Merge pull request #126 from nextstrain/feat/short-cuts

Feat/short cuts
nextstrain · Jan 10, 2024 · 8d7a3a6 · 8d7a3a6
2 parents adcee08 + 26fdb3f
commit 8d7a3a6
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Showing 21 changed files with 54 additions and 24 deletions.
diff --git a/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/CY121680/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h1n1pdm-ha-broad",
+    "flu_h1n1pdm_ha_broad",
     "nextstrain/flu/h1n1pdm/ha/california-7-2009"
   ],
   "aaMotifs": [

diff --git a/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json b/data/nextstrain/flu/h1n1pdm/ha/MW626062/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h1n1pdm-ha",
+    "flu_h1n1pdm_ha",
     "nextstrain/flu/h1n1pdm",
     "nextstrain/flu/h1n1pdm/ha",
     "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"

diff --git a/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json b/data/nextstrain/flu/h1n1pdm/na/MW626056/pathogen.json
@@ -80,7 +80,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h1n1pdm-na",
+    "flu_h1n1pdm_na",
     "nextstrain/flu/h1n1pdm/na",
     "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
   ],

diff --git a/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json b/data/nextstrain/flu/h3n2/ha/CY163680/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h3n2-ha-broad",
+    "flu_h3n2_ha_broad",
     "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
   ],
   "aaMotifs": [

diff --git a/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json b/data/nextstrain/flu/h3n2/ha/EPI1857216/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h3n2-ha",
+    "flu_h3n2_ha",
     "nextstrain/flu/h3n2",
     "nextstrain/flu/h3n2/ha",
     "nextstrain/flu/h3n2/ha/darwin-6-2021"

diff --git a/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json b/data/nextstrain/flu/h3n2/na/EPI1857215/pathogen.json
@@ -80,7 +80,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h3n2-na",
+    "flu_h3n2_na",
     "nextstrain/flu/h3n2/na",
     "nextstrain/flu/h3n2/na/darwin-6-2021"
   ],

diff --git a/data/nextstrain/flu/vic/ha/KX058884/pathogen.json b/data/nextstrain/flu/vic/ha/KX058884/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-vic-ha",
+    "flu_vic_ha",
     "nextstrain/flu/vic",
     "nextstrain/flu/vic/ha",
     "nextstrain/flu/vic/ha/brisbane-60-2008"

diff --git a/data/nextstrain/flu/vic/na/CY073894/pathogen.json b/data/nextstrain/flu/vic/na/CY073894/pathogen.json
@@ -80,7 +80,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-vic-na",
+    "flu_vic_na",
     "nextstrain/flu/vic/na",
     "nextstrain/flu/vic/na/brisbane-60-2008"
   ],

diff --git a/data/nextstrain/rsv/a/EPI_ISL_412866/pathogen.json b/data/nextstrain/rsv/a/EPI_ISL_412866/pathogen.json
@@ -21,6 +21,11 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "shortcuts": [
+    "rsv_a",
+    "nextstrain/rsv/a",
+    "nextstrain/rsv/a/hRSV-A-England-397-2017"
+  ],
   "qc": {
     "privateMutations": {
       "enabled": true,

diff --git a/data/nextstrain/rsv/b/EPI_ISL_1653999/pathogen.json b/data/nextstrain/rsv/b/EPI_ISL_1653999/pathogen.json
@@ -21,6 +21,11 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "shortcuts": [
+    "rsv_b",
+    "nextstrain/rsv/b",
+    "nextstrain/rsv/b/hRSV-B-Australia-VIC-RCH056-2019"
+  ],
   "qc": {
     "privateMutations": {
       "enabled": true,

diff --git a/data_output/index.json b/data_output/index.json
@@ -382,7 +382,7 @@
         {
           "path": "nextstrain/flu/h1n1pdm/ha/CY121680",
           "shortcuts": [
-            "flu-h1n1pdm-ha-broad",
+            "flu_h1n1pdm_ha_broad",
             "nextstrain/flu/h1n1pdm/ha/california-7-2009"
           ],
           "enabled": true,
@@ -453,7 +453,7 @@
         {
           "path": "nextstrain/flu/h1n1pdm/ha/MW626062",
           "shortcuts": [
-            "flu-h1n1pdm-ha",
+            "flu_h1n1pdm_ha",
             "nextstrain/flu/h1n1pdm",
             "nextstrain/flu/h1n1pdm/ha",
             "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"
@@ -526,7 +526,7 @@
         {
           "path": "nextstrain/flu/h1n1pdm/na/MW626056",
           "shortcuts": [
-            "flu-h1n1pdm-na",
+            "flu_h1n1pdm_na",
             "nextstrain/flu/h1n1pdm/na",
             "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
           ],
@@ -598,7 +598,7 @@
         {
           "path": "nextstrain/flu/h3n2/ha/CY163680",
           "shortcuts": [
-            "flu-h3n2-ha-broad",
+            "flu_h3n2_ha_broad",
             "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
           ],
           "enabled": true,
@@ -669,7 +669,7 @@
         {
           "path": "nextstrain/flu/h3n2/ha/EPI1857216",
           "shortcuts": [
-            "flu-h3n2-ha",
+            "flu_h3n2_ha",
             "nextstrain/flu/h3n2",
             "nextstrain/flu/h3n2/ha",
             "nextstrain/flu/h3n2/ha/darwin-6-2021"
@@ -743,7 +743,7 @@
         {
           "path": "nextstrain/flu/h3n2/na/EPI1857215",
           "shortcuts": [
-            "flu-h3n2-na",
+            "flu_h3n2_na",
             "nextstrain/flu/h3n2/na",
             "nextstrain/flu/h3n2/na/darwin-6-2021"
           ],
@@ -815,7 +815,7 @@
         {
           "path": "nextstrain/flu/vic/ha/KX058884",
           "shortcuts": [
-            "flu-vic-ha",
+            "flu_vic_ha",
             "nextstrain/flu/vic",
             "nextstrain/flu/vic/ha",
             "nextstrain/flu/vic/ha/brisbane-60-2008"
@@ -888,7 +888,7 @@
         {
           "path": "nextstrain/flu/vic/na/CY073894",
           "shortcuts": [
-            "flu-vic-na",
+            "flu_vic_na",
             "nextstrain/flu/vic/na",
             "nextstrain/flu/vic/na/brisbane-60-2008"
           ],
@@ -1026,6 +1026,11 @@
         },
         {
           "path": "nextstrain/rsv/a/EPI_ISL_412866",
+          "shortcuts": [
+            "rsv_a",
+            "nextstrain/rsv/a",
+            "nextstrain/rsv/a/hRSV-A-England-397-2017"
+          ],
           "enabled": true,
           "attributes": {
             "name": "RSV-A",
@@ -1089,6 +1094,11 @@
         },
         {
           "path": "nextstrain/rsv/b/EPI_ISL_1653999",
+          "shortcuts": [
+            "rsv_b",
+            "nextstrain/rsv/b",
+            "nextstrain/rsv/b/hRSV-B-Australia-VIC-RCH056-2019"
+          ],
           "enabled": true,
           "attributes": {
             "name": "RSV-B",

diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/CY121680/unreleased/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h1n1pdm-ha-broad",
+    "flu_h1n1pdm_ha_broad",
     "nextstrain/flu/h1n1pdm/ha/california-7-2009"
   ],
   "aaMotifs": [

diff --git a/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/ha/MW626062/unreleased/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h1n1pdm-ha",
+    "flu_h1n1pdm_ha",
     "nextstrain/flu/h1n1pdm",
     "nextstrain/flu/h1n1pdm/ha",
     "nextstrain/flu/h1n1pdm/ha/wisconsin-588-2019"

diff --git a/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json b/data_output/nextstrain/flu/h1n1pdm/na/MW626056/unreleased/pathogen.json
@@ -80,7 +80,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h1n1pdm-na",
+    "flu_h1n1pdm_na",
     "nextstrain/flu/h1n1pdm/na",
     "nextstrain/flu/h1n1pdm/na/wisconsin-588-2019"
   ],

diff --git a/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/CY163680/unreleased/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h3n2-ha-broad",
+    "flu_h3n2_ha_broad",
     "nextstrain/flu/h3n2/ha/wisconsin-67-2005"
   ],
   "aaMotifs": [

diff --git a/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/ha/EPI1857216/unreleased/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h3n2-ha",
+    "flu_h3n2_ha",
     "nextstrain/flu/h3n2",
     "nextstrain/flu/h3n2/ha",
     "nextstrain/flu/h3n2/ha/darwin-6-2021"

diff --git a/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json b/data_output/nextstrain/flu/h3n2/na/EPI1857215/unreleased/pathogen.json
@@ -80,7 +80,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-h3n2-na",
+    "flu_h3n2_na",
     "nextstrain/flu/h3n2/na",
     "nextstrain/flu/h3n2/na/darwin-6-2021"
   ],

diff --git a/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json b/data_output/nextstrain/flu/vic/ha/KX058884/unreleased/pathogen.json
@@ -81,7 +81,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-vic-ha",
+    "flu_vic_ha",
     "nextstrain/flu/vic",
     "nextstrain/flu/vic/ha",
     "nextstrain/flu/vic/ha/brisbane-60-2008"

diff --git a/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json b/data_output/nextstrain/flu/vic/na/CY073894/unreleased/pathogen.json
@@ -80,7 +80,7 @@
   "nucMutLabelMap": {},
   "nucMutLabelMapReverse": {},
   "shortcuts": [
-    "flu-vic-na",
+    "flu_vic_na",
     "nextstrain/flu/vic/na",
     "nextstrain/flu/vic/na/brisbane-60-2008"
   ],

diff --git a/data_output/nextstrain/rsv/a/EPI_ISL_412866/unreleased/pathogen.json b/data_output/nextstrain/rsv/a/EPI_ISL_412866/unreleased/pathogen.json
@@ -21,6 +21,11 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "shortcuts": [
+    "rsv_a",
+    "nextstrain/rsv/a",
+    "nextstrain/rsv/a/hRSV-A-England-397-2017"
+  ],
   "qc": {
     "privateMutations": {
       "enabled": true,

diff --git a/data_output/nextstrain/rsv/b/EPI_ISL_1653999/unreleased/pathogen.json b/data_output/nextstrain/rsv/b/EPI_ISL_1653999/unreleased/pathogen.json
@@ -21,6 +21,11 @@
     "reference": "reference.fasta",
     "treeJson": "tree.json"
   },
+  "shortcuts": [
+    "rsv_b",
+    "nextstrain/rsv/b",
+    "nextstrain/rsv/b/hRSV-B-Australia-VIC-RCH056-2019"
+  ],
   "qc": {
     "privateMutations": {
       "enabled": true,