<commit_before><webconfig>
  <class className="org.flymine.model.genomic.DataSet">
    <fields>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.Publication">
    <fields>
      <fieldconfig fieldExpr="firstAuthor"/>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="year"/>
      <fieldconfig fieldExpr="journal"/>
      <fieldconfig fieldExpr="volume"/>
      <fieldconfig fieldExpr="pages"/>
      <fieldconfig fieldExpr="pubMedId"/>
    </fields>

    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Author">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.Analysis">
    <fields>
      <fieldconfig fieldExpr="publication.title"/>
      <fieldconfig fieldExpr="publication.firstAuthor"/>
      <fieldconfig fieldExpr="publication.journal"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.Clone">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.DataSource">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
    <longdisplayers>
      <displayer src="/model/dataSourceLong.jsp"/>
    </longdisplayers>
    <tabledisplayer src="/model/dataSourceShort.jsp"/>
  </class>

  <class className="org.flymine.model.genomic.Organism">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="taxonId" />
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.LocatedSequenceFeature">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
    <longdisplayers>
      <displayer src="/model/locatedSequenceFeatureImage.jsp"/>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
    <bagdisplayers>
      <graphdisplayer title="Chromosome Distribution" domainLabel="Chromosome" rangeLabel="Count" dataSetLoader="org.intermine.bio.web.widget.ChromosomeDistributionDataSetLdr"
                      toolTipGen="org.intermine.web.logic.widget.ToolTipGenerator" urlGen="org.intermine.bio.web.widget.ChromosomeDistributionGraphURLGenerator"
                      description="Actual: number of features in this list found on each chromosome.  Expected: given the total number of featres on the chromosome and the number in this list, the number of features expected to be found on each chromosome." 
                      graphType="BarChart"/>
    </bagdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Exon">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="chromosomeLocation"  displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInInlineCollection="false"/>
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Comment">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="text"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.CDS">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInInlineCollection="false"/>
      <fieldconfig fieldExpr="organism.name"/>
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Gene">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
      <displayer src="/model/locatedSequenceFeatureImage.jsp"/>
    </longdisplayers>
    <bagdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
 
      <graphdisplayer title="Chromosome Distribution" domainLabel="Chromosome" rangeLabel="Gene Count" dataSetLoader="org.intermine.bio.web.widget.ChromosomeDistributionDataSetLdr" 
	 	      toolTipGen="org.intermine.web.logic.widget.ToolTipGenerator" urlGen="org.intermine.bio.web.widget.ChromosomeDistributionGraphURLGenerator" 
	 	      description="Actual: number of genes in this list found on each chromosome.  Expected: given the total number of genes on the chromosome and the number of genes in this list, the number of genes expected to be found on each chromosome."  
	 	      graphType="BarChart"/> 
      

      <bagtabledisplayer title="Pathway Information (KEGG)" type="Pathway" collectionName="pathways" urlGen="org.intermine.bio.web.widget.PathwayURLQuery" 
	 	         description="Most common &lt;a href=&quot;http://www.genome.jp/kegg/&quot; target=&quot;_new&quot;&gt;KEGG pathways&lt;/a&gt; for this list." /> 
      

      <enrichmentwidgetdisplayer title="Gene Ontology Enrichment"
                                 link="org.intermine.bio.web.widget.GoStatURLQuery"
                                 ldr="org.intermine.bio.web.widget.GoStatLdr"
                                 descr="Go terms enriched for genes in this list."
                                 label="GO Term"
                                 filters="biological_process,cellular_component,molecular_function"
                                 filterLabel="Ontology"
                                 max="0.10" />

<!--
      <enrichmentwidgetdisplayer title="Protein Domain Enrichment"
                                 link="org.flymine.web.widget.ProteinDomainURLQuery"
                                 ldr="org.flymine.web.widget.ProteinDomainLdr"
                                 label="Protein Domain"
                                 descr="Protein Domains enriched for genes in this list."
                                 filters=""
                                 filterLabel=""
                                 max="0.10"  />
-->
                                 
      <enrichmentwidgetdisplayer title="Publication Enrichment"
                                 link="org.intermine.bio.web.widget.PublicationURLQuery"
                                 ldr="org.intermine.bio.web.widget.PublicationLdr"
                                 label="Publication"
                                 descr="Publications enriched for genes in this list."
                                 filters=""
                                 filterLabel=""
                                 max="0.10"  />

      <!-- removed until we can optimise the query  
	   <enrichmentwidgetdisplayer title="Tiffin Motif Enrichment"  
	 	                      link="org.flymine.web.widget.TiffinURLQuery"  
	 	                      controller="org.flymine.web.widget.TiffinLdr"  
	 	                      description="Tiffin Motifs enriched for genes in this list."  
	 	                      max="0.10"  
	 	                      externalLink="http://servlet.sanger.ac.uk/tiffin/motif.jsp?acc=" 
	 	                      append=".2" /> 
	   --> 
      <commit_msg>Removed KEGG widget from modmine.<commit_after><webconfig>
  <class className="org.flymine.model.genomic.DataSet">
    <fields>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.Publication">
    <fields>
      <fieldconfig fieldExpr="firstAuthor"/>
      <fieldconfig fieldExpr="title"/>
      <fieldconfig fieldExpr="year"/>
      <fieldconfig fieldExpr="journal"/>
      <fieldconfig fieldExpr="volume"/>
      <fieldconfig fieldExpr="pages"/>
      <fieldconfig fieldExpr="pubMedId"/>
    </fields>

