Merge pull request #88 from umccr/feature/70-variant-tracks-and-types…

…cript direct htsget + typescript
umccr · Jan 13, 2022 · edc83f7 · edc83f7
2 parents ea92957 + 9d7411b
commit edc83f7
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Showing 11 changed files with 3,007 additions and 2,049 deletions.
diff --git a/.eslintignore b/.eslintignore
@@ -0,0 +1 @@
+/**/*.d.ts
diff --git a/.gitignore b/.gitignore
@@ -26,3 +26,4 @@ yarn-error.log*
 
 local_ignore/
 .eslintcache
+/.idea/
diff --git a/babel.config.js b/babel.config.js
@@ -1,4 +1,4 @@
 module.exports = {
-  presets: ['@babel/preset-env', '@babel/preset-react'],
+  presets: ['@babel/preset-env', '@babel/preset-react', '@babel/preset-typescript'],
   plugins: ['@babel/plugin-proposal-class-properties'],
 };
diff --git a/docker-compose.yml b/docker-compose.yml
@@ -10,5 +10,7 @@ services:
     volumes:
       - ./htsget-config-local.json:/htsget-config-local.json
       - ~/.aws:/root/.aws:ro
+      - ./vcfs:/vcfs:ro
+      - ./bams:/bams:ro
     environment:
       - AWS_PROFILE=dev
diff --git a/htsget-config-local.json b/htsget-config-local.json
@@ -36,6 +36,10 @@
           {
             "pattern": "^umccr-primary-data(?P<accession>.*)$",
             "path": "s3://umccr-primary-data{accession}"
+          },
+          {
+            "pattern": "^local/(?P<accession>.*)$",
+            "path": "/bams/{accession}"
           }
         ]
       },
@@ -78,6 +82,10 @@
           {
             "pattern": "^umccr-primary-data(?P<accession>.*)$",
             "path": "s3://umccr-primary-data{accession}"
+          },
+          {
+            "pattern": "^local/(?P<accession>.*)$",
+            "path": "/vcfs/{accession}"
           }
         ]
       },
@@ -98,4 +106,4 @@
       }
     }
   }
-}
+}
diff --git a/package.json b/package.json
@@ -5,6 +5,8 @@
   "dependencies": {
     "@material-ui/core": "^4.12.3",
     "@material-ui/icons": "^4.11.2",
+    "@types/react-router-dom": "^5.3.2",
+    "@types/url-parse": "^1.4.6",
     "aws-amplify": "^4.3.8",
     "aws-amplify-react": "^5.1.9",
     "classnames": "^2.3.1",
@@ -28,7 +30,8 @@
     "react-transition-group": "^4.4.2",
     "recharts": "^2.1.6",
     "redux": "^4.1.2",
-    "redux-thunk": "^2.4.0"
+    "redux-thunk": "^2.4.0",
+    "url-parse": "^1.5.4"
   },
   "scripts": {
     "start": "source start.sh",
@@ -52,6 +55,7 @@
     "@babel/plugin-proposal-class-properties": "^7.16.0",
     "@babel/preset-env": "^7.16.4",
     "@babel/preset-react": "^7.16.0",
+    "@babel/preset-typescript": "^7.16.7",
     "@typescript-eslint/eslint-plugin": "^5.4.0",
     "@typescript-eslint/parser": "^5.4.0",
     "babel-eslint": "^10.1.0",
Original file line number	Diff line number	Diff line change
Expand Up		@@ -26,3 +26,4 @@ yarn-error.log*

		local_ignore/
		.eslintcache
		/.idea/