From 4be097a06530260d820f5c759f0432c217484c3b Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 18:09:00 -0400
Subject: [PATCH 01/23] temp

---
 package-lock.json | 197 +++++++++++++++++++++++++++++++++++++++-------
 package.json      |   2 +-
 2 files changed, 169 insertions(+), 30 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 7ba99706f..ae69b1d78 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -5,14 +5,15 @@
   "requires": true,
   "packages": {
     "": {
+      "name": "bento_web",
       "version": "0.2.0",
       "license": "LGPL-3.0-only",
       "dependencies": {
         "@babel/plugin-proposal-class-properties": "^7.12.1",
         "antd": "^3.26.19",
-        "cross-fetch": "^3.0.6",
+        "cross-fetch": "^3.1.5",
         "file-saver": "^2.0.5",
-        "igv": "https://github.com/bento-platform/igv.js/archive/bento.2020-10-30.tar.gz",
+        "igv": "^2.10.1",
         "iso8601-duration": "^1.2.0",
         "prop-types": "^15.7.2",
         "query-string": "^6.13.7",
@@ -20,7 +21,6 @@
         "react-dom": "^16.14.0",
         "react-json-view": "^1.21.1",
         "react-redux": "^7.2.2",
-        "react-router": "^5.2.0",
         "react-router-dom": "^5.2.0",
         "react-router-prop-types": "^1.0.5",
         "react-syntax-highlighter": "^13.5.3",
@@ -43,6 +43,7 @@
         "css-loader": "^5.0.0",
         "eslint": "^7.12.0",
         "eslint-plugin-react": "^7.21.5",
+        "file-loader": "^6.2.0",
         "html-webpack-plugin": "^4.5.0",
         "style-loader": "^2.0.0",
         "webpack": "^4.44.2",
@@ -1784,9 +1785,9 @@
       "dev": true
     },
     "node_modules/@types/json-schema": {
-      "version": "7.0.7",
-      "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.7.tgz",
-      "integrity": "sha512-cxWFQVseBm6O9Gbw1IWb8r6OS4OhSt3hPZLkFApLjM8TEXROBuQGLAH2i2gZpcXdLBIrpXuTDhH7Vbm1iXmNGA==",
+      "version": "7.0.11",
+      "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.11.tgz",
+      "integrity": "sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==",
       "dev": true
     },
     "node_modules/@types/node": {
@@ -3619,11 +3620,11 @@
       }
     },
     "node_modules/cross-fetch": {
-      "version": "3.1.4",
-      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.4.tgz",
-      "integrity": "sha512-1eAtFWdIubi6T4XPy6ei9iUFoKpUkIF971QLN8lIvvvwueI65+Nw5haMNKUwfJxabqlIIDODJKGrQ66gxC0PbQ==",
+      "version": "3.1.5",
+      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.5.tgz",
+      "integrity": "sha512-lvb1SBsI0Z7GDwmuid+mU3kWVBwTVUbe7S0H52yaaAdQOXq2YktTCZdlAcNKFzE6QtRz0snpw9bNiPeOIkkQvw==",
       "dependencies": {
-        "node-fetch": "2.6.1"
+        "node-fetch": "2.6.7"
       }
     },
     "node_modules/cross-spawn": {
@@ -5130,6 +5131,58 @@
         "node": "^10.12.0 || >=12.0.0"
       }
     },
+    "node_modules/file-loader": {
+      "version": "6.2.0",
+      "resolved": "https://registry.npmjs.org/file-loader/-/file-loader-6.2.0.tgz",
+      "integrity": "sha512-qo3glqyTa61Ytg4u73GultjHGjdRyig3tG6lPtyX/jOEJvHif9uB0/OCI2Kif6ctF3caQTW2G5gym21oAsI4pw==",
+      "dev": true,
+      "dependencies": {
+        "loader-utils": "^2.0.0",
+        "schema-utils": "^3.0.0"
+      },
+      "engines": {
+        "node": ">= 10.13.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/webpack"
+      },
+      "peerDependencies": {
+        "webpack": "^4.0.0 || ^5.0.0"
+      }
+    },
+    "node_modules/file-loader/node_modules/loader-utils": {
+      "version": "2.0.2",
+      "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.2.tgz",
+      "integrity": "sha512-TM57VeHptv569d/GKh6TAYdzKblwDNiumOdkFnejjD0XwTH87K90w3O7AiJRqdQoXygvi1VQTJTLGhJl7WqA7A==",
+      "dev": true,
+      "dependencies": {
+        "big.js": "^5.2.2",
+        "emojis-list": "^3.0.0",
+        "json5": "^2.1.2"
+      },
+      "engines": {
+        "node": ">=8.9.0"
+      }
+    },
+    "node_modules/file-loader/node_modules/schema-utils": {
+      "version": "3.1.1",
+      "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.1.1.tgz",
+      "integrity": "sha512-Y5PQxS4ITlC+EahLuXaY86TXfR7Dc5lw294alXOq86JAHCihAIZfqv8nNCWvaEJvaC51uN9hbLGeV0cFBdH+Fw==",
+      "dev": true,
+      "dependencies": {
+        "@types/json-schema": "^7.0.8",
+        "ajv": "^6.12.5",
+        "ajv-keywords": "^3.5.2"
+      },
+      "engines": {
+        "node": ">= 10.13.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/webpack"
+      }
+    },
     "node_modules/file-saver": {
       "version": "2.0.5",
       "resolved": "https://registry.npmjs.org/file-saver/-/file-saver-2.0.5.tgz",
@@ -5835,10 +5888,9 @@
       }
     },
     "node_modules/igv": {
-      "version": "2.6.8",
-      "resolved": "https://github.com/bento-platform/igv.js/archive/bento.2020-10-30.tar.gz",
-      "integrity": "sha1-ZIYfMCook25+sMMgtmE2cCGuwoU= sha512-B0XbuB0keZVzTZO0+m/8vtI9IU3gApgCEAiy/zcsrvO8q2ftD5rt3+IM51QmQsrOLCSaDFzwoLEzT9kdi1Vm/Q==",
-      "license": "MIT"
+      "version": "2.13.1",
+      "resolved": "https://registry.npmjs.org/igv/-/igv-2.13.1.tgz",
+      "integrity": "sha512-XqFqHLfDxgl6WSk6Cy2hSMfjg5mhzWFRxk+6joTKkZHXcprSvfYNNLB+ggjrTLkNPBf1p9JikHqwirEIJIdSqg=="
     },
     "node_modules/immutable": {
       "version": "3.7.6",
@@ -6901,11 +6953,22 @@
       }
     },
     "node_modules/node-fetch": {
-      "version": "2.6.1",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.1.tgz",
-      "integrity": "sha512-V4aYg89jEoVRxRb2fJdAg8FHvI7cEyYdVAh94HH0UIK8oJxUfkjlDQN9RbMx+bEjP7+ggMiFRprSti032Oipxw==",
+      "version": "2.6.7",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
+      "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==",
+      "dependencies": {
+        "whatwg-url": "^5.0.0"
+      },
       "engines": {
         "node": "4.x || >=6.0.0"
+      },
+      "peerDependencies": {
+        "encoding": "^0.1.0"
+      },
+      "peerDependenciesMeta": {
+        "encoding": {
+          "optional": true
+        }
       }
     },
     "node_modules/node-libs-browser": {
@@ -10287,6 +10350,11 @@
       "resolved": "https://registry.npmjs.org/toggle-selection/-/toggle-selection-1.0.6.tgz",
       "integrity": "sha1-bkWxJj8gF/oKzH2J14sVuL932jI="
     },
+    "node_modules/tr46": {
+      "version": "0.0.3",
+      "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
+      "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw=="
+    },
     "node_modules/ts-essentials": {
       "version": "2.0.12",
       "resolved": "https://registry.npmjs.org/ts-essentials/-/ts-essentials-2.0.12.tgz",
