<commit_before><project>
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="flymine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="flymine-static" type="intermine-items-xml-file">
      <property name="tgt.xml.file" location="datasets.xml"/>
    </source>
    <source name="flybase-dmel-gff" type="flybase-gff">
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/gff"/>
      <property name="gff3.taxonId" value="7227"/>
      <property name="flybase.small" value="true"/>
    </source>
    <source name="flybase-dpse-gff" type="flybase-gff">
      <property name="src.data.dir" location="/shared/data/flybase/Drosophila_pseudoobscura/dpse_r20_20051018/gff"/>
      <property name="gff3.taxonId" value="7237"/>
      <property name="flybase.small" value="true"/>
    </source>
    <source name="flybase-dmel-chromosome-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="dmel-all-chromosome-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/fasta"/>
    </source>
    <source name="flybase-dmel-chromosome-fasta" type="fasta">
      <property name="fasta.taxonId" value="7237"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="dpse-all-chromosome-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dpse/release_2_0/fasta"/>
    </source>
    <!--
    <source name="ensembl-anopheles" type="ensembl">
      <property name="organism" value="AGP"/>
    </source>
    <source name="uniprot-dros" type="uniprot">
      <property name="uniprot.organisms" value="7227"/>
      <property name="src.data.dir" location="/shared/data/uniprot/7.7"/>
    </source>
    <source name="uniprot-malaria" type="uniprot">
      <property name="uniprot.organisms" value="5833"/>
      <property name="src.data.dir" location="/shared/data/uniprot/7.7"/>
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="6239 7165 180454"/>
      <property name="src.data.dir" location="/shared/data/uniprot/7.7"/>
    </source>
    -->
    <source name="rnai" type="rnai">
      <property name="src.data.dir" location="/shared/data/rnai/latest_data"/>
    </source>
    <source name="interpro" type="interpro">
        <!-- property name="interpro.organisms" value="6239,7165,7227,180454"/ -->
      <property name="interpro.organism.taxid.list" value="6239,7165,7227,180454"/>
      <!-- property name="interpro.organism.taxid.list" value="5833"/ -->
    </source>
    <source name="inparanoid-orthologue" type="orthologue">
      <!--property name="src.data.dir" location="/shared/data/orthologues/inparanoid/current"/-->
      <property name="src.data.dir" location="/shared/data/malaria/inparanoid/2006-04-16/"/>
    </source>
    <source name="drosdel" type="drosdel"/>
    <source name="tiling_path" type="tiling_path">
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/shared/data/tiling"/>
    </source>
    <source name="long_oligo" type="long_oligo">
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/shared/data/long_oligo"/>
    </source>
    <source name="phenotype" type="phenotype">
      <property name="src.data.file" location="/shared/data/phenotype/phenotype.ontology"/>
    </source>
    <source name="homophila" type="homophila">
      <property name="src.data.dir" location="/shared/data/homophila/current"/>
    </source>
    <source name="flyreg" type="flyreg">
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/shared/data/flyreg"/>
    </source>
    <source name="protein_structure" type="protein_structure">
      <!-- property name="src.data.dir" location="/shared/data/kenji/data/pfam-3d/model/1557"/ -->
      <property name="src.data.dir" location="/shared/data/kenji"/>
      <property name="data.location" location="/shared/data/kenji/data/pfam-3d/model"/>
    </source>
    <source name="psi-intact" type="psi">
      <property name="src.data.dir" location="/shared/data/malaria/psi/intact/2006-05-26"/>
      <property name="organisms" value="4896 5833 36329"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="/shared/data/gene_ontology/gene_ontology.obo"/>
    </source>
    <source name="go-annotation-gene-identifier" type="go-annotation">
      <property name="ontologyfile" location="/shared/data/gene_ontology/gene_ontology.obo"/>
      <property name="geneattribute" value="identifier"/>
      <!-- currently need to group all files that set Gene.identifier together -->
      <property name="src.data.dir" location="/shared/data/malaria/go-annotation"/>
    </source>
    <source name="go-annotation-gene-organismDbId" type="go-annotation">
      <property name="ontologyfile" location="/shared/data/gene_ontology/gene_ontology.obo"/>
      <property name="geneattribute" value="organismDbId"/>
      <!-- currently need to group all files that set Gene.identifier together -->
      <property name="src.data.dir" location="/shared/data/go-annotation/gene-organismDbId"/>
    </source>
    <!--
      fasta is a bit wierd - tasks depend on the production model and
      retrieve and translate are noops
    -->
    <source name="flybase-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Gene"/>
      <property name="fasta.include" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/fasta"/>
    </source>
    <source name="flybase-cds-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.idSuffix" value="_CDS"/>
      <property name="fasta.className" value="org.flymine.model.genomic.CDS"/>
      <property name="fasta.include" value="dmel-all-CDS-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/fasta"/>
    </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="tgt.xml.file" location="build/organisms.xml"/>
    </source>
  </sources>

