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adapting-mags.md

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Adapting MAGs View to a different MAG catalog

The app ships with a baked-in set of MAG metadata (the table on the Genomes page) and per-genome detail JSON files (used on each genome detail page). To swap in another catalog, update both pieces of data so they stay in sync.

1) Prepare the MAG metadata CSV

The genome table is powered by a CSV string embedded in src/Data/Blobs/MAGs.elm. Create a CSV file with the following header row and columns:

id,samples_id,taxonomy,completeness,contamination,genome_size,#16s_rrna,#5s_rrna,#23s_rrna,#trna,nr_contigs,nr_genes,is_representative,binning_tool,assembly_method,comment,file_size,file_sha256

Notes:

  • samples_id accepts comma-separated sample identifiers (e.g., S001,S002).
  • is_representative should be True or False (capitalized) to match the Elm decoder.
  • Numeric columns must be parseable as numbers; leave comment empty if not applicable.

Once the CSV looks correct, replace the string literal assigned to magsBlob in src/Data/Blobs/MAGs.elm with the new CSV content (keep the surrounding String.trim """ ... """ structure intact). The LoadData.loadData helper will parse it at startup.

2) Add per-genome JSON files

Each genome detail page fetches /genome-data/<MAG_ID>.json from the static/genome-data folder. For every id in the CSV, create a matching JSON file named <MAG_ID>.json with this structure:

{
  "16S": [
    { "Seq": "<16S_sequence>", "OTU": "<otu_metadata>" }
  ],
  "ARGs": [
    {
      "Sequence": "<amino_acid_sequence>",
      "ArgName": "<ARG_name>",
      "ARO": "<ARO_identifier>",
      "Cut_Off": "<e.g., Perfect/Strict>",
      "Identity": <float>,
      "Coverage": <float>,
      "InResfinder": <true|false>,
      "Drug Class": "<drug_class_label>"
    }
  ]
}

You can include multiple entries in the 16S and ARGs arrays. Make sure the JSON is compact or pretty-printed—Elm’s decoder only depends on the field names and types.

3) Verify locally

After updating the CSV and JSON files:

  1. Run npx elm-land server to rebuild the site.
  2. Visit /genomes and click into a genome to ensure the metadata and ARG/16S sections render without parse errors.

Keep the CSV and JSON files in sync: every MAG listed in the CSV should have a matching JSON file, and vice versa.