@@ -11175,6 +11243,11 @@
         "node": ">=0.10"
       }
     },
+    "node_modules/webidl-conversions": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
+      "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ=="
+    },
     "node_modules/webpack": {
       "version": "4.46.0",
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.46.0.tgz",
@@ -11353,6 +11426,15 @@
       "resolved": "https://registry.npmjs.org/whatwg-fetch/-/whatwg-fetch-3.6.2.tgz",
       "integrity": "sha512-bJlen0FcuU/0EMLrdbJ7zOnW6ITZLrZMIarMUVmdKtsGvZna8vxKYaexICWPfZ8qwf9fzNq+UEIZrnSaApt6RA=="
     },
+    "node_modules/whatwg-url": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
+      "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+      "dependencies": {
+        "tr46": "~0.0.3",
+        "webidl-conversions": "^3.0.0"
+      }
+    },
     "node_modules/which": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
@@ -12735,9 +12817,9 @@
       "dev": true
     },
     "@types/json-schema": {
-      "version": "7.0.7",
-      "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.7.tgz",
-      "integrity": "sha512-cxWFQVseBm6O9Gbw1IWb8r6OS4OhSt3hPZLkFApLjM8TEXROBuQGLAH2i2gZpcXdLBIrpXuTDhH7Vbm1iXmNGA==",
+      "version": "7.0.11",
+      "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.11.tgz",
+      "integrity": "sha512-wOuvG1SN4Us4rez+tylwwwCV1psiNVOkJeM3AUWUNWg/jDQY2+HE/444y5gc+jBmRqASOm2Oeh5c1axHobwRKQ==",
       "dev": true
     },
     "@types/node": {
@@ -14320,11 +14402,11 @@
       }
     },
     "cross-fetch": {
-      "version": "3.1.4",
-      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.4.tgz",
-      "integrity": "sha512-1eAtFWdIubi6T4XPy6ei9iUFoKpUkIF971QLN8lIvvvwueI65+Nw5haMNKUwfJxabqlIIDODJKGrQ66gxC0PbQ==",
+      "version": "3.1.5",
+      "resolved": "https://registry.npmjs.org/cross-fetch/-/cross-fetch-3.1.5.tgz",
+      "integrity": "sha512-lvb1SBsI0Z7GDwmuid+mU3kWVBwTVUbe7S0H52yaaAdQOXq2YktTCZdlAcNKFzE6QtRz0snpw9bNiPeOIkkQvw==",
       "requires": {
-        "node-fetch": "2.6.1"
+        "node-fetch": "2.6.7"
       }
     },
     "cross-spawn": {
@@ -15555,6 +15637,40 @@
         "flat-cache": "^3.0.4"
       }
     },
+    "file-loader": {
+      "version": "6.2.0",
+      "resolved": "https://registry.npmjs.org/file-loader/-/file-loader-6.2.0.tgz",
+      "integrity": "sha512-qo3glqyTa61Ytg4u73GultjHGjdRyig3tG6lPtyX/jOEJvHif9uB0/OCI2Kif6ctF3caQTW2G5gym21oAsI4pw==",
+      "dev": true,
+      "requires": {
+        "loader-utils": "^2.0.0",
+        "schema-utils": "^3.0.0"
+      },
+      "dependencies": {
+        "loader-utils": {
+          "version": "2.0.2",
+          "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-2.0.2.tgz",
+          "integrity": "sha512-TM57VeHptv569d/GKh6TAYdzKblwDNiumOdkFnejjD0XwTH87K90w3O7AiJRqdQoXygvi1VQTJTLGhJl7WqA7A==",
+          "dev": true,
+          "requires": {
+            "big.js": "^5.2.2",
+            "emojis-list": "^3.0.0",
+            "json5": "^2.1.2"
+          }
+        },
+        "schema-utils": {
+          "version": "3.1.1",
+          "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.1.1.tgz",
+          "integrity": "sha512-Y5PQxS4ITlC+EahLuXaY86TXfR7Dc5lw294alXOq86JAHCihAIZfqv8nNCWvaEJvaC51uN9hbLGeV0cFBdH+Fw==",
+          "dev": true,
+          "requires": {
+            "@types/json-schema": "^7.0.8",
+            "ajv": "^6.12.5",
+            "ajv-keywords": "^3.5.2"
+          }
+        }
+      }
+    },
     "file-saver": {
       "version": "2.0.5",
       "resolved": "https://registry.npmjs.org/file-saver/-/file-saver-2.0.5.tgz",
@@ -16092,8 +16208,9 @@
       "dev": true
     },
     "igv": {
-      "version": "https://github.com/bento-platform/igv.js/archive/bento.2020-10-30.tar.gz",
-      "integrity": "sha1-ZIYfMCook25+sMMgtmE2cCGuwoU= sha512-B0XbuB0keZVzTZO0+m/8vtI9IU3gApgCEAiy/zcsrvO8q2ftD5rt3+IM51QmQsrOLCSaDFzwoLEzT9kdi1Vm/Q=="
+      "version": "2.13.1",
+      "resolved": "https://registry.npmjs.org/igv/-/igv-2.13.1.tgz",
+      "integrity": "sha512-XqFqHLfDxgl6WSk6Cy2hSMfjg5mhzWFRxk+6joTKkZHXcprSvfYNNLB+ggjrTLkNPBf1p9JikHqwirEIJIdSqg=="
     },
     "immutable": {
       "version": "3.7.6",
@@ -16931,9 +17048,12 @@
       }
     },
     "node-fetch": {
-      "version": "2.6.1",
-      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.1.tgz",
-      "integrity": "sha512-V4aYg89jEoVRxRb2fJdAg8FHvI7cEyYdVAh94HH0UIK8oJxUfkjlDQN9RbMx+bEjP7+ggMiFRprSti032Oipxw=="
+      "version": "2.6.7",
+      "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
+      "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==",
+      "requires": {
+        "whatwg-url": "^5.0.0"
+      }
     },
     "node-libs-browser": {
       "version": "2.2.1",
@@ -19735,6 +19855,11 @@
       "resolved": "https://registry.npmjs.org/toggle-selection/-/toggle-selection-1.0.6.tgz",
       "integrity": "sha1-bkWxJj8gF/oKzH2J14sVuL932jI="
     },
+    "tr46": {
+      "version": "0.0.3",
+      "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz",
+      "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw=="
+    },
     "ts-essentials": {
       "version": "2.0.12",
       "resolved": "https://registry.npmjs.org/ts-essentials/-/ts-essentials-2.0.12.tgz",
@@ -20536,6 +20661,11 @@
         }
       }
     },
+    "webidl-conversions": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz",
+      "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ=="
+    },
     "webpack": {
       "version": "4.46.0",
       "resolved": "https://registry.npmjs.org/webpack/-/webpack-4.46.0.tgz",
@@ -20658,6 +20788,15 @@
       "resolved": "https://registry.npmjs.org/whatwg-fetch/-/whatwg-fetch-3.6.2.tgz",
       "integrity": "sha512-bJlen0FcuU/0EMLrdbJ7zOnW6ITZLrZMIarMUVmdKtsGvZna8vxKYaexICWPfZ8qwf9fzNq+UEIZrnSaApt6RA=="
     },
+    "whatwg-url": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz",
+      "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==",
+      "requires": {
+        "tr46": "~0.0.3",
+        "webidl-conversions": "^3.0.0"
+      }
+    },
     "which": {
       "version": "2.0.2",
       "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
diff --git a/package.json b/package.json
index 31bdc8eb6..9d7717b28 100644
--- a/package.json
+++ b/package.json
@@ -6,7 +6,7 @@
   "dependencies": {
     "@babel/plugin-proposal-class-properties": "^7.12.1",
     "antd": "^3.26.19",
-    "cross-fetch": "^3.0.6",
+    "cross-fetch": "^3.1.5",
     "file-saver": "^2.0.5",
     "igv": "^2.10.1",
     "iso8601-duration": "^1.2.0",

