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Fix order of exported colorings from augur export v2 when color by metadata is used #1177

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Fix order of exported colorings from augur export v2 when color by metadata is used #1177

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e68be8d
Add test for export with color by metadata
huddlej Mar 10, 2023
41b399e
Pretty print DeepDiff output
huddlej Mar 10, 2023
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20 changes: 12 additions & 8 deletions scripts/diff_jsons.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
parser.add_argument("--significant-digits", type=int, default=5, help="number of significant digits to use when comparing numeric values")
parser.add_argument("--exclude-paths", nargs="+", help="list of paths to exclude from consideration when performing a diff", default=["root['generated_by']['version']"])
parser.add_argument("--exclude-regex-paths", nargs="+", help="list of path regular expressions to exclude from consideration when performing a diff")
parser.add_argument("--pretty", action="store_true", help="use DeepDiff's pretty method when printing differences")

args = parser.parse_args()

Expand All @@ -24,12 +25,15 @@
with open(args.second_json, "r") as fh:
second_json = json.load(fh)

print(
deepdiff.DeepDiff(
first_json,
second_json,
significant_digits=args.significant_digits,
exclude_paths=args.exclude_paths,
exclude_regex_paths=args.exclude_regex_paths,
)
difference = deepdiff.DeepDiff(
first_json,
second_json,
significant_digits=args.significant_digits,
exclude_paths=args.exclude_paths,
exclude_regex_paths=args.exclude_regex_paths,
)

if args.pretty:
difference = difference.pretty()

print(difference)
16 changes: 16 additions & 0 deletions tests/functional/export_v2.t
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Original file line number Diff line number Diff line change
Expand Up @@ -166,5 +166,21 @@ Run export with metadata and external colors TSV that contains zero values.
{}
$ rm -f "$TMP/dataset6.json"

Run export with metadata and color by a metadata column ("custom_trait") in addition to colorings defined in the node data.

$ ${AUGUR} export v2 \
> --tree export_v2/tree.nwk \
> --metadata export_v2/dataset1_metadata_with_strain.tsv \
> --node-data export_v2/div_node-data.json export_v2/location_node-data.json \
> --auspice-config export_v2/auspice_config1.json \
> --maintainers "Nextstrain Team" \
> --color-by-metadata custom_trait \
> --output "$TMP/dataset_with_color_from_metadata.json" > /dev/null
WARNING: [config file] Trait 'custom_trait' is missing type information. We've guessed 'categorical'.
\s{0} (re)

$ python3 "$TESTDIR/../../scripts/diff_jsons.py" export_v2/dataset_with_color_from_metadata.json "$TMP/dataset_with_color_from_metadata.json" \
> --exclude-paths "root['meta']['updated']" "root['meta']['maintainers']" --pretty
$ rm -f "$TMP/dataset1.json"

$ popd > /dev/null
14 changes: 7 additions & 7 deletions tests/functional/export_v2/dataset1_metadata_with_strain.tsv
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
strain div mutation_length
tipA 1 1
tipB 3 1
tipC 3 1
tipD 8 3
tipE 9 4
tipF 6 1
strain div mutation_length custom_trait
tipA 1 1 A
tipB 3 1 A
tipC 3 1 B
tipD 8 3 B
tipE 9 4 C
tipF 6 1 D
248 changes: 248 additions & 0 deletions tests/functional/export_v2/dataset_with_color_from_metadata.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,248 @@
{
"meta": {
"colorings": [
{
"key": "location",
"legend": [
{
"display": "\u03b1",
"value": "alpha"
},
{
"value": "beta"
}
],
"scale": [
[
"beta",
"#bd0026"
],
[
"gamma",
"#6a51a3"
]
],
"title": "Location",
"type": "categorical"
},
{
"key": "mutation_length",
"legend": [
{
"bounds": [
-1,
2
],
"display": "0-2",
"value": 1
},
{
"bounds": [
2,
5
],
"display": "3-5",
"value": 3
},
{
"bounds": [
5,
10
],
"display": ">5",
"value": 5
}
],
"scale": [
[
1,
"#081d58"
],
[
3,
"#1d91c0"
],
[
5,
"#c7e9b4"
]
],
"title": "Mutations per branch",
"type": "continuous"
},
{
"key": "location",
"legend": [
{
"display": "\u03b1",
"value": "alpha"
},
{
"value": "beta"
}
],
"scale": [
[
"beta",
"#bd0026"
],
[
"gamma",
"#6a51a3"
]
],
"title": "Location",
"type": "categorical"
},
{
"key": "custom_trait",
"title": "custom_trait",
"type": "categorical"
}
],
"filters": [
"location",
"custom_trait"
],
"panels": [
"tree"
],
"updated": "2021-06-09"
},
"tree": {
"branch_attrs": {},
"children": [
{
"branch_attrs": {},
"name": "tipA",
"node_attrs": {
"div": 1,
"location": {
"value": "delta"
},
"mutation_length": {
"value": 1
},
"custom_trait": {
"value": "A"
}
}
},
{
"branch_attrs": {},
"children": [
{
"branch_attrs": {},
"name": "tipB",
"node_attrs": {
"div": 3,
"location": {
"value": "gamma"
},
"mutation_length": {
"value": 1
},
"custom_trait": {
"value": "A"
}
}
},
{
"branch_attrs": {},
"name": "tipC",
"node_attrs": {
"div": 3,
"location": {
"value": "gamma"
},
"mutation_length": {
"value": 1
},
"custom_trait": {
"value": "B"
}
}
}
],
"name": "internalBC",
"node_attrs": {
"div": 2,
"mutation_length": {
"value": 2
}
}
},
{
"branch_attrs": {},
"children": [
{
"branch_attrs": {},
"name": "tipD",
"node_attrs": {
"div": 8,
"location": {
"value": "alpha"
},
"mutation_length": {
"value": 3
},
"custom_trait": {
"value": "B"
}
}
},
{
"branch_attrs": {},
"name": "tipE",
"node_attrs": {
"div": 9,
"location": {
"value": "alpha"
},
"mutation_length": {
"value": 4
},
"custom_trait": {
"value": "C"
}
}
},
{
"branch_attrs": {},
"name": "tipF",
"node_attrs": {
"div": 6,
"location": {
"value": "beta"
},
"mutation_length": {
"value": 1
},
"custom_trait": {
"value": "D"
}
}
}
],
"name": "internalDEF",
"node_attrs": {
"div": 5,
"location": {
"value": "alpha"
},
"mutation_length": {
"value": 5
}
}
}
],
"name": "ROOT",
"node_attrs": {
"div": 0,
"mutation_length": {
"value": 0
}
}
},
"version": "v2"
}