-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge branch 'uniparc_light_xml' into uniparc_light_vd_v2
- Loading branch information
Showing
10 changed files
with
405 additions
and
74 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
81 changes: 81 additions & 0 deletions
81
xml-parser/src/main/java/org/uniprot/core/xml/CrossReferenceConverterUtils.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| package org.uniprot.core.xml; | ||
|
|
||
| import com.google.common.base.Strings; | ||
| import org.uniprot.core.uniparc.impl.UniParcCrossReferenceBuilder; | ||
| import org.uniprot.core.uniprotkb.taxonomy.Organism; | ||
| import org.uniprot.core.uniprotkb.taxonomy.impl.OrganismBuilder; | ||
| import org.uniprot.cv.taxonomy.TaxonomicNode; | ||
| import org.uniprot.cv.taxonomy.TaxonomyRepo; | ||
|
|
||
| import java.util.Optional; | ||
|
|
||
| public class CrossReferenceConverterUtils { | ||
| public static final String PROPERTY_GENE_NAME = "gene_name"; | ||
| public static final String PROPERTY_PROTEIN_NAME = "protein_name"; | ||
| public static final String PROPERTY_CHAIN = "chain"; | ||
| public static final String PROPERTY_NCBI_GI = "NCBI_GI"; | ||
| public static final String PROPERTY_PROTEOME_ID = "proteome_id"; | ||
| public static final String PROPERTY_COMPONENT = "component"; | ||
| public static final String PROPERTY_NCBI_TAXONOMY_ID = "NCBI_taxonomy_id"; | ||
| public static final String PROPERTY_UNIPROTKB_ACCESSION = "UniProtKB_accession"; | ||
|
|
||
| private CrossReferenceConverterUtils(){} | ||
|
|
||
| public static void populateUniParcCrossReferenceBuilder(String propertyType, String propertyValue, UniParcCrossReferenceBuilder builder, TaxonomyRepo taxonomyRepo) { | ||
| switch (propertyType) { | ||
| case PROPERTY_GENE_NAME: | ||
| builder.geneName(propertyValue); | ||
| break; | ||
| case PROPERTY_PROTEIN_NAME: | ||
| builder.proteinName(propertyValue); | ||
| break; | ||
| case PROPERTY_CHAIN: | ||
| builder.chain(propertyValue); | ||
| break; | ||
| case PROPERTY_NCBI_GI: | ||
| builder.ncbiGi(propertyValue); | ||
| break; | ||
| case PROPERTY_PROTEOME_ID: | ||
| builder.proteomeId(propertyValue); | ||
| break; | ||
| case PROPERTY_COMPONENT: | ||
| builder.component(propertyValue); | ||
| break; | ||
| case PROPERTY_NCBI_TAXONOMY_ID: | ||
| builder.organism(CrossReferenceConverterUtils.convertTaxonomy(propertyValue, taxonomyRepo)); | ||
| break; | ||
| case PROPERTY_UNIPROTKB_ACCESSION: | ||
| builder.propertiesAdd(PROPERTY_UNIPROTKB_ACCESSION, propertyValue); | ||
| break; | ||
| default: | ||
| throw new XmlReaderException( | ||
| "Unable to read xml property: " | ||
| + propertyType | ||
| + "value: " | ||
| + propertyValue); | ||
| } | ||
| } | ||
|
|
||
| private static Organism convertTaxonomy(String taxId, TaxonomyRepo taxonomyRepo) { | ||
| OrganismBuilder builder = new OrganismBuilder().taxonId(Long.parseLong(taxId)); | ||
| Optional<TaxonomicNode> opNode = getTaxonomyNode(taxId, taxonomyRepo); | ||
| if (opNode.isPresent()) { | ||
| TaxonomicNode node = opNode.get(); | ||
| builder.scientificName(node.scientificName()); | ||
| if (!Strings.isNullOrEmpty(node.commonName())) { | ||
| builder.commonName(node.commonName()); | ||
| } | ||
| if (!Strings.isNullOrEmpty(node.synonymName())) { | ||
| builder.synonymsAdd(node.synonymName()); | ||
| } | ||
| } | ||
|
|
||
| return builder.build(); | ||
| } | ||
|
|
||
| private static Optional<TaxonomicNode> getTaxonomyNode(String taxId, TaxonomyRepo taxonomyRepo) { | ||
