLinesToSkip = 1, delimiter = ',')
     public void testGetOboVersionReturnsVersionIriIfPresent(String ontologyIri, String versionIri, String versionInfo, String computedVersionIri, String computedVersion) {
-        final Version version = new Version();
-        version.setOwlOntologyIri(ontologyIri);
-        version.setOwlVersionIri(versionIri);
-        version.setOwlVersionInfo(versionInfo);
-        Assertions.assertEquals(computedVersion, version.getVersion());
-        Assertions.assertEquals(computedVersionIri, version.getOboVersionIri());
+        final OntologyHeader header = new OntologyHeader();
+        header.setOwlOntologyIri(ontologyIri);
+        header.setOwlVersionIri(versionIri);
+        header.setOwlVersionInfo(versionInfo);
+        Assertions.assertEquals(computedVersion, header.getVersion());
+        Assertions.assertEquals(computedVersionIri, header.getOboVersionIri());
     }
 }
diff --git a/...ionextractor/TestOWLVersionExtractor.java → .../sio2/obo/extractor/TestOWLExtractor.java b/...ionextractor/TestOWLVersionExtractor.java → .../sio2/obo/extractor/TestOWLExtractor.java
@@ -1,7 +1,6 @@
-package cz.sio2.obo.versionextractor;
+package cz.sio2.obo.extractor;
 
-import cz.sio2.obo.Version;
-import cz.sio2.obo.versionextractor.FSVersionExtractor;
+import cz.sio2.obo.OntologyHeader;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.CsvFileSource;
@@ -12,7 +11,7 @@
 import java.nio.file.Paths;
 import java.util.Objects;
 
-public class TestOWLVersionExtractor {
+public class TestOWLExtractor {
 
     @ParameterizedTest
     @CsvFileSource(resources = "/owl-testcases.csv", numLinesToSkip = 1, delimiter = ',')
@@ -22,8 +21,8 @@ public void testExtractVersionIriFromXMLExtractsVersionInfoCorrectlyIfPresent(
             String versionIri,
             String versionInfo) throws URISyntaxException, IOException {
         final String s = Files.readString(Paths.get(Objects.requireNonNull(getClass().getResource("/owl-testcases/" + file)).toURI()));
-        final Version version = new Version();
-        new FSVersionExtractor().extract(s, version);
+        final OntologyHeader version = new OntologyHeader();
+        new FSExtractor().extract(s, version);
         Assertions.assertEquals(ontologyIri, version.getOwlOntologyIri());
         Assertions.assertEquals(versionIri, version.getOwlVersionIri());
         Assertions.assertEquals(versionInfo, version.getOwlVersionInfo());

diff --git a/...extractor/TestRDFXMLVersionExtractor.java → ...o2/obo/extractor/TestRDFXMLExtractor.java b/...extractor/TestRDFXMLVersionExtractor.java → ...o2/obo/extractor/TestRDFXMLExtractor.java
@@ -1,7 +1,6 @@
-package cz.sio2.obo.versionextractor;
+package cz.sio2.obo.extractor;
 
-import cz.sio2.obo.Version;
-import cz.sio2.obo.versionextractor.RDFXMLVersionExtractor;
+import cz.sio2.obo.OntologyHeader;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.CsvFileSource;
@@ -12,7 +11,7 @@
 import java.nio.file.Paths;
 import java.util.Objects;
 
-public class TestRDFXMLVersionExtractor {
+public class TestRDFXMLExtractor {
 
     @ParameterizedTest
     @CsvFileSource(resources = "/rdf-testcases.csv", numLinesToSkip = 1, delimiter = ',')
@@ -21,10 +20,10 @@ public void testExtractVersionFromVersionIriFromRDFXMLWorksCorrectly(String file
                                                                          String versionIri,
                                                                          String versionInfo) throws URISyntaxException, IOException {
         final String s = Files.readString(Paths.get(Objects.requireNonNull(getClass().getResource("/rdf-testcases/" + file)).toURI()));
-        final Version version = new Version();
-        new RDFXMLVersionExtractor().extract(s, version);
-        Assertions.assertEquals(ontologyIri, version.getOwlOntologyIri());
-        Assertions.assertEquals(versionIri, version.getOwlVersionIri());
-        Assertions.assertEquals(versionInfo, version.getOwlVersionInfo());
+        final OntologyHeader header = new OntologyHeader();
+        new RDFXMLExtractor().extract(s, header);
+        Assertions.assertEquals(ontologyIri, header.getOwlOntologyIri());
+        Assertions.assertEquals(versionIri, header.getOwlVersionIri());
+        Assertions.assertEquals(versionInfo, header.getOwlVersionInfo());
     }
 }