diff --git a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
index c5562b249b74ece02c3f1c4d858b1c5fa1a64a1a..a80ab4bd6ae5aa9100ba60750e0b30950965ad2a 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
@@ -26,168 +26,177 @@ import lcsb.mapviewer.model.map.MiriamType;
*/
public class XmlAnnotationParser extends XmlParser {
- /**
- * Deafult logger.
- */
- private static Logger logger = Logger.getLogger(XmlAnnotationParser.class.getName());
-
- /**
- * Default constructor.
- */
- public XmlAnnotationParser() {
- }
-
- /**
- * This method parse the xml string passed as an argument. All information
- * obtained by the method are stored in local variables: miriamDataSet,
- * speciesId and can be accessed later on.
- *
- * @param data
- * - xml string to be parsed
- *
- * @return collection of miriam objects that were obtained from the xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parse(String data) throws InvalidXmlSchemaException {
- // start from creating a DOM parser and parse the whole document
- Document doc = getXmlDocumentFromString(data);
-
- NodeList root = doc.getChildNodes();
-
- // process the whole schema
- return parseRdfNode(root);
- }
-
- /**
- * Retrieves set of Miriam annotation from xml rdf node.
- *
- * @param root
- * xml node list
- * @return set of miriam annotations.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
- Node rdf = getNode("rdf:RDF", root);
- return parseRdfNode(rdf);
- }
-
- /**
- * Retrieves set of Miriam annotation from xml rdf node.
- *
- * @param rdf
- * xml node
- * @return set of miriam annotations.
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parseRdfNode(Node rdf) throws InvalidXmlSchemaException {
- Set<MiriamData> miriamDataSet = new HashSet<MiriamData>();
- if (rdf != null) {
- Node description = getNode("rdf:Description", rdf.getChildNodes());
- if (description != null) {
- NodeList list = description.getChildNodes();
- for (int i = 0; i < list.getLength(); i++) {
- Node node = list.item(i);
- if (node.getNodeType() == Node.ELEMENT_NODE) {
- miriamDataSet.addAll(parseMiriamNode(node));
- }
- }
- } else {
- throw new InvalidXmlSchemaException("rdf:Description node not found");
- }
- } else {
- throw new InvalidXmlSchemaException("rdf:Rdf node not found");
- }
- return miriamDataSet;
- }
-
- /**
- * This method converts a xml node into MiriamData object (annotation of a
- * species).
- *
- * @param node
- * - xml node that contains representation of a single annotation of
- * a species
- * @return MiriamData object that represents annotation of a species
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
- */
- public Set<MiriamData> parseMiriamNode(Node node) throws InvalidXmlSchemaException {
- Set<MiriamData> result = new HashSet<MiriamData>();
- NodeList list = node.getChildNodes();
- String relationTypeString = node.getNodeName();
- MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
- Node bag = getNode("rdf:Bag", list);
- if (bag == null) {
- throw new InvalidXmlSchemaException("No rdf:Bag node found");
- }
- list = bag.getChildNodes();
- List<Node> nodes = getNodes("rdf:li", list);
- for (Node li : nodes) {
- String dataTypeUri = getNodeAttr("rdf:resource", li);
- if (dataTypeUri == null || dataTypeUri.isEmpty()) {
- throw new InvalidXmlSchemaException("rdf:li does not have a rdf:resource attribute");
- }
-
- try {
- MiriamData md = MiriamType.getMiriamByUri(dataTypeUri);
- if (relationType == null) {
- logger.warn("Unknown relation type: " + relationTypeString + ". For miriam uri: " + dataTypeUri + ".");
- } else {
- if (!MiriamType.PUBMED.equals(md.getDataType())) {
- md.setRelationType(relationType);
- }
- result.add(md);
- }
- } catch (InvalidArgumentException e) {
- logger.warn(e.getMessage());
- }
- }
- return result;
- }
-
- /**
- * This method converts a set of MiriamData into xml string that can be put to
- * CellDesigner schema.
- *
- * @param data
- * - a set of MiriamData to be converted.
