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Rename tables and columns in database #1

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lohrd opened this issue Jul 21, 2020 · 1 comment
Open

Rename tables and columns in database #1

lohrd opened this issue Jul 21, 2020 · 1 comment

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@lohrd
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lohrd commented Jul 21, 2020

  • The database's entities should be renamed so that they follow proper db naming conventions
  • This will help with readability for the columns on each table as well
  • The following changes should be implemented in database:

Tables:

  • Runs => run
  • FamilySections => family
  • AccessionSections => accession
  • FastaSections => fasta

Runs(run) Table Column Changes:

  • RunId => run_id
  • Sra => sra
  • FileName => file_name
  • Genome => genome
  • Date => date

FamilySections(family) Table Column Changes:

  • FamilySectionId => family_id
  • FamilySectionLineId => family_line_id
  • RunId => run_id
  • Sra => sra
  • Family => family_name
  • Score => score
  • Aln => aligned_reads
  • Glb => global_aligned_reads
  • PanLen => pangenome_length
  • Cvg => coverage_cartoon
  • Top => top_accession
  • TopAln => top_accession_aligned_reads
  • TopLen => top_accession_length
  • TopName => top_accession_name

AccessionSections(accession) Table Column Changes:

  • AccessionSectionId => accession_id
  • AccessionSectionLineId => accession_line_id
  • RunId => run_id
  • Sra => sra
  • Fam => family_name
  • Acc => accession_name
  • PctId => percent_identity
  • Aln => aligned_reads
  • Glb => global_aligned_reads
  • Len => length
  • CvgPct => coverage_percentage
  • Depth => depth
  • Cvg => coverage_cartoon
  • Name => study_name

FastaSections(fasta) Table Column Changes:

  • FastaSectionId => fasta_id
  • FastaSectionLineId => fasta_line_id
  • RunId => run_id
  • Sra => sra
  • SequenceId => sequence_id
  • Sequence => sequence
@victorlin
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with the naming discussion in #2 (converted to a wiki page here), we should probably change accessionreferences to use genbank.

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