Migrate to pangolin v3 and other minor dependency upgrades

.dockerignore

@@ -1,2 +1,9 @@
 frontend/node_modules
-frontend/build
+frontend/build
+frontend/.yarn/*
+!frontend/.yarn/patches
+!frontend/.yarn/releases
+!frontend/.yarn/plugins
+!frontend/.yarn/sdks
+!frontend/.yarn/versions
+frontend/.pnp.*

.vscode/c_cpp_properties.json

@@ -0,0 +1,16 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/clang",
+            "cStandard": "c11",
+            "cppStandard": "c++14",
+            "intelliSenseMode": "linux-clang-x64"
+        }
+    ],
+    "version": 4
+}

Dockerfile

@@ -1,4 +1,4 @@
-FROM node:12.16.1-alpine as build-frontend
+FROM node:14.17.6-alpine as build-frontend
 WORKDIR /app
 ENV PATH /app/node_modules/.bin:$PATH
 COPY frontend/package.json ./
@@ -11,37 +11,31 @@ RUN rm public/help
 RUN yarn run build
 
 
-FROM tiangolo/uwsgi-nginx-flask:python3.7-2020-06-08 as download-jobs
+FROM tiangolo/uwsgi-nginx-flask:python3.9-2021-09-18 as download-jobs
 RUN apt-get -y update && apt-get -y install ca-certificates && apt-get clean && rm -rf /var/lib/apt/lists/*
 WORKDIR /jobs
 RUN git clone --depth 1 https://github.com/AlgoLab/MALVIRUS-data.git .
 
 
 
-FROM tiangolo/uwsgi-nginx-flask:python3.7-2020-06-08
+FROM tiangolo/uwsgi-nginx-flask:python3.9-2021-09-18
 RUN apt-get -y update && apt-get -y install ca-certificates && apt-get clean && rm -rf /var/lib/apt/lists/*
 
-RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py37_4.9.2-Linux-x86_64.sh -O ~/miniconda.sh && \
-    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
-    rm ~/miniconda.sh && \
+RUN wget --quiet https://github.com/conda-forge/miniforge/releases/download/4.10.3-7/Mambaforge-4.10.3-7-Linux-x86_64.sh -O ~/mambaforge.sh && \
+    /bin/bash ~/mambaforge.sh -b -p /opt/conda && \
+    rm ~/mambaforge.sh && \
     ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
     echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
     echo "conda activate base" >> ~/.bashrc
 
 
-RUN git clone https://github.com/cov-lineages/pangolin.git /pangolin && \
-    cd /pangolin && \
-    git checkout v.2.4.2 && \
-    /opt/conda/bin/conda env create -f environment.yml && \
-    /opt/conda/bin/conda run --no-capture-output -n pangolin python setup.py install
-
 COPY ./environment-malva.yml environment-malva.yml
 COPY ./environment-bcftools.yml environment-bcftools.yml
 
 RUN cd /app && \
-    /opt/conda/bin/conda env create -f environment-malva.yml && \
-    /opt/conda/bin/conda env create -f environment-bcftools.yml && \
-    /opt/conda/bin/conda clean --all
+    /opt/conda/bin/mamba env create -f environment-malva.yml && \
+    /opt/conda/bin/mamba env create -f environment-bcftools.yml && \
+    /opt/conda/bin/mamba clean --all
 
 ENV PATH /opt/conda/bin:$PATH
 

environment-bcftools.yml

@@ -2,6 +2,5 @@ name: bcftools
 channels:
     - conda-forge
     - bioconda
-    - defaults
 dependencies:
     - bcftools=1.11

environment-malva.yml

@@ -2,10 +2,9 @@ name: malva-env
 channels:
     - conda-forge
     - bioconda
-    - defaults
 dependencies:
     - snakemake-minimal=5.32.2
-    - mafft=7.475
+    - mafft=7.490
     - htslib=1.10.2
     - sdsl-lite=2.1.1
     - kmc=3.1.2rc1
@@ -14,4 +13,5 @@ dependencies:
     - gffutils=0.10.1
     - snp-sites=2.5.1
     - snpeff=5.0
-    - csvkit=1.0.5
+    - csvkit=1.0.5
+    - pangolin=3.1.16

frontend/.vscode/extensions.json

@@ -0,0 +1,7 @@
+{
+  "recommendations": [
+    "arcanis.vscode-zipfs",
+    "dbaeumer.vscode-eslint",
+    "esbenp.prettier-vscode"
+  ]
+}

frontend/.vscode/settings.json

@@ -0,0 +1,8 @@
+{
+  "search.exclude": {
+    "**/.yarn": true,
+    "**/.pnp.*": true
+  },
+  "eslint.nodePath": ".yarn/sdks",
+  "prettier.prettierPath": ".yarn/sdks/prettier/index.js"
+}