From 3d1faab1a58af2887d59615af074fcb61c4def70 Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 18:28:05 -0400
Subject: [PATCH 02/23] Increased line size to 120

---
 package.json | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 31bdc8eb6..a68d8ae38 100644
--- a/package.json
+++ b/package.json
@@ -67,6 +67,7 @@
     "trailingComma": "es5",
     "tabWidth": 4,
     "semi": true,
-    "singleQuote": false
+    "singleQuote": false,
+    "printWidth": 120
   }
 }

From 59258c13f210c98dea18b1de55f7f4688521e053 Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 18:28:39 -0400
Subject: [PATCH 03/23] Changed Contact info

---
 src/components/datasets/DatasetForm.js | 90 ++++++++++++++------------
 1 file changed, 48 insertions(+), 42 deletions(-)

diff --git a/src/components/datasets/DatasetForm.js b/src/components/datasets/DatasetForm.js
index ccfebd9b0..dd968cfed 100644
--- a/src/components/datasets/DatasetForm.js
+++ b/src/components/datasets/DatasetForm.js
@@ -1,51 +1,57 @@
-import React, {Component} from "react";
+import React from "react";
 import PropTypes from "prop-types";
 
-import {Form, Input} from "antd";
+import { Form, Input } from "antd";
+const { Item } = Form;
 
 import DataUseInput from "../DataUseInput";
 
-import {DATA_USE_PROP_TYPE_SHAPE, INITIAL_DATA_USE_VALUE} from "../../duo";
-import {simpleDeepCopy} from "../../utils/misc";
+import { DATA_USE_PROP_TYPE_SHAPE, INITIAL_DATA_USE_VALUE } from "../../duo";
+import { simpleDeepCopy } from "../../utils/misc";
 
-
-class DatasetForm extends Component {
-    render() {
-        return <Form style={this.props.style || {}}>
-            <Form.Item label="Title">
-                {this.props.form.getFieldDecorator("title", {
-                    initialValue: (this.props.initialValue || {title: ""}).title || "",
-                    rules: [{required: true}, {min: 3}]
+const DatasetForm = ({ style, initialValue, form }) => {
+    return (
+        <Form style={style || {}}>
+            <Item label="Title">
+                {form.getFieldDecorator("title", {
+                    initialValue: (initialValue || { title: "" }).title || "",
+                    rules: [{ required: true }, { min: 3 }],
                 })(<Input placeholder="My Dataset" size="large" />)}
-            </Form.Item>
-            <Form.Item label="Description">
-                {this.props.form.getFieldDecorator("description", {
-                    initialValue: (this.props.initialValue || {description: ""}).description || "",
-                    rules: [{required: true}]
+            </Item>
+            <Item label="Description">
+                {form.getFieldDecorator("description", {
+                    initialValue: (initialValue || { description: "" }).description || "",
+                    rules: [{ required: true }],
                 })(<Input.TextArea placeholder="This is a dataset" />)}
-            </Form.Item>
-            <Form.Item label="Contact Information">
-                {this.props.form.getFieldDecorator("contact_info", {
-                    initialValue: (this.props.initialValue || {contact_info: ""}).contact_info || "",
-                })(<Input.TextArea placeholder={"David Lougheed\ndavid.lougheed@mail.mcgill.ca"} />)}
-            </Form.Item>
-            <Form.Item label="Consent Code and Data Use Requirements">
-                {this.props.form.getFieldDecorator("data_use", {
-                    initialValue: ((this.props.initialValue ||
-                        {data_use: simpleDeepCopy(INITIAL_DATA_USE_VALUE)}).data_use ||
-                        simpleDeepCopy(INITIAL_DATA_USE_VALUE)),
-                    rules: [{required: true}, (rule, value, callback) => {
-                        if (!(value.consent_code || {}).primary_category) {
-                            callback(["Please specify one primary consent code"]);
-                            return;
-                        }
-                        callback([]);
-                    }]
+            </Item>
+            <Item label="Contact Information">
+                {form.getFieldDecorator("contact_info", {
+                    initialValue: (initialValue || { contact_info: "" }).contact_info || "",
+                })(<Input.TextArea placeholder={"Name\nInfo@c3g.ca"} />)}
+            </Item>
+            <Item label="Consent Code and Data Use Requirements">
+                {form.getFieldDecorator("data_use", {
+                    initialValue:
+                        (
+                            initialValue || {
+                                data_use: simpleDeepCopy(INITIAL_DATA_USE_VALUE),
+                            }
+                        ).data_use || simpleDeepCopy(INITIAL_DATA_USE_VALUE),
+                    rules: [
+                        { required: true },
+                        (rule, value, callback) => {
+                            if (!(value.consent_code || {}).primary_category) {
+                                callback(["Please specify one primary consent code"]);
+                                return;
+                            }
+                            callback([]);
+                        },
+                    ],
                 })(<DataUseInput />)}
-            </Form.Item>
-        </Form>;
-    }
-}
+            </Item>
+        </Form>
+    );
+};
 
 DatasetForm.propTypes = {
     style: PropTypes.object,
@@ -53,8 +59,8 @@ DatasetForm.propTypes = {
         title: PropTypes.string,
         description: PropTypes.string,
         contact_info: PropTypes.string,
-        data_use: DATA_USE_PROP_TYPE_SHAPE,  // TODO: Shared shape for data use
-    })
+        data_use: DATA_USE_PROP_TYPE_SHAPE, // TODO: Shared shape for data use
+    }),
 };
 
-export default Form.create({name: "dataset_form"})(DatasetForm);
+export default Form.create({ name: "dataset_form" })(DatasetForm);

From 587c4cc25b6f41ba47e950253fdd4ce26adc9668 Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 19:13:05 -0400
Subject: [PATCH 04/23] converted to function based

---
 src/components/datasets/DatasetTables.js | 353 ++++++++++-------------
 1 file changed, 159 insertions(+), 194 deletions(-)

diff --git a/src/components/datasets/DatasetTables.js b/src/components/datasets/DatasetTables.js
index a1cca80e1..26abc4204 100644
--- a/src/components/datasets/DatasetTables.js
+++ b/src/components/datasets/DatasetTables.js
@@ -1,10 +1,9 @@
-import React, {Component} from "react";
+import React, { useState } from "react";
 import PropTypes from "prop-types";
 
-import {bindActionCreators} from "redux";
-import {connect} from "react-redux";
+import { useSelector, useDispatch } from "react-redux";
 
-import {Button, Col, Row, Table, Typography} from "antd";
+import { Button, Col, Row, Table, Typography } from "antd";
 
 import TableAdditionModal from "./table/TableAdditionModal";
 import TableDeletionModal from "./table/TableDeletionModal";
@@ -12,173 +11,181 @@ import TableDeletionModal from "./table/TableDeletionModal";
 import {
     addProjectTable,
     deleteProjectTableIfPossible,
-    fetchProjectsWithDatasetsAndTables
+    fetchProjectsWithDatasetsAndTables,
 } from "../../modules/metadata/actions";
-import {nop} from "../../utils/misc";
-import {fetchTableSummaryIfPossible} from "../../modules/tables/actions";
+import { nop } from "../../utils/misc";
+import { fetchTableSummaryIfPossible } from "../../modules/tables/actions";
 import TableSummaryModal from "./table/TableSummaryModal";
-import {datasetPropTypesShape, projectPropTypesShape, serviceInfoPropTypesShape} from "../../propTypes";
+import { datasetPropTypesShape, projectPropTypesShape } from "../../propTypes";
 
+const NA_TEXT = <span style={{ color: "#999", fontStyle: "italic" }}>N/A</span>;
 
-const NA_TEXT = (<span style={{color: "#999", fontStyle: "italic"}}>N/A</span>);
+const DatasetTables = ({ isPrivate, project, dataset, onTableIngest, isFetchingTables }) => {
+    const dispatch = useDispatch();
 
-class DatasetTables extends Component {
-    constructor(props) {
-        super(props);
+    const chordServicesByArtifact = useSelector((state) => state.chordServices.itemsByArtifact);
+    const serviceInfoByArtifact = useSelector((state) => state.services.itemsByArtifact);
 
-        this.state = {
-            additionModalVisible: false,
-            deletionModalVisible: false,
-            tableSummaryModalVisible: false,
-            selectedTable: null,
-        };
+    const [additionModalVisible, setAdditionModalVisible] = useState(false);
+    const [deletionModalVisible, setDeletionModalVisible] = useState(false);
+    const [tableSummaryModalVisible, setTableSummaryModalVisible] = useState(false);
+    const [selectedTable, setSelectedTable] = useState(null);
 
