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Add seasonal-flu/open and seasonal-flu/gisaid #1374

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8e759c4
manifest: Split seasonal-flu into gisaid vs open builds
joverlee521 Aug 17, 2026
62ce573
Update seasonal-flu redirects
joverlee521 Aug 17, 2026
5f4a68e
Fix tests for seasonal-flu redirects
joverlee521 Aug 17, 2026
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287 changes: 187 additions & 100 deletions data/manifest_core.json
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Original file line number Diff line number Diff line change
Expand Up @@ -865,110 +865,197 @@
}
},
"seasonal-flu": {
"lineage": {
"h3n2": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
}
},
"h1n1pdm": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"pandemic": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"pandemic": "",
"default": "2y"
}
},
"default": "ha"
}
},
"vic": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
"data_source": {
"gisaid": {
"lineage": {
"h3n2": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
}
},
"h1n1pdm": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"pandemic": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"pandemic": "",
"default": "2y"
}
},
"default": "ha"
}
},
"vic": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
}
},
"yam": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
}
},
"default": "h3n2"
}
},
"yam": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
"open":{
"lineage": {
"h3n2": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
}
},
"h1n1pdm": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"pandemic": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"pandemic": "",
"default": "2y"
}
},
"default": "ha"
}
},
"vic": {
"segment": {
"ha": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"na": {
"resolution": {
"6m": "",
"2y": "",
"3y": "",
"6y": "",
"12y": "",
"default": "2y"
}
},
"default": "ha"
}
},
"default": "h3n2"
}
},
"default": "h3n2"
"default": "gisaid"
}
},
"tb": {
Expand Down
2 changes: 1 addition & 1 deletion docs/resource-collection.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ The handling of new revision numbers in Heroku review apps is currently still
handled manually.

Once you've pushed up the changes to the revision number in the config, run
the `index-resource.yml workflow <https://github.com/nextstrain/nextstrain.org/actions/workflows/index-resources.yml>__`
the `index-resource.yml workflow <https://github.com/nextstrain/nextstrain.org/actions/workflows/index-resources.yml>`__
using your branch.

After the new index resources JSON has been uploaded to S3, then open the PR for
Expand Down
4 changes: 2 additions & 2 deletions env/production/config.json
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Expand Up @@ -110,6 +110,6 @@
"OIDC_GROUPS_CLAIM": "cognito:groups",
"SESSION_COOKIE_DOMAIN": "nextstrain.org",
"GROUPS_DATA_FILE": "groups.json",
"RESOURCE_INDEX": "s3://nextstrain-inventories/resources/v11.json.gz",
"RESOURCE_INDEX": "s3://nextstrain-inventories/resources/v12.json.gz",
"PLAUSIBLE_ANALYTICS_DOMAIN": "nextstrain.org"
}
}
4 changes: 2 additions & 2 deletions env/testing/config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -108,5 +108,5 @@
"OIDC_USERNAME_CLAIM": "cognito:username",
"OIDC_GROUPS_CLAIM": "cognito:groups",
"GROUPS_DATA_FILE": "groups.json",
"RESOURCE_INDEX": "s3://nextstrain-inventories/resources/v11.json.gz"
}
"RESOURCE_INDEX": "s3://nextstrain-inventories/resources/v12.json.gz"
}
8 changes: 7 additions & 1 deletion src/redirects.js
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Expand Up @@ -172,7 +172,13 @@ const datasetRedirectPatterns = [
* both under flu/ so that avian-flu is more discoverable
*/
['/flu/avian(.*)', '/avian-flu(.*)'],
['/flu/seasonal(.*)', '/seasonal-flu(.*)'],
/**
* Prior to Sept 2026, the core seasonal-flu build were exclusively GISAID builds.
* Since we now have GISAID and open builds, add redirects for the old URLs to
* point to the new GISAID URLs.
*/
['/flu/seasonal/:lineage(h3n2|h1n1pdm|vic|yam)/(.*)', '/seasonal-flu/gisaid/:lineage/(.*)'],
['/seasonal-flu/:lineage(h3n2|h1n1pdm|vic|yam)/(.*)', '/seasonal-flu/gisaid/:lineage/(.*)'],

/**
* Redirect /flu URL itself. We choose seasonal-flu to mimic historical behaviour
Expand Down
14 changes: 7 additions & 7 deletions test/auspice_client_requests.json
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
[
{
"name": "Fetch core Nextstrain dataset (seasonal-flu/h3n2/ha/2y)",
"url": "/charon/getDataset?prefix=/seasonal-flu/h3n2/ha/2y",
"name": "Fetch core Nextstrain dataset (seasonal-flu/gisaid/h3n2/ha/2y)",
"url": "/charon/getDataset?prefix=/seasonal-flu/gisaid/h3n2/ha/2y",
"expectStatusCode": 200,
"responseIsJson": true,
"__comment": "We could define JSON schemas for each API and validate the response here"
Expand All @@ -11,7 +11,7 @@
"url": "/charon/getDataset?prefix=/seasonal-flu",
"expectStatusCode": 307,
"responseIsJson": false,
"redirectsTo": "/charon/getDataset?prefix=seasonal-flu%2Fh3n2%2Fha%2F2y"
"redirectsTo": "/charon/getDataset?prefix=seasonal-flu%2Fgisaid%2Fh3n2%2Fha%2F2y"
},
{
"name": "/flu URLs are not redirected in the charon API (but they are in the RESTful API)",
Expand Down Expand Up @@ -94,13 +94,13 @@
},
{
"name": "Check getDataset API for sidecar file tip-frequencies",
"url": "/charon/getDataset?prefix=/seasonal-flu/h3n2/ha/2y&type=tip-frequencies",
"url": "/charon/getDataset?prefix=/seasonal-flu/gisaid/h3n2/ha/2y&type=tip-frequencies",
"expectStatusCode": 200,
"responseIsJson": true
},
{
"name": "Fetch dataset using /fetch URLs (from S3 staging bucket)",
"url": "/charon/getDataset?prefix=/fetch/staging.nextstrain.org/seasonal-flu_h3n2_ha_2y.json",
"url": "/charon/getDataset?prefix=/fetch/staging.nextstrain.org/seasonal-flu_gisaid_h3n2_ha_2y.json",
"expectStatusCode": 200,
"responseIsJson": true
},
Expand All @@ -122,7 +122,7 @@
},
{
"name": "Fetch sidecar file using /fetch URLs (root-sequence JSON from S3 staging bucket)",
"url": "/charon/getDataset?prefix=/fetch/staging.nextstrain.org/seasonal-flu_h3n2_ha_2y.json&type=root-sequence",
"url": "/charon/getDataset?prefix=/fetch/staging.nextstrain.org/seasonal-flu_gisaid_h3n2_ha_2y.json&type=root-sequence",
"expectStatusCode": 200,
"responseIsJson": true
},
Expand Down Expand Up @@ -216,4 +216,4 @@
"url": "/charon/getNarrative?prefix=/groups/blab/narratives/test_fixture",
"expectStatusCode": 400
}
]
]
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