- * @return xml string representation of the input data
- */
- public String dataSetToXmlString(Collection<MiriamData> data) {
- StringBuilder result = new StringBuilder("");
- result.append(
- "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" " + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\" "
- + "xmlns:dcterms=\"http://purl.org/dc/terms/\" " + "xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" "
- + "xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" " + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n");
- result.append("<rdf:Description rdf:about=\"#\">\n");
- for (MiriamData miriamData : data) {
- result.append(miriamDataToXmlString(miriamData));
- }
- result.append("</rdf:Description>\n");
- result.append("</rdf:RDF>\n");
- return result.toString();
- }
-
- /**
- * This method converts a single MiriamData into xml string that can be put to
- * CellDesigner schema.
- *
- * @param data
- * - a MiriamData to be converted.
- * @return xml string representation of the input data
- */
- public String miriamDataToXmlString(MiriamData data) {
- StringBuilder result = new StringBuilder("");
- result.append("<" + data.getRelationType().getStringRepresentation() + ">\n");
- result.append("<rdf:Bag>\n");
- result.append("<rdf:li rdf:resource=\"" + data.getDataType().getUris().get(0) + ":" + data.getResource().replaceAll(":", "%3A") + "\"/>\n");
- result.append("</rdf:Bag>\n");
- result.append("</" + data.getRelationType().getStringRepresentation() + ">\n");
-
- return result.toString();
- }
+ /**
+ * Deafult logger.
+ */
+ private static Logger logger = Logger.getLogger(XmlAnnotationParser.class.getName());
+
+ /**
+ * Default constructor.
+ */
+ public XmlAnnotationParser() {
+ }
+
+ /**
+ * This method parse the xml string passed as an argument. All information
+ * obtained by the method are stored in local variables: miriamDataSet,
+ * speciesId and can be accessed later on.
+ *
+ * @param data
+ * - xml string to be parsed
+ *
+ * @return collection of miriam objects that were obtained from the xml node
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parse(String data) throws InvalidXmlSchemaException {
+ // start from creating a DOM parser and parse the whole document
+ Document doc = getXmlDocumentFromString(data);
+
+ NodeList root = doc.getChildNodes();
+
+ // process the whole schema
+ return parseRdfNode(root);
+ }
+
+ /**
+ * Retrieves set of Miriam annotation from xml rdf node.
+ *
+ * @param root
+ * xml node list
+ * @return set of miriam annotations.
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parseRdfNode(NodeList root) throws InvalidXmlSchemaException {
+ Node rdf = getNode("rdf:RDF", root);
+ return parseRdfNode(rdf);
+ }
+
+ /**
+ * Retrieves set of Miriam annotation from xml rdf node.
+ *
+ * @param rdf
+ * xml node
+ * @return set of miriam annotations.
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parseRdfNode(Node rdf) throws InvalidXmlSchemaException {
+ Set<MiriamData> miriamDataSet = new HashSet<>();
+ if (rdf != null) {
+ Node description = getNode("rdf:Description", rdf.getChildNodes());
+ if (description != null) {
+ NodeList list = description.getChildNodes();
+ for (int i = 0; i < list.getLength(); i++) {
+ Node node = list.item(i);
+ if (node.getNodeType() == Node.ELEMENT_NODE) {
+ String relationTypeString = node.getNodeName();
+ MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
+ if (relationType != null) {
+ miriamDataSet.addAll(parseMiriamNode(node));
+ } else {
+ logger.warn("RDF relation type is not supported: " + relationTypeString);
+ }
+ }
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Description node not found");
+ }
+ } else {
+ throw new InvalidXmlSchemaException("rdf:Rdf node not found");
+ }
+ return miriamDataSet;
+ }
+
+ /**
+ * This method converts a xml node into MiriamData object (annotation of a
+ * species).