-        this.handleAdditionClick = this.handleAdditionClick.bind(this);
-        this.handleAdditionCancel = this.handleAdditionCancel.bind(this);
-        this.handleAdditionSubmit = this.handleAdditionSubmit.bind(this);
-
-        this.handleTableDeletionClick = this.handleTableDeletionClick.bind(this);
-        this.handleTableDeletionCancel = this.handleTableDeletionCancel.bind(this);
-        this.handleTableDeletionSubmit = this.handleTableDeletionSubmit.bind(this);
-
-        this.showTableSummaryModal = this.showTableSummaryModal.bind(this);
-    }
-
-    handleAdditionClick() {
-        this.setState({additionModalVisible: true});
-    }
-
-    handleAdditionCancel() {
-        this.setState({additionModalVisible: false});
-    }
-
-    async handleAdditionSubmit(values) {
+    const handleAdditionSubmit = async (values) => {
         const [serviceArtifact, dataTypeID] = values.dataType.split(":");
-        const serviceInfo = this.props.serviceInfoByArtifact[serviceArtifact];
-        await this.props.addProjectTable(this.props.dataset.identifier, serviceInfo, dataTypeID, values.name);
-
-        await this.props.fetchProjectsWithDatasetsAndTables();  // TODO: If needed / only this project...
-
-        this.setState({additionModalVisible: false});
-    }
-
-    handleTableDeletionClick(t) {
-        this.setState({deletionModalVisible: true, selectedTable: t});
-    }
-
-    handleTableDeletionCancel() {
-        this.setState({deletionModalVisible: false});
-    }
-
-    async handleTableDeletionSubmit() {
-        if (this.state.selectedTable === null) return;
-        await this.props.deleteProjectTable(this.state.selectedTable);
-
-        await this.props.fetchProjectsWithDatasetsAndTables();  // TODO: If needed / only this project...
-
-        this.setState({deletionModalVisible: false});
-    }
-
-    showTableSummaryModal(table) {
-        this.props.fetchTableSummaryIfPossible(this.props.chordServicesByArtifact[table.service_artifact],
-            this.props.serviceInfoByArtifact[table.service_artifact], table.table_id);  // TODO
-        this.setState({tableSummaryModalVisible: true, selectedTable: table});
-    }
-
-    render() {
-        const tableListColumns = [
-            {
-                title: "ID",
-                dataIndex: "table_id",
-                render: (tableID, t) => this.props.isPrivate
-                    ? <a style={{fontFamily: "monospace"}} onClick={() => this.showTableSummaryModal(t)}>{tableID}</a>
-                    : <span style={{fontFamily: "monospace"}}>tableID</span>,
-            },
-            {
-                title: "Name",
-                dataIndex: "name",
-                render: n => (n ? n : NA_TEXT),
-                defaultSortOrder: "ascend",
-                sorter: (a, b) => (a.name && b.name)
-                    ? a.name.localeCompare(b.name)
-                    : a.table_id.localeCompare(b.table_id)
-            },
-            {title: "Data Type", dataIndex: "data_type"},
-            ...(this.props.isPrivate ? [
-                {
-                    title: "Actions",
-                    key: "actions",
-                    width: 230, /*330,*/
-                    render: t => (
-                        <Row gutter={10}>
-                            <Col span={12}>
-                                <Button icon="import"
-                                        style={{width: "100%"}}
-                                        onClick={() => (this.props.onTableIngest || nop)(this.props.project, t)}>
-                                    Ingest
-                                </Button>
-                            </Col>
-                            {/* TODO: Edit Table Name: v0.2 */}
-                            {/*<Col span={8}><Button icon="edit" style={{width: "100%"}}>Edit</Button></Col>*/}
-                            {t.manageable !== false ? (
-                                <Col span={12}><Button type="danger"
-                                                       icon="delete"
-                                                       onClick={() => this.handleTableDeletionClick(t)}
-                                                       style={{width: "100%"}}>Delete</Button></Col>
-                            ) : null}
-                        </Row>
-                    )
-                }
-            ] : [])
-        ];
-
-        const dataset = this.props.dataset || {};
-        const tables = (dataset.tables || []).map(t => ({...t, name: t.name || null}));
-        return <>
+        const serviceInfo = serviceInfoByArtifact[serviceArtifact];
+        await dispatch(addProjectTable(project, dataset.identifier, serviceInfo, dataTypeID, values.name));
+
+        await dispatch(fetchProjectsWithDatasetsAndTables()); // TODO: If needed / only this project...
+
+        setAdditionModalVisible(false);
+    };
+
+    const handleTableDeletionClick = (t) => {
+        setDeletionModalVisible(true);
+        setSelectedTable(t);
+    };
+
+    const handleTableDeletionSubmit = async () => {
+        if (selectedTable === null) return;
+        await dispatch(deleteProjectTableIfPossible(project, selectedTable));
+        await dispatch(fetchProjectsWithDatasetsAndTables()); // TODO: If needed / only this project...
+
+        setDeletionModalVisible(false);
+    };
+
+    const showTableSummaryModal = (table) => {
+        dispatch(
+            fetchTableSummaryIfPossible(
+                chordServicesByArtifact[table.service_artifact],
+                serviceInfoByArtifact[table.service_artifact],
+                table.table_id
+            )
+        );
+        setTableSummaryModalVisible(true);
+        setSelectedTable(table);
+    };
+
+    const tableListColumns = [
+        {
+            title: "ID",
+            dataIndex: "table_id",
+            render: (tableID, t) =>
+                isPrivate ? (
+                    <a style={{ fontFamily: "monospace" }} onClick={() => showTableSummaryModal(t)}>
+                        {tableID}
+                    </a>
+                ) : (
+                    <span style={{ fontFamily: "monospace" }}>tableID</span>
+                ),
+        },
+        {
+            title: "Name",
+            dataIndex: "name",
+            render: (n) => (n ? n : NA_TEXT),
+            defaultSortOrder: "ascend",
+            sorter: (a, b) => (a.name && b.name ? a.name.localeCompare(b.name) : a.table_id.localeCompare(b.table_id)),
+        },
+        { title: "Data Type", dataIndex: "data_type" },
+        ...(isPrivate
+            ? [
+                  {
+                      title: "Actions",
+                      key: "actions",
+                      width: 230 /*330,*/,
+                      render: (t) => (
+                          <Row gutter={10}>
+                              <Col span={12}>
+                                  <Button
+                                      icon="import"
+                                      style={{ width: "100%" }}
+                                      onClick={() => (onTableIngest || nop)(project, t)}
+                                  >
+                                      Ingest
+                                  </Button>
+                              </Col>
+                              {/* TODO: Edit Table Name: v0.2 */}
+                              {/*<Col span={8}><Button icon="edit" style={{width: "100%"}}>Edit</Button></Col>*/}
+                              {t.manageable !== false ? (
+                                  <Col span={12}>
+                                      <Button
+                                          type="danger"
+                                          icon="delete"
+                                          onClick={() => handleTableDeletionClick(t)}
+                                          style={{ width: "100%" }}
+                                      >
+                                          Delete
+                                      </Button>
+                                  </Col>
+                              ) : null}
+                          </Row>
+                      ),
+                  },
+              ]
+            : []),
+    ];
+
+    dataset = dataset || {};
+    const tables = (dataset.tables || []).map((t) => ({
+        ...t,
+        name: t.name || null,
+    }));
+    return (
+        <>
             <Typography.Title level={4}>
                 Tables
-                {this.props.isPrivate ? (
-                    <div style={{float: "right"}}>
+                {isPrivate ? (
+                    <div style={{ float: "right" }}>
                         {/* TODO: Implement v0.2
-                            {(this.props.strayTables || []).length > 0 ? (
+                            {(strayTables || []).length > 0 ? (
                                 <Button icon="import" style={{verticalAlign: "top", marginRight: "10px"}}>
-                                    Adopt Stray Tables ({this.props.strayTables.length})
+                                    Adopt Stray Tables ({strayTables.length})
                                 </Button>
                             ) : null} */}
-                        <Button icon="plus"
-                                style={{verticalAlign: "top"}}
-                                type="primary"
-                                onClick={() => this.handleAdditionClick()}>
+                        <Button
+                            icon="plus"
+                            style={{ verticalAlign: "top" }}
+                            type="primary"
+                            onClick={() => setAdditionModalVisible(true)}
+                        >
                             Add Table
                         </Button>
                     </div>
                 ) : null}
             </Typography.Title>
 
