diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java index 4335f7160cfb8f884cfced584239e99ad97f5a29..10e11f24de3fb581c5c486fea946a696de59aff1 100644 --- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java +++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java @@ -98,7 +98,7 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade * </ul> * The first parenthesis group is */ - public static final String defaultAnnotationPattern = "http://identifiers.org/([^/]+)/(.*)"; + public static final String defaultAnnotationPattern = "https?://identifiers.org/([^/]+)/(.*)"; /** * Constructor diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriter.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriter.java index b24b425da5c4a80042f8dfb00ccff0d81ac065f8..1e971c1c1e04461ca3c24f3ad2fa1b49960f79b5 100644 --- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriter.java +++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriter.java @@ -81,7 +81,7 @@ public class AnnotationWriter implements PackageWriter, AdditionalDataTag { /** * The default URL pattern for the annotations */ - public static final String DEFAULT_URL_BASE = "http://identifiers.org/"; + public static final String DEFAULT_URL_BASE = "https://identifiers.org/"; /** * The user defined URL pattern for the annotations diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriterTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriterTest.java index 1aca694fe5e2371062753cdf5d9ab717f0205748..0c8acfbb151d49a4bda57ad8374dfffbfc619c0d 100644 --- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriterTest.java +++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/writer/plugin/AnnotationWriterTest.java @@ -189,7 +189,7 @@ public class AnnotationWriterTest { assertNotNull(s1); - assertTrue(s1.getAnnotationString().contains("http://identifiers.org/kegg.reaction/id2")); + assertTrue(s1.getAnnotationString().contains("https://identifiers.org/kegg.reaction/id2")); } @@ -213,7 +213,7 @@ public class AnnotationWriterTest { assertNotNull(s1); assertTrue(s1.getAnnotationString() - .contains("<rdf:li rdf:resource=\"http://identifiers.org/pubchem.compound/puchem123\"/>")); + .contains("<rdf:li rdf:resource=\"https://identifiers.org/pubchem.compound/puchem123\"/>")); } @@ -225,10 +225,10 @@ public class AnnotationWriterTest { assertNotNull(s1); assertTrue(s1.getAnnotationString() - .contains("<rdf:li rdf:resource=\"http://identifiers.org/pubmed/23456\"/>")); + .contains("<rdf:li rdf:resource=\"https://identifiers.org/pubmed/23456\"/>")); assertTrue(s1.getAnnotationString() - .contains("<rdf:li rdf:resource=\"http://identifiers.org/pubmed/12345\"/>")); + .contains("<rdf:li rdf:resource=\"https://identifiers.org/pubmed/12345\"/>")); } @@ -239,7 +239,7 @@ public class AnnotationWriterTest { assertNotNull(r1); - assertTrue(r1.getAnnotationString().contains("http://identifiers.org/kegg.reaction/id1")); + assertTrue(r1.getAnnotationString().contains("https://identifiers.org/kegg.reaction/id1")); } @@ -250,7 +250,7 @@ public class AnnotationWriterTest { assertNotNull(r1); - assertTrue(r1.getAnnotationString().contains("http://identifiers.org/ec-code/1.2.3.4")); + assertTrue(r1.getAnnotationString().contains("https://identifiers.org/ec-code/1.2.3.4")); } @@ -262,10 +262,10 @@ public class AnnotationWriterTest { assertNotNull(r1); assertTrue(r1.getAnnotationString() - .contains("<rdf:li rdf:resource=\"http://identifiers.org/pubmed/23456\"/>")); + .contains("<rdf:li rdf:resource=\"https://identifiers.org/pubmed/23456\"/>")); assertTrue(r1.getAnnotationString() - .contains("<rdf:li rdf:resource=\"http://identifiers.org/pubmed/12345\"/>")); + .contains("<rdf:li rdf:resource=\"https://identifiers.org/pubmed/12345\"/>")); }