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prevent self referencing. Refs #472
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Julie Sullivan committed Dec 10, 2013
1 parent c1ac71e commit 49f8d48
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Showing 2 changed files with 66 additions and 94 deletions.
2 changes: 1 addition & 1 deletion bio/sources/orthodb/main/src/org/intermine/bio/dataconversion/OrthodbConverter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ private void processHomologuePair(GeneHolder gene, GeneHolder homologue)
final String refId1 = getGene(gene);
final String refId2 = getGene(homologue);

if (refId1 == null || refId2 == null) {
if (refId1 == null || refId2 == null || refId1.equals(refId2)) {
// will happen if ID resolver fails to find a match
return;
}
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158 changes: 65 additions & 93 deletions bio/sources/orthodb/test/resources/OrthodbConverterTest_tgt.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,107 +2,63 @@
<item id="8_1" class="OrthologueEvidence">
<reference name="evidenceCode" ref_id="7_1"/>
</item>
<item id="4_4" class="Organism">
<attribute name="taxonId" value="198094"/>
</item>
<item id="3_3" class="Gene">
<attribute name="primaryIdentifier" value="GBAA2196"/>
<reference name="organism" ref_id="4_3"/>
<item id="3_2" class="Gene">
<attribute name="primaryIdentifier" value="BAS2041"/>
<reference name="organism" ref_id="4_2"/>
<reference name="sequenceOntologyTerm" ref_id="5_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
</item>
<item id="3_1" class="Gene">
<attribute name="primaryIdentifier" value="BAMEG_2400"/>
<reference name="organism" ref_id="4_1"/>
<reference name="sequenceOntologyTerm" ref_id="5_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<item id="4_4" class="Organism">
<attribute name="taxonId" value="198094"/>
</item>
<item id="6_3" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_1"/>
<reference name="homologue" ref_id="3_3"/>
<reference name="homologue" ref_id="3_4"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="2_1" class="DataSet">
<attribute name="name" value="OrthoDB data set"/>
<reference name="dataSource" ref_id="1_1"/>
</item>
<item id="4_1" class="Organism">
<attribute name="taxonId" value="568206"/>
</item>
<item id="3_4" class="Gene">
<attribute name="primaryIdentifier" value="BA_2196"/>
<reference name="organism" ref_id="4_4"/>
<item id="3_1" class="Gene">
<attribute name="primaryIdentifier" value="BAMEG_2400"/>
<reference name="organism" ref_id="4_1"/>
<reference name="sequenceOntologyTerm" ref_id="5_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
</item>
<item id="6_15" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_4"/>
<reference name="homologue" ref_id="3_3"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_8" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_2"/>
<reference name="homologue" ref_id="3_4"/>
<item id="3_3" class="Gene">
<attribute name="primaryIdentifier" value="GBAA2196"/>
<reference name="organism" ref_id="4_3"/>
<reference name="sequenceOntologyTerm" ref_id="5_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="4_2" class="Organism">
<attribute name="taxonId" value="260799"/>
<item id="4_3" class="Organism">
<attribute name="taxonId" value="261594"/>
</item>
<item id="0_1" class="Ontology">
<attribute name="name" value="Sequence Ontology"/>
<attribute name="url" value="http://www.sequenceontology.org"/>
<item id="7_1" class="OrthologueEvidenceCode">
<attribute name="abbreviation" value="AA"/>
<attribute name="name" value="Amino acid sequence comparison"/>
</item>
<item id="6_9" class="Homologue">
<item id="6_1" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_3"/>
<reference name="gene" ref_id="3_1"/>
<reference name="homologue" ref_id="3_2"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_6" class="Homologue">
<item id="6_11" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_2"/>
<reference name="gene" ref_id="3_4"/>
<reference name="homologue" ref_id="3_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_4" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_1"/>
<reference name="homologue" ref_id="3_4"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="3_2" class="Gene">
<attribute name="primaryIdentifier" value="BAS2041"/>
<reference name="organism" ref_id="4_2"/>
<reference name="sequenceOntologyTerm" ref_id="5_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
</item>
<item id="4_3" class="Organism">
<attribute name="taxonId" value="261594"/>
</item>
<item id="6_12" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_3"/>
<reference name="homologue" ref_id="3_4"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="7_1" class="OrthologueEvidenceCode">
<attribute name="abbreviation" value="AA"/>
<attribute name="name" value="Amino acid sequence comparison"/>
<item id="2_1" class="DataSet">
<attribute name="name" value="OrthoDB data set"/>
<reference name="dataSource" ref_id="1_1"/>
</item>
<item id="6_1" class="Homologue">
<item id="6_2" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_1"/>
<reference name="homologue" ref_id="3_2"/>
<reference name="homologue" ref_id="3_3"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
Expand All @@ -111,61 +67,77 @@
<reference name="ontology" ref_id="0_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
</item>
<item id="6_16" class="Homologue">
<attribute name="type" value="paralogue"/>
<reference name="gene" ref_id="3_4"/>
<reference name="homologue" ref_id="3_4"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
<item id="4_1" class="Organism">
<attribute name="taxonId" value="568206"/>
</item>
<item id="1_1" class="DataSource">
<attribute name="name" value="OrthoDB"/>
</item>
<item id="6_10" class="Homologue">
<item id="3_4" class="Gene">
<attribute name="primaryIdentifier" value="BA_2196"/>
<reference name="organism" ref_id="4_4"/>
<reference name="sequenceOntologyTerm" ref_id="5_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
</item>
<item id="6_9" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_3"/>
<reference name="homologue" ref_id="3_1"/>
<reference name="homologue" ref_id="3_4"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_13" class="Homologue">
<item id="6_7" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_4"/>
<reference name="gene" ref_id="3_3"/>
<reference name="homologue" ref_id="3_2"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_11" class="Homologue">
<attribute name="type" value="paralogue"/>
<reference name="gene" ref_id="3_3"/>
<reference name="homologue" ref_id="3_3"/>
<item id="6_6" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_2"/>
<reference name="homologue" ref_id="3_4"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_7" class="Homologue">
<item id="6_12" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_2"/>
<reference name="gene" ref_id="3_4"/>
<reference name="homologue" ref_id="3_3"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_5" class="Homologue">
<attribute name="type" value="paralogue"/>
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_2"/>
<reference name="homologue" ref_id="3_3"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_10" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_4"/>
<reference name="homologue" ref_id="3_2"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_2" class="Homologue">
<attribute name="type" value="paralogue"/>
<reference name="gene" ref_id="3_1"/>
<item id="6_8" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_3"/>
<reference name="homologue" ref_id="3_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
</item>
<item id="6_14" class="Homologue">
<item id="0_1" class="Ontology">
<attribute name="name" value="Sequence Ontology"/>
<attribute name="url" value="http://www.sequenceontology.org"/>
</item>
<item id="4_2" class="Organism">
<attribute name="taxonId" value="260799"/>
</item>
<item id="6_4" class="Homologue">
<attribute name="type" value="orthologue"/>
<reference name="gene" ref_id="3_4"/>
<reference name="gene" ref_id="3_2"/>
<reference name="homologue" ref_id="3_1"/>
<collection name="dataSets"><reference ref_id="2_1"/></collection>
<collection name="evidence"><reference ref_id="8_1"/></collection>
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