-            <Table bordered
-                   dataSource={tables}
-                   rowKey="table_id"
-                   // expandedRowRender={() => (<span>TODO: List of files</span>)} TODO: Implement v0.2
-                   columns={tableListColumns}
-                   loading={this.props.isFetchingTables} />
-
-            <TableSummaryModal visible={this.state.tableSummaryModalVisible}
-                               table={this.state.selectedTable}
-                               onCancel={() => this.setState({tableSummaryModalVisible: false})} />
-
-            <TableAdditionModal visible={this.state.additionModalVisible}
-                                project={this.props.project}
-                                dataset={dataset}
-                                onSubmit={vs => this.handleAdditionSubmit(vs)}
-                                onCancel={() => this.handleAdditionCancel()} />
-
-            <TableDeletionModal visible={this.state.deletionModalVisible}
-                                table={dataset}
-                                onSubmit={() => this.handleTableDeletionSubmit()}
-                                onCancel={() => this.handleTableDeletionCancel()} />
-        </>;
-    }
-}
+            <Table
+                bordered
+                dataSource={tables}
+                rowKey="table_id"
+                // expandedRowRender={() => (<span>TODO: List of files</span>)} TODO: Implement v0.2
+                columns={tableListColumns}
+                loading={isFetchingTables}
+            />
+
+            <TableSummaryModal
+                visible={tableSummaryModalVisible}
+                table={selectedTable}
+                onCancel={() => setTableSummaryModalVisible(false)}
+            />
+
+            <TableAdditionModal
+                visible={additionModalVisible}
+                project={project}
+                dataset={dataset}
+                onSubmit={handleAdditionSubmit}
+                onCancel={() => setAdditionModalVisible(false)}
+            />
+
+            <TableDeletionModal
+                visible={deletionModalVisible}
+                table={dataset}
+                onSubmit={handleTableDeletionSubmit}
+                onCancel={() => setDeletionModalVisible(false)}
+            />
+        </>
+    );
+};
 
 DatasetTables.propTypes = {
     isPrivate: PropTypes.bool,
@@ -186,48 +193,6 @@ DatasetTables.propTypes = {
     dataset: datasetPropTypesShape,
     onTableIngest: PropTypes.func,
     isFetchingTables: PropTypes.bool,
-
-    chordServicesByArtifact: PropTypes.objectOf(PropTypes.shape({
-        apt_dependencies: PropTypes.arrayOf(PropTypes.string),
-        data_service: PropTypes.bool,
-        manageable_tables: PropTypes.string,
-        python_callable: PropTypes.string,
-        python_module: PropTypes.string,
-        repository: PropTypes.string,
-        run_environment: PropTypes.objectOf(PropTypes.string),
-        service_runnable: PropTypes.string,
-        type: PropTypes.shape({
-            artifact: PropTypes.string.isRequired,
-            language: PropTypes.string,
-            organization: PropTypes.string,
-        }),
-        wsgi: PropTypes.bool,
-
-        post_stop_commands: PropTypes.arrayOf(PropTypes.string),
-        post_start_commands: PropTypes.arrayOf(PropTypes.string),
-        pre_install_commands: PropTypes.arrayOf(PropTypes.string),
-        pre_start_commands: PropTypes.arrayOf(PropTypes.string),
-    })),
-    serviceInfoByArtifact: PropTypes.objectOf(serviceInfoPropTypesShape),
-
-    addProjectTable: PropTypes.func,
-    deleteProjectTable: PropTypes.func,
-    fetchProjectsWithDatasetsAndTables: PropTypes.func,
-    fetchTableSummaryIfPossible: PropTypes.func,
 };
 
-const mapStateToProps = state => ({
-    chordServicesByArtifact: state.chordServices.itemsByArtifact,
-    serviceInfoByArtifact: state.services.itemsByArtifact,
-});
-
-const mapDispatchToProps = (dispatch, ownProps) => ({
-    addProjectTable: (ds, s, dt, name) => dispatch(addProjectTable(ownProps.project, ds, s, dt, name)),
-    deleteProjectTable: table => dispatch(deleteProjectTableIfPossible(ownProps.project, table)),
-    ...bindActionCreators({
-        fetchProjectsWithDatasetsAndTables,
-        fetchTableSummaryIfPossible,
-    }, dispatch),
-});
-
-export default connect(mapStateToProps, mapDispatchToProps)(DatasetTables);
+export default DatasetTables;

From fca740e9bb17c44ff05e7ec776aeb0edeaaf1a33 Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 19:13:53 -0400
Subject: [PATCH 05/23] resolved id interpolation issue

---
 src/components/datasets/DatasetTables.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/datasets/DatasetTables.js b/src/components/datasets/DatasetTables.js
index 26abc4204..66f4d3f53 100644
--- a/src/components/datasets/DatasetTables.js
+++ b/src/components/datasets/DatasetTables.js
@@ -76,7 +76,7 @@ const DatasetTables = ({ isPrivate, project, dataset, onTableIngest, isFetchingT
                         {tableID}
                     </a>
                 ) : (
-                    <span style={{ fontFamily: "monospace" }}>tableID</span>
+                    <span style={{ fontFamily: "monospace" }}>{tableID}</span>
                 ),
         },
         {

From 816f1c7d70fd8a1d3f3630a297ea7cfddf3c174d Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 19:39:48 -0400
Subject: [PATCH 06/23] converted to function based

---
 src/components/overview/VariantsSummary.js | 129 +++++----------------
 1 file changed, 30 insertions(+), 99 deletions(-)

diff --git a/src/components/overview/VariantsSummary.js b/src/components/overview/VariantsSummary.js
index 255c149fb..16db82a5a 100644
--- a/src/components/overview/VariantsSummary.js
+++ b/src/components/overview/VariantsSummary.js
@@ -1,111 +1,42 @@
-import React, {Component} from "react";
-import {connect} from "react-redux";
+import React from "react";
+import { connect } from "react-redux";
 import PropTypes from "prop-types";
-import {Col, Row, Spin, Statistic, Typography, Icon} from "antd";
+import { Col, Row, Spin, Statistic, Typography, Icon } from "antd";
 
-const mapStateToProps = state => ({
-    tableSummaries: state.tableSummaries,
-});
-
-const actionCreators = {};
-
-class VariantsSummary extends Component {
-
-    static propTypes = {
-        tableSummaries : PropTypes.shape({
-            isFetching: PropTypes.bool,
-            summariesByServiceArtifactAndTableID: PropTypes.object,
-        }),
-    };
-
-    constructor(props) {
-        super(props);
-        this.state = {
-            activeIndex: 0,
-            sexChartActiveIndex: 0,
-            diseaseChartActiveIndex: 0,
-            biosamplesChartActiveIndex: 0,
-            phenotypicFeaturesThresholdSliderValue: 0.01,
-            chartPadding:  "1rem",
-            chartWidthHeight: 500,
-            chartLabelPaddingTop: 3,
-            chartLabelPaddingLeft: 3,
-        };
-    }
+const VariantsSummary = ({ tableSummaries }) => {
+    const fetchingTableSummaries = tableSummaries?.isFetching;
 
-    render() {
-        const fetchingTableSummaries = this.props.tableSummaries?.isFetching;
-        const variantTableSummaries =
-            this.props.tableSummaries?.summariesByServiceArtifactAndTableID?.variant;
+    const numVCFs = 0;
 