  <post-processing>
    <create-utr-references/>
    <calculate-locations/>
    <create-references/>
    <update-orthologues/>
    <make-spanning-locations/>
    <create-chromosome-locations-and-lengths/>
    <create-symmetrical-relation-references/>
    <transfer-sequences/>

    <do-sources/>

    <set-collection-counts/>
    <create-flybase-to-uniprot-refs/>  

    <!-- set-name-and-wildtypefunction/
    TODO: Convert to datasource
   <target name="set-name-and-wildtypefunction" depends="compile-genomic-java-from-db">
     <taskdef name="tsv-file-reader" classname="org.flymine.task.TSVFileReaderWithSynonymTask">
       <classpath refid="models.class.path"/>
     </taskdef>
     <tsv-file-reader oswAlias="osw.production" organismAbbreviation="DM"
                      configurationFile="model/genomic/resources/flymine/drosophila_fullname_reader.properties"
                      dataSourceName="FlyBase">
       <fileset dir="${flybase.chado.melanogaster}">
         <include name="flyBaseFullNameWT.txt"/>
       </fileset>
     </tsv-file-reader>
   </target>

    -->
    <!-- create-overlap-relations-flymine/
    TODO - CORE:
  <target name="create-overlap-relations-flymine" depends="compile-genomic-java-from-db">
    <taskdef name="create-overlap-relations"
             classname="org.flymine.postprocess.CreateOverlapRelationsTask">
      <classpath refid="models.class.path"/>
    </taskdef>
    <create-overlap-relations objectStoreWriter="osw.production"
                              ignoreSelfMatches="false"
                              classesToIgnore="Primer, Contig, CDS, Chromosome, ChromosomeBand, Enhancer, Exon, FivePrimeUTR, Intron, MRNA, PCRProduct, PolyASite, Pseudogene, RRNA, RegulatoryRegion, RepeatRegion, Supercontig, ThreePrimeUTR, TranscriptionStartSite, TransposableElementInsertionSite"/>
  </target>
    -->
    <!-- create-flybase-to-uniprot-refs/
    TODO: Convert to datasource
  <target name="create-flybase-to-uniprot-refs" depends="compile-genomic-java-from-db">
    <taskdef name="fb-uniprot-refs" classname="org.flymine.postprocess.FlyBaseUniProtRefsTask">
      <classpath refid="models.class.path"/>
    </taskdef>
    <fb-uniprot-refs linkFile="${flybase.uniprot.link.file}"
                     objectStoreWriter="osw.production"/>
  </target>

    -->
    <!-- update-publications/
    TODO - CORE:
  <target name="update-publications" depends="compile-genomic-java-from-db">
    <taskdef name="mappings" classname="org.flymine.postprocess.PostProcessTask">
      <classpath refid="models.class.path"/>
    </taskdef>
    <mappings operation="update-publications" objectStore="os.production" outputFile="${build.tmp}/publications.xml"/>

    <taskdef name="load-xml-data"
      classname="org.intermine.dataloader.XmlDataLoaderTask">
      <classpath refid="models.class.path"/>
    </taskdef>

    <load-xml-data integrationWriter="integration.production"
                   xmlFile="${build.tmp}/publications.xml"
                   sourceName="pubmed"
                   ignoreDuplicates="true"/>
  </target>
    -->
    <!-- grant-db-production/
    TODO: Not really post processing but just has to be done sometime...
  <target name="grant-db-production" depends="prepare" - ->
    <!- - grant 'public' user select permission on production db - ->
    <taskdef name="grant" classname="org.intermine.task.GrantTask">
      <classpath refid="models.class.path"/>
    </taskdef>