    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Author">
    <fields>
      <fieldconfig fieldExpr="name"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.Analysis">
    <fields>
      <fieldconfig fieldExpr="publication.title"/>
      <fieldconfig fieldExpr="publication.firstAuthor"/>
      <fieldconfig fieldExpr="publication.journal"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.Clone">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.DataSource">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="url" doNotTruncate="true"/>
    </fields>
    <longdisplayers>
      <displayer src="/model/dataSourceLong.jsp"/>
    </longdisplayers>
    <tabledisplayer src="/model/dataSourceShort.jsp"/>
  </class>

  <class className="org.flymine.model.genomic.Organism">
    <fields>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="taxonId" />
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.LocatedSequenceFeature">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
    <longdisplayers>
      <displayer src="/model/locatedSequenceFeatureImage.jsp"/>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
    <bagdisplayers>
      <graphdisplayer title="Chromosome Distribution" domainLabel="Chromosome" rangeLabel="Count" dataSetLoader="org.intermine.bio.web.widget.ChromosomeDistributionDataSetLdr"
                      toolTipGen="org.intermine.web.logic.widget.ToolTipGenerator" urlGen="org.intermine.bio.web.widget.ChromosomeDistributionGraphURLGenerator"
                      description="Actual: number of features in this list found on each chromosome.  Expected: given the total number of featres on the chromosome and the number in this list, the number of features expected to be found on each chromosome." 
                      graphType="BarChart"/>
    </bagdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Exon">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="chromosomeLocation"  displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInInlineCollection="false"/>
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Comment">
    <fields>
      <fieldconfig fieldExpr="type"/>
      <fieldconfig fieldExpr="text"/>
    </fields>
  </class>

  <class className="org.flymine.model.genomic.CDS">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
      <fieldconfig fieldExpr="gene.primaryIdentifier" showInInlineCollection="false"/>
      <fieldconfig fieldExpr="organism.name"/>
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
    </longdisplayers>
  </class>

  <class className="org.flymine.model.genomic.Gene">
    <fields>
      <fieldconfig fieldExpr="primaryIdentifier"/>
      <fieldconfig fieldExpr="secondaryIdentifier"/>
      <fieldconfig fieldExpr="symbol"/>
      <fieldconfig fieldExpr="name"/>
      <fieldconfig fieldExpr="chromosomeLocation" displayer="/model/chromosomeLocDisplayer.jsp" showInResults="false" />
      <fieldconfig fieldExpr="length" displayer="/model/sequenceShortDisplayerWithField.jsp" />
    </fields>
    <longdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
      <displayer src="/model/locatedSequenceFeatureImage.jsp"/>
    </longdisplayers>
    <bagdisplayers>
      <displayer src="attributeLinkDisplayer.tile"/>
 
      <graphdisplayer title="Chromosome Distribution" domainLabel="Chromosome" rangeLabel="Gene Count" dataSetLoader="org.intermine.bio.web.widget.ChromosomeDistributionDataSetLdr" 
	 	      toolTipGen="org.intermine.web.logic.widget.ToolTipGenerator" urlGen="org.intermine.bio.web.widget.ChromosomeDistributionGraphURLGenerator" 
	 	      description="Actual: number of genes in this list found on each chromosome.  Expected: given the total number of genes on the chromosome and the number of genes in this list, the number of genes expected to be found on each chromosome."  
	 	      graphType="BarChart"/> 
      

      <enrichmentwidgetdisplayer title="Gene Ontology Enrichment"
                                 link="org.intermine.bio.web.widget.GoStatURLQuery"
                                 ldr="org.intermine.bio.web.widget.GoStatLdr"
                                 descr="Go terms enriched for genes in this list."
                                 label="GO Term"
                                 filters="biological_process,cellular_component,molecular_function"
                                 filterLabel="Ontology"
                                 max="0.10" />

<!--
      <enrichmentwidgetdisplayer title="Protein Domain Enrichment"
                                 link="org.flymine.web.widget.ProteinDomainURLQuery"
                                 ldr="org.flymine.web.widget.ProteinDomainLdr"
                                 label="Protein Domain"
                                 descr="Protein Domains enriched for genes in this list."
                                 filters=""
                                 filterLabel=""
                                 max="0.10"  />
-->
                                 
      <enrichmentwidgetdisplayer title="Publication Enrichment"
                                 link="org.intermine.bio.web.widget.PublicationURLQuery"
                                 ldr="org.intermine.bio.web.widget.PublicationLdr"
                                 label="Publication"
                                 descr="Publications enriched for genes in this list."
                                 filters=""
                                 filterLabel=""
                                 max="0.10"  />

{'fraction_non_alphanumeric': 0.11705706849488987, 'fraction_numerical': 0.0013965593855138703, 'mean_word_length': 2.638337182448037, 'pattern_counts': {'":': 0, '<': 250, '<?xml version=': 0, '>': 250, 'https://': 0, 'lorem ipsum': 0, 'www.': 1, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 42, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3106729', 'n_tokens_mistral': 4380, 'n_tokens_neox': 4159, 'n_words': 736}