From bf4e39eeebfd361a32c1c896d2ba0399a22d84ae Mon Sep 17 00:00:00 2001 From: Richard Neher Date: Fri, 21 Jun 2024 12:21:58 +0200 Subject: [PATCH] data: run migration script to include ref_node info --- .../flu/h1n1pdm/ha/CY121680/tree.json | 11 +-- .../flu/h1n1pdm/ha/MW626062/tree.json | 11 +-- .../flu/h3n2/ha/EPI1857216/tree.json | 3 +- data/nextstrain/sars-cov-2/BA.2.86/tree.json | 75 ++++++------------- data/nextstrain/sars-cov-2/BA.2/tree.json | 75 ++++++------------- data/nextstrain/sars-cov-2/XBB/tree.json | 75 ++++++------------- .../sars-cov-2/wuhan-hu-1/orfs/tree.json | 75 ++++++------------- .../sars-cov-2/wuhan-hu-1/proteins/tree.json | 75 ++++++------------- 8 files changed, 124 insertions(+), 276 deletions(-) diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json index 8199c1bd..1b2baa89 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json +++ b/data/nextstrain/flu/h1n1pdm/ha/CY121680/tree.json @@ -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": { diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json index 3b46a08b..11d2a236 100644 --- a/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json +++ b/data/nextstrain/flu/h1n1pdm/ha/MW626062/tree.json @@ -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": { diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json index 5d09b79e..b475384a 100644 --- a/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json +++ b/data/nextstrain/flu/h3n2/ha/EPI1857216/tree.json @@ -163,7 +163,8 @@ { "name": "short-clade", "displayName": "short-clade", - "description": "" + "description": "", + "skipAsReference": true } ], "ref_nodes": { diff --git a/data/nextstrain/sars-cov-2/BA.2.86/tree.json b/data/nextstrain/sars-cov-2/BA.2.86/tree.json index f783c0ba..354b5cac 100644 --- a/data/nextstrain/sars-cov-2/BA.2.86/tree.json +++ b/data/nextstrain/sars-cov-2/BA.2.86/tree.json @@ -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", @@ -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" } @@ -1875,14 +1885,19 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "name": [ - "NODE_0000000" + "B.1" ] } ] @@ -1914,7 +1929,7 @@ "node": [ { "name": [ - "NODE_0000862" + "XBB.1.16" ] } ] @@ -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)", @@ -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" - ] - } - ] - } - ] } ] } diff --git a/data/nextstrain/sars-cov-2/BA.2/tree.json b/data/nextstrain/sars-cov-2/BA.2/tree.json index 0d67ad39..dfeac5bf 100644 --- a/data/nextstrain/sars-cov-2/BA.2/tree.json +++ b/data/nextstrain/sars-cov-2/BA.2/tree.json @@ -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", @@ -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" } @@ -1875,14 +1885,19 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "name": [ - "NODE_0000000" + "B.1" ] } ] @@ -1914,7 +1929,7 @@ "node": [ { "name": [ - "NODE_0000862" + "XBB.1.16" ] } ] @@ -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)", @@ -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" - ] - } - ] - } - ] } ] } diff --git a/data/nextstrain/sars-cov-2/XBB/tree.json b/data/nextstrain/sars-cov-2/XBB/tree.json index 10ccbce0..b7182c3f 100644 --- a/data/nextstrain/sars-cov-2/XBB/tree.json +++ b/data/nextstrain/sars-cov-2/XBB/tree.json @@ -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", @@ -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" } @@ -1875,14 +1885,19 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "name": [ - "NODE_0000000" + "B.1" ] } ] @@ -1914,7 +1929,7 @@ "node": [ { "name": [ - "NODE_0000862" + "XBB.1.16" ] } ] @@ -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)", @@ -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" - ] - } - ] - } - ] } ] } diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json index 9295df28..b157eda1 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/orfs/tree.json @@ -2350,14 +2350,14 @@ "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", @@ -2389,14 +2389,24 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ], "searchAlgo": "ancestor-earliest" } @@ -2447,14 +2457,19 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "name": [ - "NODE_0000000" + "B.1" ] } ] @@ -2486,7 +2501,7 @@ "node": [ { "name": [ - "NODE_0000862" + "XBB.1.16" ] } ] @@ -2517,29 +2532,6 @@ } ] }, - { - "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)", @@ -2562,29 +2554,6 @@ ] } ] - }, - { - "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" - ] - } - ] - } - ] } ] } diff --git a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/tree.json b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/tree.json index 66df0d66..54770aad 100644 --- a/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/tree.json +++ b/data/nextstrain/sars-cov-2/wuhan-hu-1/proteins/tree.json @@ -2463,14 +2463,14 @@ "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", @@ -2502,14 +2502,24 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ], "searchAlgo": "ancestor-earliest" } @@ -2560,14 +2570,19 @@ "qry": [ { "clade": [ - "20A" + "20A", + "20B", + "20C", + "20E", + "20F", + "20G" ] } ], "node": [ { "name": [ - "NODE_0000000" + "B.1" ] } ] @@ -2599,7 +2614,7 @@ "node": [ { "name": [ - "NODE_0000862" + "XBB.1.16" ] } ] @@ -2630,29 +2645,6 @@ } ] }, - { - "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)", @@ -2675,29 +2667,6 @@ ] } ] - }, - { - "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" - ] - } - ] - } - ] } ] }