    <grant database="db.production" user="PUBLIC" perm="SELECT"/>

  </target>
    -->
  </post-processing>

</project>

<commit_msg>Fixes for flymine project.xml - uncomment all sources, get all of flybase GFF and fix flybase-gene-fasta and flybase-cds-fasta properties.<commit_after><project>
  <property name="target.model" value="genomic"/>
  <property name="common.os.prefix" value="common"/>
  <property name="intermine.properties.file" value="flymine.properties"/>
  <property name="default.intermine.properties.file" location="../default.intermine.integrate.properties"/>
  <sources>
    <source name="flymine-static" type="intermine-items-xml-file">
      <property name="tgt.xml.file" location="datasets.xml"/>
    </source>
    <source name="flybase-dmel-gff" type="flybase-gff">
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/gff"/>
      <property name="gff3.taxonId" value="7227"/>
    </source>
    <source name="flybase-dpse-gff" type="flybase-gff">
      <property name="src.data.dir" location="/shared/data/flybase/dpse/release_2_0/gff"/>
      <property name="gff3.taxonId" value="7237"/>
    </source>
    <source name="flybase-dmel-chromosome-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="dmel-all-chromosome-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/fasta"/>
    </source>
    <source name="flybase-dmel-chromosome-fasta" type="fasta">
      <property name="fasta.taxonId" value="7237"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Chromosome"/>
      <property name="fasta.includes" value="dpse-all-chromosome-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dpse/release_2_0/fasta"/>
    </source>
    <source name="ensembl-anopheles" type="ensembl">
      <property name="organism" value="AGP"/>
    </source>
    <source name="uniprot-dros" type="uniprot">
      <property name="uniprot.organisms" value="7227"/>
      <property name="src.data.dir" location="/shared/data/uniprot/7.7"/>
    </source>
    <source name="uniprot-malaria" type="uniprot">
      <property name="uniprot.organisms" value="5833"/>
      <property name="src.data.dir" location="/shared/data/uniprot/7.7"/>
    </source>
    <source name="uniprot" type="uniprot">
      <property name="uniprot.organisms" value="6239 7165 180454"/>
      <property name="src.data.dir" location="/shared/data/uniprot/7.7"/>
    </source>
    <source name="rnai" type="rnai">
      <property name="src.data.dir" location="/shared/data/rnai/latest_data"/>
    </source>
    <source name="interpro" type="interpro">
      <!-- property name="interpro.organisms" value="6239,7165,7227,180454"/ -->
      <property name="interpro.organism.taxid.list" value="6239,7165,7227,180454"/>
      <!-- property name="interpro.organism.taxid.list" value="5833"/ -->
    </source>
    <source name="inparanoid-orthologue" type="orthologue">
      <!--property name="src.data.dir" location="/shared/data/orthologues/inparanoid/current"/-->
      <property name="src.data.dir" location="/shared/data/malaria/inparanoid/2006-04-16/"/>
    </source>
    <source name="drosdel" type="drosdel"/>
    <source name="tiling_path" type="tiling_path">
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/shared/data/tiling"/>
    </source>
    <source name="long_oligo" type="long_oligo">
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/shared/data/long_oligo"/>
    </source>
    <source name="phenotype" type="phenotype">
      <property name="src.data.file" location="/shared/data/phenotype/phenotype.ontology"/>
    </source>
    <source name="homophila" type="homophila">
      <property name="src.data.dir" location="/shared/data/homophila/current"/>
    </source>
    <source name="flyreg" type="flyreg">
      <property name="gff3.taxonId" value="7227"/>
      <property name="src.data.dir" location="/shared/data/flyreg"/>
    </source>
    <source name="protein_structure" type="protein_structure">
      <!-- property name="src.data.dir" location="/shared/data/kenji/data/pfam-3d/model/1557"/ -->
      <property name="src.data.dir" location="/shared/data/kenji"/>
      <property name="data.location" location="/shared/data/kenji/data/pfam-3d/model"/>
    </source>
    <source name="psi-intact" type="psi">
      <property name="src.data.dir" location="/shared/data/malaria/psi/intact/2006-05-26"/>
      <property name="organisms" value="4896 5833 36329"/>
    </source>
    <source name="go" type="go">
      <property name="src.data.file" location="/shared/data/gene_ontology/gene_ontology.obo"/>
    </source>
    <source name="go-annotation-gene-identifier" type="go-annotation">
      <property name="ontologyfile" location="/shared/data/gene_ontology/gene_ontology.obo"/>
      <property name="geneattribute" value="identifier"/>
      <!-- currently need to group all files that set Gene.identifier together -->
      <property name="src.data.dir" location="/shared/data/malaria/go-annotation"/>
    </source>
    <source name="go-annotation-gene-organismDbId" type="go-annotation">
      <property name="ontologyfile" location="/shared/data/gene_ontology/gene_ontology.obo"/>
      <property name="geneattribute" value="organismDbId"/>
      <!-- currently need to group all files that set Gene.identifier together -->
      <property name="src.data.dir" location="/shared/data/go-annotation/gene-organismDbId"/>
    </source>
    <!--
      fasta is a bit wierd - tasks depend on the production model and
      retrieve and translate are noops
    -->
    <source name="flybase-gene-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.className" value="org.flymine.model.genomic.Gene"/>
      <property name="fasta.include" value="dmel-all-gene-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/fasta"/>
    </source>
    <source name="flybase-cds-fasta" type="fasta">
      <property name="fasta.taxonId" value="7227"/>
      <property name="fasta.idSuffix" value="_CDS"/>
      <property name="fasta.className" value="org.flymine.model.genomic.CDS"/>
      <property name="fasta.include" value="dmel-all-CDS-*.fasta"/>
      <property name="src.data.dir" location="/shared/data/flybase/dmel/release_4_2_1/fasta"/>
    </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="tgt.xml.file" location="build/organisms.xml"/>
    </source>
  </sources>

