v2.7.4 - Flu data update (#622)

* Restrict spikenuc processing to sars2

* Bump version to v2.7.4-flu-rc1

* Add missing description, fix Darwin/6 description

* Add A-Viet-Nam-1203-2004 H5 reference

* Add missing H5 HA alignment

* Update default H5 reference

* Bump to v2.7.4-flu-rc2

* Multithreaded and much more efficient flu ingest

* Change loading logo depending on site

* Add more metadata columns

* Add About page for Flu site (close #600)

* Bump version to v2.7.4-flu-rc3

* Fix extra metadata col

* Remove duplicate metadata cols

* Bump version to v2.7.4-flu-rc4

* Finalize flu update, bump to v2.7.4

config/config_flu_gisaid.yaml

@@ -50,6 +50,10 @@ consensus_fraction: 0.9
 min_reporting_fraction: 0.05
 
 metadata_cols:
+  clade:
+    title: "Clade"
+  lineage:
+    title: "Lineage"
   passage:
     title: "Passage"
   host:
@@ -64,6 +68,26 @@ metadata_cols:
     title: "Authors"
   publication:
     title: "Publication"
+  adamantanes_resistance_geno:
+    title: "Adamantanes Resistance Genotype"
+  oseltamivir_resistance_geno:
+    title: "Oseltamivir Resistance Genotype"
+  zanamivir_resistance_geno:
+    title: "Zanamivir Resistance Genotype"
+  peramivir_resistance_geno:
+    title: "Peramivir Resistance Genotype"
+  other_resistance_geno:
+    title: "Other Resistance Genotype"
+  adamantanes_resistance_pheno:
+    title: "Adamantanes Resistance Phenotype"
+  oseltamivir_resistance_pheno:
+    title: "Oseltamivir Resistance Phenotype"
+  zanamivir_resistance_pheno:
+    title: "Zanamivir Resistance Phenotype"
+  peramivir_resistance_pheno:
+    title: "Peramivir Resistance Phenotype"
+  other_resistance_pheno:
+    title: "Other Resistance Phenotype"
   gender:
     title: "Gender"
   patient_status:
@@ -84,7 +108,7 @@ report_group_references:
   B-yam: B-Phuket-3073-2013
   H1N1: A-Wisconsin-67-2022
   H3N2: A-Darwin-6-2021
-  H5NX: A-Goose-Guangdong-1-96
+  H5NX: A-Viet-Nam-1203-2004
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
 
@@ -102,7 +126,7 @@ surv_group_references:
   B-yam: B-Phuket-3073-2013
   H1N1: A-Wisconsin-67-2022
   H3N2: A-Darwin-6-2021
-  H5NX: A-Goose-Guangdong-1-96
+  H5NX: A-Viet-Nam-1203-2004
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
 
@@ -145,7 +169,7 @@ default_references:
   B-yam: B-Phuket-3073-2013
   H1N1: A-Wisconsin-67-2022
   H3N2: A-Darwin-6-2021
-  H5NX: A-Goose-Guangdong-1-96
+  H5NX: A-Viet-Nam-1203-2004
   H7NX: A-Shanghai-02-2013
   H9NX: A-Hong-Kong-1073-99
 

config/config_flu_gisaid_dev.yaml

@@ -50,6 +50,10 @@ consensus_fraction: 0.9
 min_reporting_fraction: 0.05
 
 metadata_cols:
+  clade:
+    title: "Clade"
+  lineage:
+    title: "Lineage"
   passage:
     title: "Passage"
   host:
@@ -64,6 +68,26 @@ metadata_cols:
     title: "Authors"
   publication:
     title: "Publication"
+  adamantanes_resistance_geno:
+    title: "Adamantanes Resistance Genotype"
+  oseltamivir_resistance_geno:
+    title: "Oseltamivir Resistance Genotype"
+  zanamivir_resistance_geno:
+    title: "Zanamivir Resistance Genotype"
+  peramivir_resistance_geno:
+    title: "Peramivir Resistance Genotype"
+  other_resistance_geno:
+    title: "Other Resistance Genotype"
+  adamantanes_resistance_pheno:
+    title: "Adamantanes Resistance Phenotype"
+  oseltamivir_resistance_pheno:
+    title: "Oseltamivir Resistance Phenotype"
+  zanamivir_resistance_pheno:
+    title: "Zanamivir Resistance Phenotype"
+  peramivir_resistance_pheno:
+    title: "Peramivir Resistance Phenotype"
+  other_resistance_pheno:
+    title: "Other Resistance Phenotype"
   gender:
     title: "Gender"
   patient_status:

package.json

@@ -1,6 +1,6 @@
 {
   "name": "covidcg",
-  "version": "2.7.3",
+  "version": "2.7.4",
   "description": "",
   "engines": {
     "node": ">=8",

src/components/LoadingScreen.js

@@ -3,6 +3,7 @@ import { observer } from 'mobx-react';
 import { Transition } from 'react-transition-group';
 import { asyncDataStoreInstance } from './App';
 
+import { config } from '../config';
 import { ASYNC_STATES } from '../constants/defs.json';
 
 import ExternalLink from './Common/ExternalLink';
@@ -15,6 +16,8 @@ import {
 } from './LoadingScreen.styles';
 
 import CGLogo from '../assets/images/[email protected]';
+import FluLogo from '../assets/images/[email protected]';
+import RSVLogo from '../assets/images/[email protected]';
 
 const duration = 1000;
 
@@ -44,6 +47,12 @@ const loadingTransitionStyles = {
   exited: { opacity: 0 },
 };
 
+const siteLogos = {
+  sars2: CGLogo,
+  flu: FluLogo,
+  rsv: RSVLogo,
+};
+
 const LoadingScreen = observer(() => {
   const [progressText, setProgressText] = useState('');
 
@@ -94,7 +103,7 @@ const LoadingScreen = observer(() => {
               ...transitionStyles[state],
             }}
           >
-            <img src={CGLogo}></img>
+            <img src={siteLogos[config['virus']]}></img>
           </LogoContainer>
         )}
       </Transition>