+ *
+ * @param node
+ * - xml node that contains representation of a single annotation of a
+ * species
+ * @return MiriamData object that represents annotation of a species
+ * @throws InvalidXmlSchemaException
+ * thrown when there is a problem with xml
+ */
+ public Set<MiriamData> parseMiriamNode(Node node) throws InvalidXmlSchemaException {
+ Set<MiriamData> result = new HashSet<>();
+ NodeList list = node.getChildNodes();
+ String relationTypeString = node.getNodeName();
+ MiriamRelationType relationType = MiriamRelationType.getTypeByStringRepresentation(relationTypeString);
+ Node bag = getNode("rdf:Bag", list);
+ if (bag == null) {
+ throw new InvalidXmlSchemaException("No rdf:Bag node found");
+ }
+ list = bag.getChildNodes();
+ List<Node> nodes = getNodes("rdf:li", list);
+ for (Node li : nodes) {
+ String dataTypeUri = getNodeAttr("rdf:resource", li);
+ if (dataTypeUri == null || dataTypeUri.isEmpty()) {
+ throw new InvalidXmlSchemaException("rdf:li does not have a rdf:resource attribute");
+ }
+
+ try {
+ MiriamData md = MiriamType.getMiriamByUri(dataTypeUri);
+ if (relationType == null) {
+ logger.warn("Unknown relation type: " + relationTypeString + ". For miriam uri: " + dataTypeUri + ".");
+ } else {
+ if (!MiriamType.PUBMED.equals(md.getDataType())) {
+ md.setRelationType(relationType);
+ }
+ result.add(md);
+ }
+ } catch (InvalidArgumentException e) {
+ logger.warn(e.getMessage());
+ }
+ }
+ return result;
+ }
+
+ /**
+ * This method converts a set of MiriamData into xml string that can be put to
+ * CellDesigner schema.
+ *
+ * @param data
+ * - a set of MiriamData to be converted.
+ * @return xml string representation of the input data
+ */
+ public String dataSetToXmlString(Collection<MiriamData> data) {
+ StringBuilder result = new StringBuilder("");
+ result.append(
+ "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" "
+ + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\" "
+ + "xmlns:dcterms=\"http://purl.org/dc/terms/\" " + "xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" "
+ + "xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" "
+ + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n");
+ result.append("<rdf:Description rdf:about=\"#\">\n");
+ for (MiriamData miriamData : data) {
+ result.append(miriamDataToXmlString(miriamData));
+ }
+ result.append("</rdf:Description>\n");
+ result.append("</rdf:RDF>\n");
+ return result.toString();
+ }
+
+ /**
+ * This method converts a single MiriamData into xml string that can be put to
+ * CellDesigner schema.
+ *
+ * @param data
+ * - a MiriamData to be converted.
+ * @return xml string representation of the input data
+ */
+ public String miriamDataToXmlString(MiriamData data) {
+ StringBuilder result = new StringBuilder("");
+ result.append("<" + data.getRelationType().getStringRepresentation() + ">\n");
+ result.append("<rdf:Bag>\n");
+ result.append("<rdf:li rdf:resource=\"" + data.getDataType().getUris().get(0) + ":"
+ + data.getResource().replaceAll(":", "%3A") + "\"/>\n");
+ result.append("</rdf:Bag>\n");
+ result.append("</" + data.getRelationType().getStringRepresentation() + ">\n");
+
+ return result.toString();
+ }
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java
index 68b70d80c391bc064dba2fefeca97284f69671b0..748d392229730dc572aa6a3d0ea978f1ce00f445 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java
@@ -83,6 +83,20 @@ public class XmlAnnotationParserTest extends ConverterTestFunctions {
}
}
+ @Test
+ public void testParseRdfWithCreatorTag() throws Exception {
+ try {
+ XmlAnnotationParser xap = new XmlAnnotationParser();
+ String xml = readFile("testFiles/annotation/rdf_with_creator_tag.xml");
+
+ Set<MiriamData> set = xap.parse(xml);
+ assertTrue(set.size() > 0);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