frontend/.yarn/sdks/eslint/bin/eslint.js

@@ -0,0 +1,20 @@
+#!/usr/bin/env node
+
+const {existsSync} = require(`fs`);
+const {createRequire, createRequireFromPath} = require(`module`);
+const {resolve} = require(`path`);
+
+const relPnpApiPath = "../../../../.pnp.cjs";
+
+const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absRequire = (createRequire || createRequireFromPath)(absPnpApiPath);
+
+if (existsSync(absPnpApiPath)) {
+  if (!process.versions.pnp) {
+    // Setup the environment to be able to require eslint/bin/eslint.js
+    require(absPnpApiPath).setup();
+  }
+}
+
+// Defer to the real eslint/bin/eslint.js your application uses
+module.exports = absRequire(`eslint/bin/eslint.js`);

frontend/.yarn/sdks/eslint/lib/api.js

@@ -0,0 +1,20 @@
+#!/usr/bin/env node
+
+const {existsSync} = require(`fs`);
+const {createRequire, createRequireFromPath} = require(`module`);
+const {resolve} = require(`path`);
+
+const relPnpApiPath = "../../../../.pnp.cjs";
+
+const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absRequire = (createRequire || createRequireFromPath)(absPnpApiPath);
+
+if (existsSync(absPnpApiPath)) {
+  if (!process.versions.pnp) {
+    // Setup the environment to be able to require eslint/lib/api.js
+    require(absPnpApiPath).setup();
+  }
+}
+
+// Defer to the real eslint/lib/api.js your application uses
+module.exports = absRequire(`eslint/lib/api.js`);

frontend/.yarn/sdks/eslint/package.json

@@ -0,0 +1,6 @@
+{
+  "name": "eslint",
+  "version": "7.32.0-sdk",
+  "main": "./lib/api.js",
+  "type": "commonjs"
+}

frontend/.yarn/sdks/integrations.yml

@@ -0,0 +1,5 @@
+# This file is automatically generated by @yarnpkg/sdks.
+# Manual changes might be lost!
+
+integrations:
+  - vscode

frontend/.yarn/sdks/prettier/index.js

@@ -0,0 +1,20 @@
+#!/usr/bin/env node
+
+const {existsSync} = require(`fs`);
+const {createRequire, createRequireFromPath} = require(`module`);
+const {resolve} = require(`path`);
+
+const relPnpApiPath = "../../../.pnp.cjs";
+
+const absPnpApiPath = resolve(__dirname, relPnpApiPath);
+const absRequire = (createRequire || createRequireFromPath)(absPnpApiPath);
+
+if (existsSync(absPnpApiPath)) {
+  if (!process.versions.pnp) {
+    // Setup the environment to be able to require prettier/index.js
+    require(absPnpApiPath).setup();
+  }
+}
+
+// Defer to the real prettier/index.js your application uses
+module.exports = absRequire(`prettier/index.js`);

frontend/.yarn/sdks/prettier/package.json

@@ -0,0 +1,6 @@
+{
+  "name": "prettier",
+  "version": "2.3.2-sdk",
+  "main": "./index.js",
+  "type": "commonjs"
+}

frontend/.yarnrc.yml

@@ -2,7 +2,7 @@ plugins:
   - path: .yarn/plugins/@yarnpkg/plugin-interactive-tools.cjs
     spec: "@yarnpkg/plugin-interactive-tools"
 
-yarnPath: .yarn/releases/yarn-2.4.1.cjs
+yarnPath: .yarn/releases/yarn-3.0.2.cjs
 
 packageExtensions:
   "antd-dayjs-webpack-plugin@*":

