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Merge pull request #1746 from nextstrain/fix-metadata-index-dtype
io/read_metadata: Fix dtype for the index column
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34 changes: 34 additions & 0 deletions
34
tests/functional/export_v2/cram/metadata-with-float-strains.t
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| Setup | ||
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| $ source "$TESTDIR"/_setup.sh | ||
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| Create files for testing. | ||
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| $ cat >metadata.tsv <<~~ | ||
| > strain field_A field_B | ||
| > 1.00 AA AAA | ||
| > 2.00 BB BBB | ||
| > 3.00 CC CCC | ||
| > 4.00 DD DDD | ||
| > 5.00 EE EEE | ||
| > 6.00 FF FFF | ||
| > ~~ | ||
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| $ cat >tree.nwk <<~~ | ||
| > (1.00:1,(2.00:1,3.00:1)internalBC:2,(4.00:3,5.00:4,6.00:1)internalDEF:5)ROOT:0; | ||
| > ~~ | ||
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| Run export with tree and metadata with additional columns. | ||
| The metadata should match with the tree even though the names are floats | ||
| because we force the index column to be strings. | ||
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| $ ${AUGUR} export v2 \ | ||
| > --tree tree.nwk \ | ||
| > --metadata metadata.tsv \ | ||
| > --metadata-columns "field_A" "field_B" \ | ||
| > --maintainers "Nextstrain Team" \ | ||
| > --output dataset.json > /dev/null | ||
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| $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" "$TESTDIR/../data/dataset-with-float-strains.json" dataset.json \ | ||
| > --exclude-paths "root['meta']['updated']" "root['meta']['maintainers']" | ||
| {} |
121 changes: 121 additions & 0 deletions
121
tests/functional/export_v2/data/dataset-with-float-strains.json
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,121 @@ | ||
| { | ||
| "version": "v2", | ||
| "meta": { | ||
| "updated": "2025-02-06", | ||
| "maintainers": [ | ||
| { | ||
| "name": "Nextstrain Team" | ||
| } | ||
| ], | ||
| "colorings": [], | ||
| "filters": [], | ||
| "panels": [ | ||
| "tree" | ||
| ] | ||
| }, | ||
| "tree": { | ||
| "name": "ROOT", | ||
| "node_attrs": { | ||
| "div": 0 | ||
| }, | ||
| "branch_attrs": {}, | ||
| "children": [ | ||
| { | ||
| "name": "1.00", | ||
| "node_attrs": { | ||
| "div": 1.0, | ||
| "field_A": { | ||
| "value": "AA" | ||
| }, | ||
| "field_B": { | ||
| "value": "AAA" | ||
| } | ||
| }, | ||
| "branch_attrs": {} | ||
| }, | ||
| { | ||
| "name": "internalBC", | ||
| "node_attrs": { | ||
| "div": 2.0 | ||
| }, | ||
| "branch_attrs": {}, | ||
| "children": [ | ||
| { | ||
| "name": "2.00", | ||
| "node_attrs": { | ||
| "div": 3.0, | ||
| "field_A": { | ||
| "value": "BB" | ||
| }, | ||
| "field_B": { | ||
| "value": "BBB" | ||
| } | ||
| }, | ||
| "branch_attrs": {} | ||
| }, | ||
| { | ||
| "name": "3.00", | ||
| "node_attrs": { | ||
| "div": 3.0, | ||
| "field_A": { | ||
| "value": "CC" | ||
| }, | ||
| "field_B": { | ||
| "value": "CCC" | ||
| } | ||
| }, | ||
| "branch_attrs": {} | ||
| } | ||
| ] | ||
| }, | ||
| { | ||
| "name": "internalDEF", | ||
| "node_attrs": { | ||
| "div": 5.0 | ||
| }, | ||
| "branch_attrs": {}, | ||
| "children": [ | ||
| { | ||
| "name": "4.00", | ||
| "node_attrs": { | ||
| "div": 8.0, | ||
| "field_A": { | ||
| "value": "DD" | ||
| }, | ||
| "field_B": { | ||
| "value": "DDD" | ||
| } | ||
| }, | ||
| "branch_attrs": {} | ||
| }, | ||
| { | ||
| "name": "5.00", | ||
| "node_attrs": { | ||
| "div": 9.0, | ||
| "field_A": { | ||
| "value": "EE" | ||
| }, | ||
| "field_B": { | ||
| "value": "EEE" | ||
| } | ||
| }, | ||
| "branch_attrs": {} | ||
| }, | ||
| { | ||
| "name": "6.00", | ||
| "node_attrs": { | ||
| "div": 6.0, | ||
| "field_A": { | ||
| "value": "FF" | ||
| }, | ||
| "field_B": { | ||
| "value": "FFF" | ||
| } | ||
| }, | ||
| "branch_attrs": {} | ||
| } | ||
| ] | ||
| } | ||
| ] | ||
| } | ||
| } |