diff --git a/.aspell-api-exceptions.pws b/.aspell-api-exceptions.pws index 8589d9cecd52eebe140cd1b92130ef8ba2669f65..022b7732bd0090ad4e733c057c9923b522b25ddd 100644 --- a/.aspell-api-exceptions.pws +++ b/.aspell-api-exceptions.pws @@ -305,6 +305,7 @@ ird irefweb isbn isDefault +isDescribedBy isfinder isoform Isoform diff --git a/CHANGELOG b/CHANGELOG index 79d73f90e0344e733c768f90c51436b7f21d1ca0..86075ff0b11c99328777e0e21a9c9bf591aef9f4 100644 --- a/CHANGELOG +++ b/CHANGELOG @@ -1,8 +1,9 @@ minerva (18.1.1) stable; urgency=medium * Bug fix: SBGN-ML import/export should not use compartmentOrder for non-compartment entities (#2193) - * Bug fix: invalir relation type has been used as default + * Bug fix: invalid relation type has been used as default (bqbiol:isDescribedBy), the default is changed to: bqbiol:is (#2206) + * Bug fix: export of default compartment provide compartment name (#2208) -- Piotr Gawron <piotr.gawron@uni.lu> Wed, 05 Feb 2025 12:00:00 +0200 diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java index 1cfef66dd442c02195415b77de6c857b3250d926..228410c4d32f4fe48fd1c0d6ec683fdb7ba89774 100644 --- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java +++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentCollectionXmlParser.java @@ -1,16 +1,5 @@ package lcsb.mapviewer.converter.model.celldesigner.compartment; -import java.util.ArrayList; -import java.util.Collection; -import java.util.HashSet; -import java.util.List; -import java.util.Set; - -import org.apache.logging.log4j.LogManager; -import org.apache.logging.log4j.Logger; -import org.w3c.dom.Node; -import org.w3c.dom.NodeList; - import lcsb.mapviewer.common.Pair; import lcsb.mapviewer.common.exception.InvalidXmlSchemaException; import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection; @@ -18,12 +7,21 @@ import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompart import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement; import lcsb.mapviewer.model.map.compartment.Compartment; import lcsb.mapviewer.model.map.compartment.PathwayCompartment; +import org.apache.logging.log4j.LogManager; +import org.apache.logging.log4j.Logger; +import org.w3c.dom.Node; +import org.w3c.dom.NodeList; + +import java.util.ArrayList; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; +import java.util.Set; /** * CellDEsigner xml parser for collection of compartments. - * + * * @author Piotr Gawron - * */ public class CompartmentCollectionXmlParser { @@ -31,25 +29,24 @@ public class CompartmentCollectionXmlParser { * Default class logger. */ @SuppressWarnings("unused") - private Logger logger = LogManager.getLogger(); + private final Logger logger = LogManager.getLogger(); /** * CellDesigner xml parser for single compartment. */ - private CompartmentXmlParser compartmentParser; + private final CompartmentXmlParser compartmentParser; /** * Collection of {@link CellDesignerElement cell designer elements} parsed from * xml. */ - private CellDesignerElementCollection elements; + private final CellDesignerElementCollection elements; /** * Default constructor. - * - * @param elements - * collection of {@link CellDesignerElement cell designer elements} - * parsed from xml + * + * @param elements collection of {@link CellDesignerElement cell designer elements} + * parsed from xml */ public CompartmentCollectionXmlParser(final CellDesignerElementCollection elements) { this.elements = elements; @@ -58,14 +55,11 @@ public class CompartmentCollectionXmlParser { /** * Parse CellDEsigner xml node with collection of compartments. - * - * @param compartmentsNode - * xml node to parse + * + * @param compartmentsNode xml node to parse * @return list of compartments obtained from xml node - * @throws InvalidXmlSchemaException - * thrown when there is a problem with xml - * @throws CompartmentParserException - * thrown when there is a problem with parsing a compartment + * @throws InvalidXmlSchemaException thrown when there is a problem with xml + * @throws CompartmentParserException thrown when there is a problem with parsing a compartment */ public List<CellDesignerCompartment> parseXmlCompartmentCollection(final Node compartmentsNode) throws InvalidXmlSchemaException, CompartmentParserException { @@ -87,9 +81,8 @@ public class CompartmentCollectionXmlParser { /** * Creates CellDesigner xml string from set of compartments. - * - * @param collection - * collection of compartments to be transformed into xml + * + * @param collection collection of compartments to be transformed into xml * @return xml representation of the compartments */ public String toXml(final Collection<Compartment> collection) { @@ -104,6 +97,7 @@ public class CompartmentCollectionXmlParser { } } Compartment defaultCompartment = new Compartment("default"); + defaultCompartment.setName("default"); result.append(compartmentParser.toXml(defaultCompartment)); result.append("</listOfCompartments>\n"); return result.toString(); diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java index 5e7fb0b28095a21a90fa3e58331d1fb545f70d2f..0ba1bee9b05360521edfaae4a8beb21300da97c3 100644 --- a/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java +++ b/service/src/main/java/lcsb/mapviewer/services/impl/SearchService.java @@ -86,7 +86,7 @@ public class SearchService implements ISearchService { this.elementDao = elementDao; this.reactionDao = reactionDao; addSearchPrefix("complex", Collections.singletonList(Complex.class)); - addSearchPrefix("degrded", Collections.singletonList(Degraded.class)); + addSearchPrefix("degraded", Collections.singletonList(Degraded.class)); addSearchPrefix("drug", Collections.singletonList(Drug.class)); addSearchPrefix("gene", Collections.singletonList(Gene.class)); addSearchPrefix("ion", Collections.singletonList(Ion.class));