<commit_before><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="modmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="modmine-static" type="intermine-items-xml-file" dump="true">
      <property name="src.data.file" location="resources/projects.xml"/>
    </source>
    <source name="chado-db-flybase-dmel" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="organisms" value="7227"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.FlyBaseProcessor"/>
      <property name="converter.class" 
                value="org.intermine.bio.dataconversion.GenomeDBConverter"/>
    </source>
    <source name="chado-db-wormbase-c_elegans" type="chado-db" dump="true">
      <property name="source.db.name" value="wormbase"/>
      <property name="organisms" value="6239"/>
      <property name="dataSourceName" value="WormBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.WormBaseProcessor"/>
      <property name="converter.class" 
                value="org.intermine.bio.dataconversion.GenomeDBConverter"/>
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="7227 6239"/>
      <property name="src.data.dir" location="/shared/data/uniprot/current/split"/>
      <property name="createinterpro" value="true"/>
    </source>
    <source name="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keywlist.xml"/>
    </source>
    <source name="interpro" type="interpro" dump="true">
      <property name="src.data.dir" location="/shared/data/interpro/current"/>
    </source>
    <source name="inparanoid-orthologue" type="orthologue">
      <property name="src.data.dir" location="/shared/data/modmine/inparanoid-orthologue/current/"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="/shared/data/go-annotation/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="/shared/data/go-annotation/gene_ontology.obo"/>
      <property name="src.data.dir" location="/shared/data/modmine/go-annotation/"/>
      <property name="src.data.dir.includes" value="*/gene_association*"/>
    </source>
                <source name="fly-anatomy-ontology" type="fly-anatomy-ontology" dump="true">
      <property name="src.data.file" location="/shared/data/ontologies/fly_anatomy/current/fly_anatomy.obo"/>
    </source>
                <source name="fly-development-ontology" type="fly-development-ontology" dump="true">
      <property name="src.data.file" location="/shared/data/ontologies/fly_development/current/fly_development.obo"/>
    </source>
    <source name="fly-misc-cvterms" type="fly-misc-cvterms">
      <property name="src.data.file" location="/shared/data/ontologies/fly_cv/current/flybase_controlled_vocabulary.obo"/>
    </source>
    <source name="flybase-dmel-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Gene"/>
      <property name="fasta.includes" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
    </source>
    <source name="flybase-dmel-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.CDS"/>
      <property name="fasta.classAttribute" value="secondaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
    </source>
    <source name="flybase-dmel-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
    </source>
    <source name="flybase-dmel-3prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.ThreePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-three_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
    </source>
                <source name="wormbase-c_elegans-chromosome-fasta" type="fasta" dump="true">
      <property name="fasta.taxonId" value="6239"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="*chromosome*.fasta"/>
                        <property name="fasta.dataSetTitle" value="WormBase C. Elegans data set"/>
                        <property name="fasta.synonymSource" value="WormBase"/>
      <property name="src.data.dir" location="/shared/data/wormbase/ws175"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <!-- this source finds the taxon ids in the objectstore, retrieves
           species name and genus from Entrez into an InterMine format XML
           file, loads that file into a target items DB, then into the final
           objectstore -->
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>
    <source name="update-publications" type="update-publications">
      <!-- this source finds the publication ids (pubmed ids) in the
           objectstore, retrieves the details of the publication from Entrez
           into an InterMine format XML file, loads that file into a target
           items DB, then into the final objectstore -->
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
    <source name="modencode-metadata" type="chado-db">
      <property name="organisms" value="7227"/>
      <property name="dataSourceName" value="modENCODE"/>
      <property name="dataSetTitle" value="modENCODE submission"/>
      <property name="source.db.name" value="modencode-metadata"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
    </source><commit_msg>modmine: resolved conflict<commit_after><project type="bio">
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="modmine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="modmine-static" type="intermine-items-xml-file" dump="true">
      <property name="src.data.file" location="resources/projects.xml"/>
    </source>
    <source name="chado-db-flybase-dmel" type="chado-db" dump="true">
      <property name="source.db.name" value="flybase"/>
      <property name="organisms" value="7227"/>
      <property name="dataSourceName" value="FlyBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.FlyBaseProcessor"/>
      <property name="converter.class" 
                value="org.intermine.bio.dataconversion.GenomeDBConverter"/>
    </source>
    <source name="chado-db-wormbase-c_elegans" type="chado-db" dump="true">