frontend/package.json

@@ -4,21 +4,21 @@
   "private": true,
   "dependencies": {
     "@2fd/ant-design-icons": "2.4.1",
-    "@ant-design/icons": "4.6.2",
-    "antd": "4.16.1",
-    "core-js": "^3.13.1",
-    "dayjs": "1.10.5",
+    "@ant-design/icons": "4.7.0",
+    "antd": "4.16.13",
+    "core-js": "^3.19.1",
+    "dayjs": "1.10.7",
     "eslint-config-react-app": "^6.0.0",
-    "history": "5.0.0",
+    "history": "5.1.0",
     "markdown-to-jsx": "7.1.3",
     "react": "^17.0.2",
     "react-app-polyfill": "2.0.0",
     "react-dom": "^17.0.2",
     "react-refetch": "^3.0.1",
-    "react-router-dom": "6.0.0-beta.0",
+    "react-router-dom": "6.0.2",
     "react-scripts": "4.0.3",
     "react-window": "1.8.6",
-    "xlsx": "^0.17.0"
+    "xlsx": "^0.17.4"
   },
   "scripts": {
     "start": "craco start",
@@ -38,13 +38,14 @@
     ]
   },
   "devDependencies": {
-    "@craco/craco": "6.1.2",
+    "@craco/craco": "6.4.0",
     "antd-dayjs-webpack-plugin": "1.0.6",
     "babel-plugin-import": "1.13.3",
-    "craco-less": "1.17.1",
-    "eslint": "^7.27.0",
+    "craco-less": "1.20.0",
+    "eslint": "^7.32.0",
     "eslint-config-prettier": "8.3.0",
-    "eslint-plugin-prettier": "3.4.0",
-    "prettier": "2.3.0"
-  }
+    "eslint-plugin-prettier": "3.4.1",
+    "prettier": "2.4.1"
+  },
+  "packageManager": "[email protected]"
 }

frontend/src/components/PangolinOutput/index.jsx

@@ -28,11 +28,11 @@ function PangolinOutputDescription({ pred, labelClassName }) {
       )}
       Lineage assignment is performed with PANGOLIN. See{' '}
       <a
-        href="https://cov-lineages.org/"
+        href="https://cov-lineages.org/resources/pangolin/output.html"
         target="_blank"
         rel="noopener noreferrer"
       >
-        https://cov-lineages.org/
+        https://cov-lineages.org/resources/pangolin/output.html
       </a>{' '}
       for details.
     </>

frontend/src/components/PangolinOutput/utils.js

@@ -1,30 +1,47 @@
+const render = (x) => <kbd>{x}</kbd>;
+
 export const FIELDS = [
   {
     name: 'lineage',
     label: 'Lineage',
     render: (x, pred) => <b>{pred['Lineage name'] || x}</b>,
   },
   { name: 'probability', label: 'Assignment probability' },
-  { name: 'conflict', label: 'Assignment conflict', extra: '0 = no conflicts' },
+  {
+    name: 'conflict',
+    label: 'Assignment conflict',
+    extra:
+      '0 = no conflicts, otherwise the number of categories the sequence could fit into',
+  },
+  {
+    name: 'ambiguity_score',
+    label: 'Ambiguity score',
+    extra:
+      'A score of 1 indicates that no sites were imputed, while a score of 0 indicates that more sites were imputed than were not imputed.',
+  },
   { name: 'Date range' },
   { name: 'Days since last sampling' },
   { name: 'Most common countries' },
   { name: 'Number of taxa' },
-  { name: 'status', label: 'Status' },
+  { name: 'scorpio_call', label: 'Scorpio call' },
+  { name: 'scorpio_support', label: 'Scorpio support' },
+  { name: 'scorpio_conflict', label: 'Scorpio conflict' },
+  { name: 'version', label: 'Version', render },
+  {
+    name: 'pangolin_version',
+    label: 'Pangolin version',
+    render,
+  },
   {
     name: 'pangoLEARN_version',
     label: 'pangoLEARN version',
-    render: (x) => <kbd>{x}</kbd>,
+    render,
   },
   {
     name: 'pango_version',
     label: 'Pango version',
-    render: (x) => <kbd>{x}</kbd>,
-  },
-  {
-    name: 'pangolin_version',
-    label: 'Pangolin version',
-    render: (x) => <kbd>{x}</kbd>,
+    render,
   },
+  { name: 'status', label: 'Status' },
   { name: 'note', label: 'Note' },
 ];

frontend/src/pages/Call/Call.jsx

@@ -1,4 +1,4 @@
-import { Fragment, useCallback } from 'react';
+import { Fragment, useCallback, useEffect } from 'react';
 
 import { Button, Descriptions } from 'antd';
 import { SyncOutlined } from '@ant-design/icons';
@@ -126,6 +126,13 @@ function Call({ id, call, reloadCall }) {
     call.value.log &&
     JOB_STATUSES[call.value.log.status] &&
     JOB_STATUSES[call.value.log.status].final;
+  useEffect(() => {
+    if (noRefresh) return;
+    const interval = window.setInterval(() => {
+      reloadCall();
+    }, 5000);
+    return () => window.clearInterval(interval);
+  });
   return (
     <>
       <h1>

frontend/src/pages/CallNew/CallNew.jsx

@@ -55,7 +55,7 @@ function CallNew({ createCall, vcfs }) {
         (call) => {
           setLoading(false);
           message.success('Job submission successful!');
-          navigate(`../${call.id}`);
+          navigate(`/calls/${call.id}`);
         },
         (error) => {
           setLoading(false);