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UPDATING_EXTERNAL.md

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Update SeqCode Registry using external databases

Update data using LPSN download

  1. To protect manually modified data, run in the app folder: RAILS_ENV=production bundle exec rake lpsn:protect[/path/to/last/data.csv]
  2. Go to https://lpsn.dsmz.de/downloads
  3. Download the CSV file
  4. Run in the app folder: RAILS_ENV=production bundle exec rake lpsn:import[/path/to/data.csv]
  5. Review the names with special messages (if any)
  6. Review all newly created names

Update data using GTDB release

  1. Create a release directory and download taxonomy tables: 
    mkdir ~/gtdb_release
cd ~/gtdb_release
wget https://data.gtdb.ecogenomic.org/releases/latest/ar53_taxonomy.tsv.gz
wget https://data.gtdb.ecogenomic.org/releases/latest/bac120_taxonomy.tsv.gz
  2. Run in the app folder: RAILS_ENV=production bundle exec rake gtdb:import[$HOME/gtdb_release]
  3. Review all newly created names
  4. Update the release information in app/helpers/placements_helper.rb

Update data using NCBI Taxonomy dump

  1. Download and untarball the taxonomy dump: 
    mkdir ~/ncbi_taxdump
cd ~/ncbi_taxdump
wget https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
tar -zxvf taxdump.tar.gz
  2. Run in the app folder: RAILS_ENV=production bundle exec rake ncbi:import[$HOME/ncbi_taxdump]
  3. Review all newly created names
  4. Update the release information in app/helpers/placements_helper.rb

Update external databases with SeqCode Registry data

Update NCBI LinkOut

  1. Download the complete linkout XML: 
    wget -O resources_1.xml 'https://registry.seqco.de/names/linkout.xml?per_page=10000&page=1'
wget -O resources_2.xml 'https://registry.seqco.de/names/linkout.xml?per_page=10000&page=2'
wget -O resources_3.xml 'https://registry.seqco.de/names/linkout.xml?per_page=10000&page=3'
wget -O resources_4.xml 'https://registry.seqco.de/names/linkout.xml?per_page=10000&page=4'
  2. Upload to the private FTP

Update Wikidata

This should automatically update every day, but just in case that fails or needs to be manually performed:

  1. Run in the app folder: RAILS_ENV=production bundle exec rake wikidata:push