-        let numVCFs = 0;
-        Object.values(variantTableSummaries || []).forEach(s => {
-            numVCFs += s.data_type_specific.vcf_files;
-        });
-
-        return <>
+    return (
+        <>
             <Typography.Title level={4}>Variants</Typography.Title>
-            <Row style={{marginBottom: "24px"}} gutter={[0, 16]}>
+            <Row style={{ marginBottom: "24px" }} gutter={[0, 16]}>
                 <Col xl={2} lg={3} md={4} sm={5} xs={6}>
                     <Spin spinning={fetchingTableSummaries}>
-                        <Statistic title="VCF Files"
-                                   prefix={<Icon type="file" />}
-                                   value={numVCFs} />
+                        <Statistic
+                            title="VCF Files"
+                            prefix={<Icon type="file" />}
+                            value={numVCFs}
+                        />
                     </Spin>
                 </Col>
             </Row>
-        </>;
-    }
-
-    updateDimensions = () => {
-        if (window.innerWidth < 576) { //xs
-            this.setState({
-                chartPadding: "0rem",
-                chartWidthHeight: window.innerWidth,
-                chartLabelPaddingTop: 3,
-                chartLabelPaddingLeft: 3
-            });
-        } else if (window.innerWidth < 768) { // sm
-            this.setState({
-                chartPadding: "1rem",
-                chartWidthHeight: window.innerWidth,
-                chartLabelPaddingTop: 3,
-                chartLabelPaddingLeft: 6 });
-        } else if (window.innerWidth < 992) { // md
-            this.setState({
-                chartPadding: "2rem",
-                chartWidthHeight: window.innerWidth,
-                chartLabelPaddingTop: 3,
-                chartLabelPaddingLeft: 5 });
-        } else if (window.innerWidth < 1200) { // lg
-            this.setState({
-                chartPadding: "4rem",
-                chartWidthHeight: window.innerWidth / 2,
-                chartLabelPaddingTop: 3,
-                chartLabelPaddingLeft: 6 });
-        } else if (window.innerWidth < 1600) { // xl
-            this.setState({
-                chartPadding: "6rem",
-                chartWidthHeight: window.innerWidth / 2,
-                chartLabelPaddingTop: 3,
-                chartLabelPaddingLeft: 7 });
-        } else {
-            this.setState({
-                chartPadding: "10rem",
-                chartWidthHeight: window.innerWidth / 2,
-                chartLabelPaddingTop: 5,
-                chartLabelPaddingLeft: 7 }); // > xl
-        }
-    }
-
-    componentDidMount() {
-        this.updateDimensions();
-        window.addEventListener("resize", this.updateDimensions);
-    }
+        </>
+    );
+};
+
+VariantsSummary.propTypes = {
+    tableSummaries: PropTypes.shape({
+        isFetching: PropTypes.bool,
+        summariesByServiceArtifactAndTableID: PropTypes.object,
+    }),
+};
+
+const mapStateToProps = (state) => ({
+    tableSummaries: state.tableSummaries,
+});
 
-    componentWillUnmount() {
-        window.removeEventListener("resize", this.updateDimensions);
-    }
-}
+const actionCreators = {};
 
-export default connect(mapStateToProps, actionCreators)(VariantsSummary);
+export default connect(mapStateToProps, actionCreators)(VariantsSummary);
\ No newline at end of file

From e203cd2271649a05fbad763ecd59afc8774250fe Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Sun, 14 Aug 2022 19:51:23 -0400
Subject: [PATCH 07/23] Added vcf counts

---
 src/components/overview/VariantsSummary.js | 31 +++++-----------------
 1 file changed, 7 insertions(+), 24 deletions(-)

diff --git a/src/components/overview/VariantsSummary.js b/src/components/overview/VariantsSummary.js
index 16db82a5a..600b17c68 100644
--- a/src/components/overview/VariantsSummary.js
+++ b/src/components/overview/VariantsSummary.js
@@ -1,12 +1,12 @@
 import React from "react";
-import { connect } from "react-redux";
-import PropTypes from "prop-types";
+import { useSelector } from "react-redux";
 import { Col, Row, Spin, Statistic, Typography, Icon } from "antd";
 
-const VariantsSummary = ({ tableSummaries }) => {
-    const fetchingTableSummaries = tableSummaries?.isFetching;
+const VariantsSummary = ( ) => {
 
-    const numVCFs = 0;
+    const fetchingTableSummaries = useSelector(state => state.tableSummaries?.isFetching);
+    const numVCFs =
+        useSelector((state) => state.overviewSummary.data?.data_type_specific?.experiment_results.file_format.VCF) || 0;
 
     return (
         <>
@@ -14,11 +14,7 @@ const VariantsSummary = ({ tableSummaries }) => {
             <Row style={{ marginBottom: "24px" }} gutter={[0, 16]}>
                 <Col xl={2} lg={3} md={4} sm={5} xs={6}>
                     <Spin spinning={fetchingTableSummaries}>
-                        <Statistic
-                            title="VCF Files"
-                            prefix={<Icon type="file" />}
-                            value={numVCFs}
-                        />
+                        <Statistic title="VCF Files" prefix={<Icon type="file" />} value={numVCFs} />
                     </Spin>
                 </Col>
             </Row>
@@ -26,17 +22,4 @@ const VariantsSummary = ({ tableSummaries }) => {
     );
 };
 
-VariantsSummary.propTypes = {
-    tableSummaries: PropTypes.shape({
-        isFetching: PropTypes.bool,
-        summariesByServiceArtifactAndTableID: PropTypes.object,
-    }),
-};
-
-const mapStateToProps = (state) => ({
-    tableSummaries: state.tableSummaries,
-});
-
-const actionCreators = {};
-
-export default connect(mapStateToProps, actionCreators)(VariantsSummary);
\ No newline at end of file
+export default VariantsSummary;

From 608b65b0d9b4a03b77d7281254a287ab80ac868a Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Mon, 15 Aug 2022 10:46:09 -0400
Subject: [PATCH 08/23] lint fixed

---
 src/components/datasets/DatasetTables.js | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/components/datasets/DatasetTables.js b/src/components/datasets/DatasetTables.js
index 66f4d3f53..1260d6032 100644
--- a/src/components/datasets/DatasetTables.js
+++ b/src/components/datasets/DatasetTables.js
@@ -89,11 +89,11 @@ const DatasetTables = ({ isPrivate, project, dataset, onTableIngest, isFetchingT
         { title: "Data Type", dataIndex: "data_type" },
         ...(isPrivate
             ? [
-                  {
-                      title: "Actions",
-                      key: "actions",
-                      width: 230 /*330,*/,
-                      render: (t) => (
+                {
+                    title: "Actions",
+                    key: "actions",
+                    width: 230 /*330,*/,
+                    render: (t) => (
                           <Row gutter={10}>
                               <Col span={12}>
                                   <Button
@@ -119,9 +119,9 @@ const DatasetTables = ({ isPrivate, project, dataset, onTableIngest, isFetchingT
                                   </Col>
                               ) : null}
                           </Row>
-                      ),
-                  },
-              ]
+                    ),
+                },
+            ]
             : []),
     ];
 

From 64a5c6f82da6822de54452d51a664c8606711d2d Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Tue, 19 Jul 2022 11:38:50 -0400
Subject: [PATCH 09/23] changed get request csv to post - this now allows us to
 query multiple

---
 src/modules/explorer/actions.js | 43 +++++++++++++++++++--------------
 1 file changed, 25 insertions(+), 18 deletions(-)

diff --git a/src/modules/explorer/actions.js b/src/modules/explorer/actions.js
index 2958e378e..5a7aed72f 100644
--- a/src/modules/explorer/actions.js
+++ b/src/modules/explorer/actions.js
@@ -2,6 +2,8 @@ import {createNetworkActionTypes, networkAction} from "../../utils/actions";
 import {jsonRequest} from "../../utils/requests";
 import {extractQueriesFromDataTypeForms} from "../../utils/search";
 
+import FileSaver from "file-saver";
+
 export const PERFORM_SEARCH = createNetworkActionTypes("EXPLORER.PERFORM_SEARCH");
 export const PERFORM_INDIVIDUAL_CSV_DOWNLOAD = createNetworkActionTypes("EXPLORER.PERFORM_INDIVIDUAL_CSV_DOWNLOAD");
 export const ADD_DATA_TYPE_QUERY_FORM = "EXPLORER.ADD_DATA_TYPE_QUERY_FORM";
@@ -26,13 +28,6 @@ const performSearch = networkAction((datasetID, dataTypeQueries, excludeFromAuto
         err: "Error performing search",
     }));
 
-const performIndividualCSVDownload = networkAction((individualsUrl) => () => ({
-    types: PERFORM_INDIVIDUAL_CSV_DOWNLOAD,
-    url: individualsUrl,
-    parse: r => r.blob(),  // Parse the CSV as a binary blob rather than e.g. a JSON file
-    err: "Error performing individual csv download",
-}));
-
 export const performSearchIfPossible = (datasetID) => (dispatch, getState) => {
     if (getState().explorer.fetchingSearchByDatasetID[datasetID]) return;
 