@Test
public void testParseInvalidRdf2() throws Exception {
try {
diff --git a/converter/testFiles/annotation/rdf_with_creator_tag.xml b/converter/testFiles/annotation/rdf_with_creator_tag.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fc1d44356eaa607d7bfd5000710b639cbb24edb7
--- /dev/null
+++ b/converter/testFiles/annotation/rdf_with_creator_tag.xml
@@ -0,0 +1,74 @@
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:dcterms="http://purl.org/dc/terms/"
+ xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"
+ xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
+ xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+ <rdf:Description rdf:about="#metaid_0000002">
+ <dc:creator>
+ <rdf:Bag>
+ <rdf:li rdf:parseType="Resource">
+ <vCard:N rdf:parseType="Resource">
+ <vCard:Family>Roberts</vCard:Family>
+ <vCard:Given>Matthew Grant</vCard:Given>
+ </vCard:N>
+ <vCard:EMAIL>mroberts@embl.ac.uk</vCard:EMAIL>
+ <vCard:ORG rdf:parseType="Resource">
+ <vCard:Orgname>EMBL-EBI</vCard:Orgname>
+ </vCard:ORG>
+ </rdf:li>
+ <rdf:li rdf:parseType="Resource">
+ <vCard:N rdf:parseType="Resource">
+ <vCard:Family>Lloyd</vCard:Family>
+ <vCard:Given>Catherine</vCard:Given>
+ </vCard:N>
+ <vCard:EMAIL>c.lloyd@auckland.ac.nz</vCard:EMAIL>
+ <vCard:ORG rdf:parseType="Resource">
+ <vCard:Orgname>University of Auckland</vCard:Orgname>
+ </vCard:ORG>
+ </rdf:li>
+ </rdf:Bag>
+ </dc:creator>
+ <dcterms:created rdf:parseType="Resource">
+ <dcterms:W3CDTF>2010-06-25T13:23:00Z</dcterms:W3CDTF>
+ </dcterms:created>
+ <dcterms:modified rdf:parseType="Resource">
+ <dcterms:W3CDTF>2018-03-08T16:30:35Z</dcterms:W3CDTF>
+ </dcterms:modified>
+ <dcterms:modified rdf:parseType="Resource">
+ <dcterms:W3CDTF>2018-03-08T16:30:35Z</dcterms:W3CDTF>
+ </dcterms:modified>
+ <bqmodel:is>
+ <rdf:Bag>
+ <rdf:li
+ rdf:resource="http://identifiers.org/biomodels.db/MODEL1006230061" />
+ </rdf:Bag>
+ </bqmodel:is>
+ <bqmodel:isDescribedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/pubmed/13678598" />
+ </rdf:Bag>
+ </bqmodel:isDescribedBy>
+ <bqbiol:isVersionOf>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/go/GO:0002250" />
+ </rdf:Bag>
+ </bqbiol:isVersionOf>
+ <bqbiol:hasTaxon>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/taxonomy/9606" />
+ </rdf:Bag>
+ </bqbiol:hasTaxon>
+ <bqbiol:isDescribedBy>
+ <rdf:Bag>
+ <rdf:li rdf:resource="http://identifiers.org/pubmed/13678598" />
+ </rdf:Bag>
+ </bqbiol:isDescribedBy>
+ <bqmodel:is>
+ <rdf:Bag>
+ <rdf:li
+ rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000684" />
+ </rdf:Bag>
+ </bqmodel:is>
+ </rdf:Description>
+</rdf:RDF>
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index 16be247cdd9510a05f251e136da04c44ceea924c..94384aa60ebe99127629b5ccba12b0bc4b5fc3ef 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -108,7 +108,7 @@ public enum MiriamType {
CLINICAL_TRIALS_GOV("ClinicalTrials.gov",
"https://clinicaltrials.gov/",
new String[] { "urn:miriam:clinicaltrials" },
- new Class<?>[] { }, "MIR:00000137"),
+ new Class<?>[] {}, "MIR:00000137"),
/**
* Clusters of Orthologous Groups: https://www.ncbi.nlm.nih.gov/COG/.
@@ -178,7 +178,7 @@ public enum MiriamType {
*/
GO("Gene Ontology",
"http://amigo.geneontology.org/amigo",
- new String[] { "urn:miriam:obo.go", "urn:miriam:go" },
+ new String[] { "urn:miriam:obo.go", "urn:miriam:go", "http://identifiers.org/go/" },
new Class<?>[] { Phenotype.class, Compartment.class, Complex.class }, "MIR:00000022"),
/**
@@ -358,7 +358,7 @@ public enum MiriamType {
*/
PUBMED("PubMed",
"http://www.ncbi.nlm.nih.gov/PubMed/",
- new String[] { "urn:miriam:pubmed" },
+ new String[] { "urn:miriam:pubmed", "http://identifiers.org/pubmed/" },
new Class<?>[] { BioEntity.class }, "MIR:00000015",
new Class<?>[] { Reaction.class }),