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data: run migration script to include ref_node info
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@rneher
rneher committed Jun 21, 2024
1 parent b2fbfb4 commit bf4e39e
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Showing 8 changed files with 124 additions and 276 deletions.
11 changes: 6 additions & 5 deletions data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json
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Expand Up @@ -155,15 +155,16 @@
"extensions": {
"nextclade": {
"clade_node_attrs": [
{
"name": "short-clade",
"displayName": "short-clade",
"description": ""
},
{
"name": "subclade",
"displayName": "Subclade",
"description": "Experimental fine-grained subclade annotation."
},
{
"name": "short-clade",
"displayName": "short-clade",
"description": "",
"skipAsReference": true
}
],
"ref_nodes": {
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11 changes: 6 additions & 5 deletions data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json
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Original file line number Diff line number Diff line change
Expand Up @@ -155,15 +155,16 @@
"extensions": {
"nextclade": {
"clade_node_attrs": [
{
"name": "short-clade",
"displayName": "short-clade",
"description": ""
},
{
"name": "subclade",
"displayName": "Subclade",
"description": "Experimental fine-grained subclade annotation."
},
{
"name": "short-clade",
"displayName": "short-clade",
"description": "",
"skipAsReference": true
}
],
"ref_nodes": {
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3 changes: 2 additions & 1 deletion data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json
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Original file line number Diff line number Diff line change
Expand Up @@ -163,7 +163,8 @@
{
"name": "short-clade",
"displayName": "short-clade",
"description": ""
"description": "",
"skipAsReference": true
}
],
"ref_nodes": {
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75 changes: 22 additions & 53 deletions data/nextstrain/sars-cov-2/BA.2.86/tree.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1778,14 +1778,14 @@
"displayName": "Nextstrain Clade",
"description": "Nextstrain Clade",
"hideInWeb": true,
"skipAsReference": true
"skipAsReference": false
},
{
"name": "clade_who",
"displayName": "WHO name",
"description": "Greek letter WHO name",
"hideInWeb": true,
"skipAsReference": false
"skipAsReference": true
},
{
"name": "clade_display",
Expand Down Expand Up @@ -1817,14 +1817,24 @@
"qry": [
{
"clade": [
"20A"
"20A",
"20B",
"20C",
"20E",
"20F",
"20G"
]
}
],
"node": [
{
"clade": [
"20A"
"20A",
"20B",
"20C",
"20E",
"20F",
"20G"
],
"searchAlgo": "ancestor-earliest"
}
Expand Down Expand Up @@ -1875,14 +1885,19 @@
"qry": [
{
"clade": [
"20A"
"20A",
"20B",
"20C",
"20E",
"20F",
"20G"
]
}
],
"node": [
{
"name": [
"NODE_0000000"
"B.1"
]
}
]
Expand Down Expand Up @@ -1914,7 +1929,7 @@
"node": [
{
"name": [
"NODE_0000862"
"XBB.1.16"
]
}
]
Expand Down Expand Up @@ -1945,29 +1960,6 @@
}
]
},
{
"name": "BA.2.86",
"displayName": "BA.2.86 (23I)",
"description": "Full search by name: NODE_0000659 (only for samples having clade 22I)",
"criteria": [
{
"qry": [
{
"clade": [
"23I"
]
}
],
"node": [
{
"name": [
"NODE_0000659"
]
}
]
}
]
},
{
"name": "XBB.1.5",
"displayName": "XBB.1.5 (23A)",
Expand All @@ -1990,29 +1982,6 @@
]
}
]
},
{
"name": "BA.5",
"displayName": "BA.5 (22B)",
"description": "Full search by name: NODE_0000862 (only for samples having clade 22B)",
"criteria": [
{
"qry": [
{
"clade": [
"22B"
]
}
],
"node": [
{
"name": [
"NODE_0000862"
]
}
]
}
]
}
]
}
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75 changes: 22 additions & 53 deletions data/nextstrain/sars-cov-2/BA.2/tree.json
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Original file line number Diff line number Diff line change
Expand Up @@ -1778,14 +1778,14 @@
"displayName": "Nextstrain Clade",
"description": "Nextstrain Clade",
"hideInWeb": true,
"skipAsReference": true
"skipAsReference": false
},
{
"name": "clade_who",
"displayName": "WHO name",
"description": "Greek letter WHO name",
"hideInWeb": true,
"skipAsReference": false
"skipAsReference": true
},
{
"name": "clade_display",
Expand Down Expand Up @@ -1817,14 +1817,24 @@
"qry": [
{
"clade": [
"20A"
"20A",
"20B",
"20C",
"20E",
"20F",
"20G"
]
}
],
"node": [
{
"clade": [
"20A"
"20A",
"20B",
"20C",
"20E",
"20F",
"20G"
],
"searchAlgo": "ancestor-earliest"
}
Expand Down Expand Up @@ -1875,14 +1885,19 @@
"qry": [
{
"clade": [
"20A"
"20A",
"20B",
"20C",
"20E",
"20F",
"20G"
]
}
],
"node": [
{
"name": [
"NODE_0000000"
"B.1"
]
}
]
Expand Down Expand Up @@ -1914,7 +1929,7 @@
"node": [
{
"name": [
"NODE_0000862"
"XBB.1.16"
]
}
]
Expand Down Expand Up @@ -1945,29 +1960,6 @@
}
]
},
{
"name": "BA.2.86",
"displayName": "BA.2.86 (23I)",
"description": "Full search by name: NODE_0000659 (only for samples having clade 22I)",
"criteria": [
{
"qry": [
{
"clade": [
"23I"
]
}
],
"node": [
{
"name": [
"NODE_0000659"
]
}
]
}
]
},
{
"name": "XBB.1.5",
"displayName": "XBB.1.5 (23A)",
Expand All @@ -1990,29 +1982,6 @@
]
}
]
},
{
"name": "BA.5",
"displayName": "BA.5 (22B)",
"description": "Full search by name: NODE_0000862 (only for samples having clade 22B)",
"criteria": [
{
"qry": [
{
"clade": [
"22B"
]
}
],
"node": [
{
"name": [
"NODE_0000862"
]
}
]
}
]
}
]
}
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