| if (taxonomyRepo == null) { | ||
| return Optional.empty(); | ||
| } else return taxonomyRepo.retrieveNodeUsingTaxID(Integer.parseInt(taxId)); | ||
| } | ||
| } |
101 changes: 101 additions & 0 deletions
101
...parser/src/main/java/org/uniprot/core/xml/dbreference/UniParcCrossReferenceConverter.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,101 @@ | ||
| package org.uniprot.core.xml.dbreference; | ||
|
|
||
| import org.uniprot.core.uniparc.UniParcCrossReference; | ||
| import org.uniprot.core.uniparc.UniParcDatabase; | ||
| import org.uniprot.core.uniparc.impl.UniParcCrossReferenceBuilder; | ||
| import org.uniprot.core.util.Utils; | ||
| import org.uniprot.core.xml.Converter; | ||
| import org.uniprot.core.xml.CrossReferenceConverterUtils; | ||
| import org.uniprot.core.xml.jaxb.dbreference.DbReference; | ||
| import org.uniprot.core.xml.jaxb.dbreference.ObjectFactory; | ||
| import org.uniprot.core.xml.jaxb.dbreference.PropertyType; | ||
| import org.uniprot.core.xml.uniprot.XmlConverterHelper; | ||
| import org.uniprot.cv.taxonomy.TaxonomyRepo; | ||
|
|
||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
||
| import static org.uniprot.core.xml.CrossReferenceConverterUtils.*; | ||
|
|
||
| public class UniParcCrossReferenceConverter | ||
| implements Converter<DbReference, UniParcCrossReference> { | ||
| private final ObjectFactory xmlFactory; | ||
| private final TaxonomyRepo taxonomyRepo; | ||
|
|
||
| public UniParcCrossReferenceConverter() { | ||
| this(new ObjectFactory(), null); | ||
| } | ||
|
|
||
| public UniParcCrossReferenceConverter(ObjectFactory xmlFactory, TaxonomyRepo taxonomyRepo) { | ||
| this.xmlFactory = xmlFactory; | ||
| this.taxonomyRepo = taxonomyRepo; | ||
| } | ||
|
|
||
| @Override | ||
| public UniParcCrossReference fromXml(DbReference xmlObj) { | ||
| UniParcCrossReferenceBuilder builder = new UniParcCrossReferenceBuilder(); | ||
| builder.database(UniParcDatabase.typeOf(xmlObj.getType())) | ||
| .id(xmlObj.getId()) | ||
| .active(xmlObj.getActive().equals("Y")) | ||
| .versionI(xmlObj.getVersionI()) | ||
| .created(XmlConverterHelper.dateFromXml(xmlObj.getCreated())) | ||
| .lastUpdated(XmlConverterHelper.dateFromXml(xmlObj.getLast())); | ||
|
|
||
| for (PropertyType property : xmlObj.getProperty()) { | ||
| CrossReferenceConverterUtils.populateUniParcCrossReferenceBuilder(property.getType(), property.getValue(), builder, taxonomyRepo); | ||
| } | ||
| if (xmlObj.getVersion() != null) builder.version(xmlObj.getVersion()); | ||
| return builder.build(); | ||
| } | ||
|
|
||
| @Override | ||
| public DbReference toXml(UniParcCrossReference uniObj) { | ||
| DbReference xmlObj = xmlFactory.createDbReference(); | ||
| xmlObj.setActive(uniObj.isActive() ? "Y" : "N"); | ||
| xmlObj.setId(uniObj.getId()); | ||
| xmlObj.setType(uniObj.getDatabase().getDisplayName()); | ||
| xmlObj.setVersionI(uniObj.getVersionI()); | ||
| if (uniObj.getVersion() != null) xmlObj.setVersion(uniObj.getVersion()); | ||
| xmlObj.setCreated(XmlConverterHelper.dateToXml(uniObj.getCreated())); | ||
| xmlObj.setLast(XmlConverterHelper.dateToXml(uniObj.getLastUpdated())); | ||
|
|
||
| List<PropertyType> properties = new ArrayList<>(); | ||
| if (Utils.notNullNotEmpty(uniObj.getGeneName())) { | ||
| properties.add(createProperty(PROPERTY_GENE_NAME, uniObj.getGeneName())); | ||
| } | ||
| if (Utils.notNullNotEmpty(uniObj.getProteinName())) { | ||
| properties.add(createProperty(PROPERTY_PROTEIN_NAME, uniObj.getProteinName())); | ||
| } | ||
