preview-genomic_model-neo4j.xml does not contain all the fields for some classes

[yasharmaster]

When I try to convert all templates to cypher, some templates are not converted. For example consider the template Gene_transcriptionFactors.

<query name="Gene_transcriptionFactors" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.regulatoryRegions.primaryIdentifier Gene.regulatoryRegions.chromosome.primaryIdentifier Gene.regulatoryRegions.chromosomeLocation.end Gene.regulatoryRegions.chromosomeLocation.start Gene.regulatoryRegions.dataSets.dataSource.name Gene.regulatoryRegions.factor.primaryIdentifier Gene.regulatoryRegions.factor.symbol Gene.regulatoryRegions.sequence.residues" longDescription="Show all known transcription factors for a particular D. melanogaster gene. (Data Source: REDfly, FlyBase)." sortOrder="Gene.regulatoryRegions.primaryIdentifier asc" constraintLogic="A and C">
<constraint path="Gene.regulatoryRegions" editable="false" type="TFBindingSite" />
<constraint path="Gene" code="A" editable="true" op="LOOKUP" value="dpp" />
<constraint path="Gene.organism.name" code="C" editable="true" op="=" value="Drosophila melanogaster" />
</query>

It gives following exception,

org.intermine.pathquery.PathException: Unable to resolve path 'Gene.regulatoryRegions.factor.primaryIdentifier': field 'factor' of class 'org.intermine.model.bio.RegulatoryRegion' not found in model 'genomic'
	at org.intermine.pathquery.Path.initialise(Path.java:195)
	at org.intermine.pathquery.Path.<init>(Path.java:102)
	at org.intermine.neo4j.cypher.Helper.getAllPaths(Helper.java:131)
	at org.intermine.neo4j.cypher.tree.PathTree.<init>(PathTree.java:25)
	at org.intermine.neo4j.cypher.QueryGenerator.pathQueryToCypher(QueryGenerator.java:48)
	at TemplateParser.main(TemplateParser.java:52)

This is because this template contains a Path having factor field right after RegulatoryRegion class, but in preview-genomic_model-neo4j.xml, RegulatoryRegion does not have any field called factor. Same is the case for some other classes and their fields.

So we need to update preview-genomic_model-neo4j.xml to reflect all the FlyMine classes and their fields, so as to be able to convert all sorts of PathQueries.
@sammyjava @danielabutano @vivekkrish

[sammyjava]

Seems you're using templates from a different FlyMine than http://intermine.modencode.org/preview (currently down, and I've asked Daniela whether I should host it here so it stays up). In that mine, you have

<class name="RegulatoryRegion" extends="SequenceFeature" is-interface="true">
        <attribute name="evidenceMethod" type="java.lang.String"/>
        <reference name="gene" referenced-type="Gene" reverse-reference="regulatoryRegions"/>
</class>
<class name="SequenceFeature" extends="BioEntity" is-interface="true" neo4j-ignore="true">
        <attribute name="length" type="java.lang.Integer"/>
        <attribute name="cytoLocation" type="java.lang.String"/>
        <attribute name="scoreType" type="java.lang.String"/>
        <attribute name="score" type="java.lang.Double"/>
        <reference name="chromosome" referenced-type="Chromosome" neo4j-ignore="true"/>
        <reference name="chromosomeLocation" referenced-type="Location" neo4j-ignore="true"/>
        <reference name="sequence" referenced-type="Sequence" neo4j-ignore="true"/>
        <reference name="sequenceOntologyTerm" referenced-type="SOTerm" neo4j-relationship="HAS_TERM"/>
        <collection name="childFeatures" referenced-type="SequenceFeature" neo4j-relationship="PARENT_OF"/>
        <collection name="overlappingFeatures" referenced-type="SequenceFeature" neo4j-relationship="OVERLAPS"/>
</class>
<class name="BioEntity" is-interface="true" neo4j-ignore="true">
        <attribute name="secondaryIdentifier" type="java.lang.String"/>
        <attribute name="symbol" type="java.lang.String"/>
        <attribute name="primaryIdentifier" type="java.lang.String"/>
        <attribute name="name" type="java.lang.String"/>
        <reference name="organism" referenced-type="Organism" neo4j-relationship="PART_OF"/>
        <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject" neo4j-relationship="SYNONYM_OF"/>
        <collection name="publications" referenced-type="Publication" reverse-reference="bioEntities" neo4j-relationship="MENTIONED_IN"/>
        <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject" neo4j-relationship="ANNOTATED_BY"/>
        <collection name="interactions" referenced-type="Interaction" reverse-reference="participant1" neo4j-relationship="PARTICIPATES_IN"/>
        <collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject" neo4j-relationship="CROSS_REFERENCED_BY"/>
        <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities" neo4j-ignore="true"/>
        <collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn" neo4j-ignore="true"/>
        <collection name="locations" referenced-type="Location" reverse-reference="feature" neo4j-ignore="true"/>
</class>

But also, there is nothing special or permanent about templates - they're just example queries that are stored. There isn't really any need to convert templates to Cypher, per se, they're just good test cases for you to work with.

[yasharmaster]

Yeah @sammyjava , I downloaded these templates from http://www.flymine.org/ and not from our standard mine http://intermine.modencode.org/preview. I thought that the data model and templates of both FlyMines would be the same but I was wrong. 😅

When http://intermine.modencode.org/preview is up and running, I'll use its templates as test cases instead.

[sammyjava]

I'm pretty sure mines are like snowflakes: no two are alike. :)