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89 changes: 33 additions & 56 deletions
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biopax-validator/src/main/java/org/biopax/validator/rules/PathwayMultiOrganismRule.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,77 +1,54 @@ | ||
| package org.biopax.validator.rules; | ||
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| /* | ||
| * | ||
| */ | ||
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| import java.util.Collection; | ||
| import java.util.HashSet; | ||
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| import org.biopax.paxtools.controller.AbstractTraverser; | ||
| import org.biopax.paxtools.controller.Fetcher; | ||
| import org.biopax.paxtools.controller.PathAccessor; | ||
| import org.biopax.paxtools.controller.PropertyEditor; | ||
| import org.biopax.paxtools.util.Filter; | ||
| import org.biopax.paxtools.model.BioPAXElement; | ||
| import org.biopax.paxtools.model.Model; | ||
| import org.biopax.paxtools.controller.SimpleEditorMap; | ||
| import org.biopax.paxtools.model.level3.BioSource; | ||
| import org.biopax.paxtools.model.level3.Pathway; | ||
| import org.biopax.paxtools.util.Filter; | ||
| import org.biopax.validator.api.AbstractRule; | ||
| import org.biopax.validator.api.beans.Validation; | ||
| import org.biopax.paxtools.controller.SimpleEditorMap; | ||
| import org.springframework.stereotype.Component; | ||
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|
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| import java.util.HashSet; | ||
| import java.util.Set; | ||
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| /** | ||
| * Warn if a pathway and its component have different (not null) 'organism' values. | ||
| * What to do? (ignore, delete this value, or override nested organism properties with pathway's value) | ||
| * | ||
| * | ||
| * @author rodche | ||
| */ | ||
| @Component | ||
| public class PathwayMultiOrganismRule extends AbstractRule<Pathway> | ||
| { | ||
| private final static Filter<PropertyEditor> filter = new Filter<PropertyEditor>() { | ||
| public class PathwayMultiOrganismRule extends AbstractRule<Pathway> { | ||
| private final static Filter<PropertyEditor> filter = new Filter<PropertyEditor>() { | ||
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| public boolean filter(PropertyEditor editor) { | ||
| return !"nextStep".equals(editor.getProperty()); | ||
| } | ||
| }; | ||
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| public void check(final Validation validation, final Pathway pathway) { | ||
| final Collection<BioPAXElement> organisms = new HashSet<BioPAXElement>(); | ||
| final BioSource organism = pathway.getOrganism(); // not null - due to the canCheck method! | ||
| //but.. | ||
| if(organism==null) return; // we do not care | ||
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| AbstractTraverser runner = new AbstractTraverser( | ||
| SimpleEditorMap.L3, filter) | ||
| { | ||
| @Override | ||
| protected void visit(Object value, BioPAXElement parent, | ||
| Model model, PropertyEditor editor) | ||
| { | ||
| if(value instanceof BioSource) { | ||
| if(!((BioPAXElement) value).isEquivalent(organism)) { | ||
| organisms.add((BioPAXElement) value); | ||
| } | ||
| } | ||
| else if (value instanceof BioPAXElement) { | ||
| logger.trace("Traverse into " + value + " " | ||
| + value.getClass().getSimpleName()); | ||
| traverse((BioPAXElement) value, model); | ||
| } | ||
| } | ||
| }; | ||
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| runner.traverse(pathway, null); | ||
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| if(organisms.size()>0) { | ||
| error(validation, pathway, "multi.organism.pathway", | ||
| false, organism, organisms); | ||
| } | ||
| public boolean filter(PropertyEditor editor) { | ||
| //skip for: nextStep (those can be reached via pathwayOrder or pathwayComponent) and evidence (multi-org. is normal there) | ||
| return !("nextStep".equals(editor.getProperty()) || "evidence".equals(editor.getProperty())); | ||
| } | ||
| }; | ||
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| public void check(final Validation validation, final Pathway pathway) { | ||
| Fetcher fetcher = new Fetcher(SimpleEditorMap.L3, Fetcher.evidenceFilter, Fetcher.nextStepFilter); | ||
| fetcher.setSkipSubPathways(true); | ||
| final Set<BioSource> organisms = fetcher.fetch(pathway, BioSource.class); | ||
| //collect taxonomy IDs (from the BioSource objects that have valid xrefs) | ||
| PathAccessor accessor = new PathAccessor("BioSource/xref:UnificationXref/id"); | ||
| Set<String> taxIds = accessor.getValueFromBeans(organisms); | ||
| if (taxIds.size() > 1) { | ||
| accessor = new PathAccessor("BioSource/name"); | ||
| Set<String> names = new HashSet<String>(); | ||
| for(Object name : accessor.getValueFromBeans(organisms)) | ||
| names.add(String.valueOf(name).toLowerCase()); | ||
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| public boolean canCheck(Object thing) { | ||
| return thing instanceof Pathway | ||
| && ((Pathway)thing).getOrganism() != null; | ||
| error(validation, pathway, "multi.organism.pathway", false, taxIds, names); | ||
| } | ||
| } | ||
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| public boolean canCheck(Object thing) { | ||
| return thing instanceof Pathway; | ||
| } | ||
|
|
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| } |
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