| if (Utils.notNullNotEmpty(uniObj.getChain())) { | ||
| properties.add(createProperty(PROPERTY_CHAIN, uniObj.getChain())); | ||
| } | ||
| if (Utils.notNullNotEmpty(uniObj.getNcbiGi())) { | ||
| properties.add(createProperty(PROPERTY_NCBI_GI, uniObj.getNcbiGi())); | ||
| } | ||
| if (Utils.notNullNotEmpty(uniObj.getProteomeId())) { | ||
| properties.add(createProperty(PROPERTY_PROTEOME_ID, uniObj.getProteomeId())); | ||
| } | ||
| if (Utils.notNullNotEmpty(uniObj.getComponent())) { | ||
| properties.add(createProperty(PROPERTY_COMPONENT, uniObj.getComponent())); | ||
| } | ||
| if (Utils.notNull(uniObj.getOrganism())) { | ||
| String taxonId = String.valueOf(uniObj.getOrganism().getTaxonId()); | ||
| properties.add(createProperty(PROPERTY_NCBI_TAXONOMY_ID, taxonId)); | ||
| } | ||
| xmlObj.getProperty().addAll(properties); | ||
| if (Utils.notNullNotEmpty(uniObj.getProperties())) { | ||
| uniObj.getProperties().stream() | ||
| .map(prop -> createProperty(prop.getKey(), prop.getValue())) | ||
| .forEach(val -> xmlObj.getProperty().add(val)); | ||
| } | ||
|
|
||
| return xmlObj; | ||
| } | ||
|
|
||
| private PropertyType createProperty(String key, String value) { | ||
| PropertyType xmlObj = xmlFactory.createPropertyType(); | ||
| xmlObj.setType(key); | ||
| xmlObj.setValue(value); | ||
| return xmlObj; | ||
| } | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
48 changes: 48 additions & 0 deletions
48
xml-parser/src/main/java/org/uniprot/core/xml/uniparc/UniParcEntryLightConverter.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| package org.uniprot.core.xml.uniparc; | ||
|
|
||
| import org.uniprot.core.uniparc.UniParcEntryLight; | ||
| import org.uniprot.core.uniparc.impl.UniParcEntryLightBuilder; | ||
| import org.uniprot.core.xml.Converter; | ||
| import org.uniprot.core.xml.jaxb.uniparc.Entry; | ||
| import org.uniprot.core.xml.jaxb.uniparc.ObjectFactory; | ||
|
|
||
| public class UniParcEntryLightConverter implements Converter<Entry, UniParcEntryLight> { | ||
| private static final String UNIPARC = "uniparc"; | ||
| private final ObjectFactory xmlFactory; | ||
| private final SequenceFeatureConverter seqFeatureConverter; | ||
| private final SequenceConverter sequenceConverter; | ||
|
|
||
| public UniParcEntryLightConverter(){ | ||
| this(new ObjectFactory()); | ||
| } | ||
|
|
||
| public UniParcEntryLightConverter(ObjectFactory xmlFactory) { | ||
| this.xmlFactory = xmlFactory; | ||
| this.seqFeatureConverter = new SequenceFeatureConverter(xmlFactory); | ||
| this.sequenceConverter = new SequenceConverter(xmlFactory); | ||
| } | ||
|
|
||
| @Override | ||
| public UniParcEntryLight fromXml(Entry xmlObj) { | ||
| UniParcEntryLightBuilder builder = new UniParcEntryLightBuilder(); | ||
| builder.uniParcId(xmlObj.getAccession()) | ||
| .sequence(sequenceConverter.fromXml(xmlObj.getSequence())) | ||
| .sequenceFeaturesSet( | ||
| xmlObj.getSignatureSequenceMatch().stream() | ||
| .map(seqFeatureConverter::fromXml) | ||
| .toList()); | ||
| return builder.build(); | ||
| } | ||
|
|
||
| @Override | ||
| public Entry toXml(UniParcEntryLight uniObj) { | ||
| Entry entry = xmlFactory.createEntry(); | ||
| entry.setDataset(UNIPARC); | ||
| entry.setAccession(uniObj.getUniParcId()); | ||
| entry.setSequence(sequenceConverter.toXml(uniObj.getSequence())); | ||
| uniObj.getSequenceFeatures().stream() | ||
| .map(seqFeatureConverter::toXml) | ||
| .forEach(val -> entry.getSignatureSequenceMatch().add(val)); | ||
| return entry; | ||
| } | ||
| } |
Oops, something went wrong.