@@ -57,21 +52,33 @@ export const performSearchIfPossible = (datasetID) => (dispatch, getState) => {
 
 export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds, allSearchResults) =>
     (dispatch, getState) => {
-        console.log("Initiating PerformIndividualsDownloadCSVIfPossible");
-
-        let dataUrl = `${getState().services.itemsByArtifact.metadata.url}/api/individuals?format=csv`;
-
-        // build query string
-        // TODO: This should use the actual JS API for URL construction
+        let ids;
         if (individualIds.length > 0) { // Get only selected results
-            dataUrl += ("&page_size=" + individualIds.length);
-            individualIds.forEach(id => dataUrl += `&id=${id}`);
+            ids = individualIds;
         } else { // Get all search results
-            dataUrl += ("&page_size=" + allSearchResults.length);
-            allSearchResults.forEach(sr => dataUrl += `&id=${sr.key}`);
+            ids = allSearchResults.map(sr => sr.key);
         }
 
-        return dispatch(performIndividualCSVDownload(dataUrl));
+        const myHeaders = new Headers();
+        myHeaders.append("Content-Type", "application/json");
+
+        const raw = JSON.stringify({
+            "ids": ids
+        });
+
+        const requestOptions = {
+            method: 'POST',
+            headers: myHeaders,
+            body: raw,
+            redirect: 'follow'
+        };
+
+        fetch(`${getState().services.itemsByArtifact.metadata.url}/api/individualsgetcsv`, requestOptions)
+            .then(response => response.blob())
+            .then(result => {
+                FileSaver.saveAs(result, "data.csv");
+            })
+            .catch(error => console.log('error', error));
     };
 
 

From 3995bd6134367888f9053ba05d9ba8f83ee3dca7 Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Wed, 20 Jul 2022 14:10:00 -0400
Subject: [PATCH 10/23] lint fixed

---
 src/modules/explorer/actions.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/modules/explorer/actions.js b/src/modules/explorer/actions.js
index 5a7aed72f..bae30d340 100644
--- a/src/modules/explorer/actions.js
+++ b/src/modules/explorer/actions.js
@@ -67,10 +67,10 @@ export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds
         });
 
         const requestOptions = {
-            method: 'POST',
+            method: "POST",
             headers: myHeaders,
             body: raw,
-            redirect: 'follow'
+            redirect: "follow"
         };
 
         fetch(`${getState().services.itemsByArtifact.metadata.url}/api/individualsgetcsv`, requestOptions)
@@ -78,7 +78,7 @@ export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds
             .then(result => {
                 FileSaver.saveAs(result, "data.csv");
             })
-            .catch(error => console.log('error', error));
+            .catch(error => console.log("error", error));
     };
 
 

From d9cff5195a63bdc04c68865b32833f2d84e24231 Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Tue, 2 Aug 2022 16:22:59 -0400
Subject: [PATCH 11/23] made more readable

---
 src/modules/explorer/actions.js | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/src/modules/explorer/actions.js b/src/modules/explorer/actions.js
index bae30d340..ccd596da3 100644
--- a/src/modules/explorer/actions.js
+++ b/src/modules/explorer/actions.js
@@ -52,12 +52,8 @@ export const performSearchIfPossible = (datasetID) => (dispatch, getState) => {
 
 export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds, allSearchResults) =>
     (dispatch, getState) => {
-        let ids;
-        if (individualIds.length > 0) { // Get only selected results
-            ids = individualIds;
-        } else { // Get all search results
-            ids = allSearchResults.map(sr => sr.key);
-        }
+
+        const ids = individualIds.length ? individualIds : allSearchResults.map(sr => sr.key);
 
         const myHeaders = new Headers();
         myHeaders.append("Content-Type", "application/json");
@@ -73,7 +69,7 @@ export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds
             redirect: "follow"
         };
 
-        fetch(`${getState().services.itemsByArtifact.metadata.url}/api/individualsgetcsv`, requestOptions)
+        fetch(`${getState().services.itemsByArtifact.metadata.url}/api/batch/individuals`, requestOptions)
             .then(response => response.blob())
             .then(result => {
                 FileSaver.saveAs(result, "data.csv");

From dce8018b907bcf52669b99ed1ed880e62523ce18 Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Mon, 22 Aug 2022 09:44:03 -0400
Subject: [PATCH 12/23] API change: use `id` instead of `ids`

In Katsu all parameters used in requests for filtering are based
on field names.
---
 src/modules/explorer/actions.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/modules/explorer/actions.js b/src/modules/explorer/actions.js
index ccd596da3..38bce3a79 100644
--- a/src/modules/explorer/actions.js
+++ b/src/modules/explorer/actions.js
@@ -59,7 +59,7 @@ export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds
         myHeaders.append("Content-Type", "application/json");
 
         const raw = JSON.stringify({
-            "ids": ids
+            "id": ids
         });
 
         const requestOptions = {

From 4d889fa8b0f165d2c8e2aa5120e000542cfd9307 Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Mon, 22 Aug 2022 14:37:32 -0400
Subject: [PATCH 13/23] add `format` parameter. Use `id` for consistency.

---
 src/modules/explorer/actions.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/modules/explorer/actions.js b/src/modules/explorer/actions.js
index 38bce3a79..b89395dd4 100644
--- a/src/modules/explorer/actions.js
+++ b/src/modules/explorer/actions.js
@@ -59,7 +59,8 @@ export const performIndividualsDownloadCSVIfPossible = (datasetId, individualIds
         myHeaders.append("Content-Type", "application/json");
 
         const raw = JSON.stringify({
-            "id": ids
+            "id": ids,
+            "format": "csv"
         });
 
         const requestOptions = {

From 0568be1655f7f2c72beaa982b9ba4eccdd22f064 Mon Sep 17 00:00:00 2001
From: SanjeevLakhwani <lakhwani.sanjeev691@gmail.com>
Date: Mon, 22 Aug 2022 15:45:24 -0400
Subject: [PATCH 14/23] Added missing prettier dev dep

---
 package.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/package.json b/package.json
index a68d8ae38..6f22d2f24 100644
--- a/package.json
+++ b/package.json
@@ -40,6 +40,7 @@
     "eslint-plugin-react": "^7.21.5",
     "file-loader": "^6.2.0",
     "html-webpack-plugin": "^4.5.0",
+    "prettier": "^2.7.1",
     "style-loader": "^2.0.0",
     "webpack": "^4.44.2",
     "webpack-cli": "^4.1.0",

From cc748e87bd128896323bae7df1c173e7c1d0279b Mon Sep 17 00:00:00 2001
From: SanjeevLakhwani <lakhwani.sanjeev691@gmail.com>
Date: Mon, 22 Aug 2022 16:05:11 -0400
Subject: [PATCH 15/23] enabled bigwigs download

---
 src/components/explorer/IndividualExperiments.js | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/components/explorer/IndividualExperiments.js b/src/components/explorer/IndividualExperiments.js
index 4f4d47ced..7bfe4e2aa 100644
--- a/src/components/explorer/IndividualExperiments.js
+++ b/src/components/explorer/IndividualExperiments.js
@@ -305,8 +305,7 @@ const IndividualExperiments = ({ individual }) => {
 
 // expand here accordingly
 const isDownloadable = (result) =>
-    result.file_format?.toLowerCase() === "vcf" ||
-    result.file_format?.toLowerCase() === "cram";
+    ["vcf", "cram", "bw", "bigwig"].includes(result.file_format?.toLowerCase());
 
 IndividualExperiments.propTypes = {
     individual: individualPropTypesShape,

From c567e50c368ccc81b2e1a5e8ba898a2d2222e93d Mon Sep 17 00:00:00 2001
From: Sanjeev Lakhwani <sanjeev.lakhwani@gmail.com>
Date: Wed, 24 Aug 2022 13:42:28 -0400
Subject: [PATCH 16/23] displayed N/A when no url