      <property name="source.db.name" value="wormbase"/>
      <property name="organisms" value="6239"/>
      <property name="dataSourceName" value="WormBase"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.WormBaseProcessor"/>
      <property name="converter.class" 
                value="org.intermine.bio.dataconversion.GenomeDBConverter"/>
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="7227 6239"/>
      <property name="src.data.dir" location="/shared/data/uniprot/current/split"/>
      <property name="createinterpro" value="true"/>
    </source>
    <source name="uniprot-keywords" type="uniprot-keywords">
      <property name="src.data.dir" location="/shared/data/uniprot/current"/>
      <property name="src.data.dir.includes" value="keywlist.xml"/>
    </source>
    <source name="interpro" type="interpro" dump="true">
      <property name="src.data.dir" location="/shared/data/interpro/current"/>
    </source>
    <source name="inparanoid-orthologue" type="orthologue">
      <property name="src.data.dir" location="/shared/data/modmine/inparanoid-orthologue/current/"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="/shared/data/go-annotation/gene_ontology.obo"/>
    </source>
    <source name="go-annotation" type="go-annotation" dump="true">
      <property name="ontologyfile" location="/shared/data/go-annotation/gene_ontology.obo"/>
      <property name="src.data.dir" location="/shared/data/modmine/go-annotation/"/>
      <property name="src.data.dir.includes" value="*/gene_association*"/>
    </source>
                <source name="fly-anatomy-ontology" type="fly-anatomy-ontology" dump="true">
      <property name="src.data.file" location="/shared/data/ontologies/fly_anatomy/current/fly_anatomy.obo"/>
    </source>
                <source name="fly-development-ontology" type="fly-development-ontology" dump="true">
      <property name="src.data.file" location="/shared/data/ontologies/fly_development/current/fly_development.obo"/>
    </source>
    <source name="fly-misc-cvterms" type="fly-misc-cvterms">
      <property name="src.data.file" location="/shared/data/ontologies/fly_cv/current/flybase_controlled_vocabulary.obo"/>
    </source>
    <source name="flybase-dmel-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Gene"/>
      <property name="fasta.includes" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
    </source>
    <source name="flybase-dmel-cds-fasta" type="fasta">
      <property name="fasta.loaderClassName"
                value="org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.CDS"/>
      <property name="fasta.classAttribute" value="secondaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-CDS-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
    </source>
    <source name="flybase-dmel-5prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.FivePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-five_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
    </source>
    <source name="flybase-dmel-3prime-utr-fasta" type="fasta">
      <property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask"/>
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.ThreePrimeUTR"/>
      <property name="fasta.classAttribute" value="primaryIdentifier"/>
      <property name="fasta.includes" value="dmel-all-three_prime_UTR-*.fasta"/>
      <property name="fasta.dataSetTitle" value="FlyBase Drosophila melanogaster data set"/>
      <property name="fasta.synonymSource" value="FlyBase"/>
      <property name="src.data.dir" location="/shared/data/flybase/current/fasta"/>
    </source>
                <source name="wormbase-c_elegans-chromosome-fasta" type="fasta" dump="true">
      <property name="fasta.taxonId" value="6239"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="*chromosome*.fasta"/>
                        <property name="fasta.dataSetTitle" value="WormBase C. Elegans data set"/>
                        <property name="fasta.synonymSource" value="WormBase"/>
      <property name="src.data.dir" location="/shared/data/wormbase/ws175"/>
    </source>
    <source name="entrez-organism" type="entrez-organism">
      <!-- this source finds the taxon ids in the objectstore, retrieves
           species name and genus from Entrez into an InterMine format XML
           file, loads that file into a target items DB, then into the final
           objectstore -->
      <property name="src.data.file" location="build/organisms.xml"/>
    </source>
    <source name="update-publications" type="update-publications">
      <!-- this source finds the publication ids (pubmed ids) in the
           objectstore, retrieves the details of the publication from Entrez
           into an InterMine format XML file, loads that file into a target
           items DB, then into the final objectstore dump="true"-->
      <property name="src.data.file" location="build/publications.xml"/>
    </source>
<source name="modencode-metadata" type="chado-db" dump="true">
      <property name="organisms" value="7227"/>
      <property name="dataSourceName" value="modENCODE"/>
      <property name="dataSetTitle" value="modENCODE submission"/>
      <property name="source.db.name" value="modencode-metadata"/>
      <property name="processors"
                value="org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor"/>
      <property name="converter.class"
                value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
    </source>
{'fraction_non_alphanumeric': 0.15711610486891386, 'fraction_numerical': 0.0056179775280898875, 'mean_word_length': 3.793836026331538, 'pattern_counts': {'":': 0, '<': 237, '<?xml version=': 0, '>': 237, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 10}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1027145', 'n_tokens_mistral': 4977, 'n_tokens_neox': 4760, 'n_words': 813}