  <post-processing>
    <create-utr-references/>
    <calculate-locations/>
    <create-references/>
    <update-orthologues/>
    <make-spanning-locations/>
    <create-chromosome-locations-and-lengths/>
    <create-symmetrical-relation-references/>
    <transfer-sequences/>

    <do-sources/>

    <set-collection-counts/>
    <create-flybase-to-uniprot-refs/>  

    <!-- set-name-and-wildtypefunction/
    TODO: Convert to datasource
   <target name="set-name-and-wildtypefunction" depends="compile-genomic-java-from-db">
     <taskdef name="tsv-file-reader" classname="org.flymine.task.TSVFileReaderWithSynonymTask">
       <classpath refid="models.class.path"/>
     </taskdef>
     <tsv-file-reader oswAlias="osw.production" organismAbbreviation="DM"
                      configurationFile="model/genomic/resources/flymine/drosophila_fullname_reader.properties"
                      dataSourceName="FlyBase">
       <fileset dir="${flybase.chado.melanogaster}">
         <include name="flyBaseFullNameWT.txt"/>
       </fileset>
     </tsv-file-reader>
   </target>

    -->
    <!-- create-overlap-relations-flymine/
    TODO - CORE:
  <target name="create-overlap-relations-flymine" depends="compile-genomic-java-from-db">
    <taskdef name="create-overlap-relations"
             classname="org.flymine.postprocess.CreateOverlapRelationsTask">
      <classpath refid="models.class.path"/>
    </taskdef>
    <create-overlap-relations objectStoreWriter="osw.production"
                              ignoreSelfMatches="false"
                              classesToIgnore="Primer, Contig, CDS, Chromosome, ChromosomeBand, Enhancer, Exon, FivePrimeUTR, Intron, MRNA, PCRProduct, PolyASite, Pseudogene, RRNA, RegulatoryRegion, RepeatRegion, Supercontig, ThreePrimeUTR, TranscriptionStartSite, TransposableElementInsertionSite"/>
  </target>
    -->
    <!-- create-flybase-to-uniprot-refs/
    TODO: Convert to datasource
  <target name="create-flybase-to-uniprot-refs" depends="compile-genomic-java-from-db">
    <taskdef name="fb-uniprot-refs" classname="org.flymine.postprocess.FlyBaseUniProtRefsTask">
      <classpath refid="models.class.path"/>
    </taskdef>
    <fb-uniprot-refs linkFile="${flybase.uniprot.link.file}"
                     objectStoreWriter="osw.production"/>
  </target>

    -->
    <!-- update-publications/
    TODO - CORE:
  <target name="update-publications" depends="compile-genomic-java-from-db">
    <taskdef name="mappings" classname="org.flymine.postprocess.PostProcessTask">
      <classpath refid="models.class.path"/>
    </taskdef>
    <mappings operation="update-publications" objectStore="os.production" outputFile="${build.tmp}/publications.xml"/>

    <taskdef name="load-xml-data"
      classname="org.intermine.dataloader.XmlDataLoaderTask">
      <classpath refid="models.class.path"/>
    </taskdef>

    <load-xml-data integrationWriter="integration.production"
                   xmlFile="${build.tmp}/publications.xml"
                   sourceName="pubmed"
                   ignoreDuplicates="true"/>
  </target>
    -->
    <!-- grant-db-production/
    TODO: Not really post processing but just has to be done sometime...
  <target name="grant-db-production" depends="prepare" - ->
    <!- - grant 'public' user select permission on production db - ->
    <taskdef name="grant" classname="org.intermine.task.GrantTask">
      <classpath refid="models.class.path"/>
    </taskdef>

    <grant database="db.production" user="PUBLIC" perm="SELECT"/>

  </target>
    -->
  </post-processing>

</project>


{'fraction_non_alphanumeric': 0.16593406593406593, 'fraction_numerical': 0.015671285236502627, 'mean_word_length': 3.487778730703259, 'pattern_counts': {'":': 0, '<': 358, '<?xml version=': 0, '>': 358, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 21}, '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': '6569632', 'n_tokens_mistral': 7013, 'n_tokens_neox': 6627, 'n_words': 1061}