---
 src/components/ServiceList.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/ServiceList.js b/src/components/ServiceList.js
index 42bdd1f73..318ed8222 100644
--- a/src/components/ServiceList.js
+++ b/src/components/ServiceList.js
@@ -42,7 +42,7 @@ const serviceColumns = (isOwner) => [
     {
         title: "URL",
         dataIndex: "serviceInfo.url",
-        render: (url) => <a href={`${url}/service-info`}>{`${url}/service-info`}</a>,
+        render: (url) => url ? <a href={`${url}/service-info`}>{`${url}/service-info`}</a> : "N/A",
     },
     {
         title: "Status",

From 11ab38871df80d76e0725bf5e6a80a0c31338c7e Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Mon, 29 Aug 2022 11:08:11 -0400
Subject: [PATCH 17/23] add comment on undefined value

---
 src/components/ServiceList.js | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/src/components/ServiceList.js b/src/components/ServiceList.js
index 318ed8222..324fae5f7 100644
--- a/src/components/ServiceList.js
+++ b/src/components/ServiceList.js
@@ -42,6 +42,8 @@ const serviceColumns = (isOwner) => [
     {
         title: "URL",
         dataIndex: "serviceInfo.url",
+        // url is undefined when service-registry does not receive replies from
+        // the container.
         render: (url) => url ? <a href={`${url}/service-info`}>{`${url}/service-info`}</a> : "N/A",
     },
     {

From 538e34278567a246dd63ab3461fb914bf36389f6 Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Fri, 2 Sep 2022 09:15:32 -0400
Subject: [PATCH 18/23] adapt tableSearchResults to latest API

The latest API exports the results with only the required fields and
avoids most of the nested entries.
This avoids reprocessing the entirety of the results.
---
 .../explorer/ExplorerDatasetSearch.js         |  6 +-
 src/modules/explorer/reducers.js              | 67 +++----------------
 2 files changed, 14 insertions(+), 59 deletions(-)

diff --git a/src/components/explorer/ExplorerDatasetSearch.js b/src/components/explorer/ExplorerDatasetSearch.js
index 67e570eac..3f1d138d9 100644
--- a/src/components/explorer/ExplorerDatasetSearch.js
+++ b/src/components/explorer/ExplorerDatasetSearch.js
@@ -46,7 +46,7 @@ const SEARCH_RESULT_COLUMNS = [
         dataIndex: "biosamples",
         render: samples => <>
             {samples.length} Sample{samples.length === 1 ? "" : "s"}{samples.length ? ": " : ""}
-            {samples.map(b => b.id).join(", ")}
+            {samples.join(", ")}
         </>,
         sorter: (a, b) => a.biosamples.length - b.biosamples.length,
         sortDirections: ["descend", "ascend", "descend"],
@@ -54,8 +54,8 @@ const SEARCH_RESULT_COLUMNS = [
     {
         title: "Experiments",
         dataIndex: "experiments",
-        render: experiments => <>{experiments.length} Experiment{experiments.length === 1 ? "" : "s"}</>,
-        sorter: (a, b) => a.experiments.length - b.experiments.length,
+        render: experiments => <>{experiments} Experiment{experiments === 1 ? "" : "s"}</>,
+        sorter: (a, b) => a.experiments - b.experiments,
         sortDirections: ["descend", "ascend", "descend"],
     },
 ];
diff --git a/src/modules/explorer/reducers.js b/src/modules/explorer/reducers.js
index 9baf197d1..eb28853f1 100644
--- a/src/modules/explorer/reducers.js
+++ b/src/modules/explorer/reducers.js
@@ -204,64 +204,19 @@ export const explorer = (
 // helpers
 
 const tableSearchResults = (searchResults) => {
-    const results = (searchResults || {}).results || {};
-    const tableResultSet = {};
+    const results = (searchResults || {}).results || [];
 
-    // Collect all experiments (which have a biosample, not necessarily unique
-    // - one can perform multiple experiments on the same biosample) in arrays
-    // by their biosample ID.
-    const experimentsByBiosample = {};
-    (results.experiment ?? []).forEach(experiment => {
-        const biosampleID = experiment.biosample;
-        if (!experimentsByBiosample.hasOwnProperty(biosampleID)) {
-            experimentsByBiosample[biosampleID] = [];
-        }
-        experimentsByBiosample[biosampleID].push(experiment);
-    });
-
-    // First, collect different data from phenopackets and sort them into an object for an individual
-    (results.phenopacket || []).forEach(p => {
-        const individualID = p.subject.id;
-        if (!tableResultSet.hasOwnProperty(individualID)) {
-            // We DO NOT initialize diseases, PFs, experiments etc. here because we may have
-            // multiple phenopackets on the same individual, and we want to combine this
-            // into one record for the individual. It gets populated separately below.
-            tableResultSet[individualID] = {
-                key: individualID,
-                individual: p.subject,
-                biosamples: {},  // Only includes biosamples from the phenopackets that matched the search query.
-                diseases: {},  // Only includes diseases from "
-                phenotypic_features: {},
-                experiments: {},  // Filled from all the experiments conducted on the biosamples
-            };
-        }
-
-        // Accumulate biosamples based on individual ID and experiments by that biosample
-        // ID, de-duplicating in the process to event overlap if multiple phenopackets
-        // have the same biosample(s) or something weird.
-        (p.biosamples ?? []).forEach(b => {
-            tableResultSet[individualID].biosamples[b.id] = b;
-            (experimentsByBiosample[b.id] ?? []).forEach(e => tableResultSet[individualID].experiments[e.id] = e);
-        });
-
-        // Accumulate diseases and phenotypic features in the same manner.
-        (p.diseases ?? []).forEach(d => tableResultSet[individualID].diseases[d.id] = d);
-        (p.phenotypic_features ?? []).forEach(pf => tableResultSet[individualID].phenotypic_features[pf.type.id] = pf);
+    return results.map((p) => {
+        return {
+            key: p.subject_id,
+            individual: {
+                id: p.subject_id,
+                alternate_ids: p.alternate_ids ?? []
+            },
+            biosamples: p.biosamples,
+            experiments: p.num_experiments
+        };
     });
-
-    // Now that the biosamples/diseases/PFs/experiments are de-duplicated, turn
-    // them into arrays and sort them in a consistent manner. Also flatten the
-    // stuff-by-individual object into a sorted array.
-    return Object.values(tableResultSet).map(i => ({
-        ...i,
-        biosamples: Object.values(i.biosamples).sort((b1, b2) => b1.id.localeCompare(b2.id)),
-        diseases: Object.values(i.diseases).sort(
-            (d1, d2) => d1.id.toString().localeCompare(d2.id.toString())),
-        phenotypic_features: Object.values(i.phenotypic_features).sort(
-            (pf1, pf2) => pf1.type.id.localeCompare(pf2.type.id)),
-        experiments: Object.values(i.experiments).sort(
-            (e1, e2) => e1.id.toString().localeCompare(e2.id.toString())),
-    })).sort((i1, i2) => i1.key.localeCompare(i2.key));
 };
 
 

From 57b35be0d0c0166caf3a19cf29cc01838297da8b Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Wed, 7 Sep 2022 14:05:35 -0400
Subject: [PATCH 19/23] give full-text search same shape as advanced search

---
 src/modules/explorer/actions.js  |  3 ++-
 src/modules/explorer/reducers.js | 15 +++------------
 2 files changed, 5 insertions(+), 13 deletions(-)

diff --git a/src/modules/explorer/actions.js b/src/modules/explorer/actions.js
index b89395dd4..21141db4b 100644
--- a/src/modules/explorer/actions.js
+++ b/src/modules/explorer/actions.js
@@ -128,7 +128,8 @@ export const neutralizeAutoQueryPageTransition = () => ({
 const performFreeTextSearch = networkAction((datasetID, term) => (dispatch, getState) => ({
     types: FREE_TEXT_SEARCH,
     params: {datasetID},
-    url: `${getState().services.metadataService.url}/api/individuals?search=${term}&page_size=10000`,
+    url: `${getState().services.metadataService.url}/api/individuals?search=${term}&page_size=10000` +
+        "&format=bento_search_result",
     err: `Error searching in all records with term ${term}`,
 }));
 
diff --git a/src/modules/explorer/reducers.js b/src/modules/explorer/reducers.js
index eb28853f1..ee77c0214 100644
--- a/src/modules/explorer/reducers.js
+++ b/src/modules/explorer/reducers.js
@@ -246,21 +246,12 @@ function freeTextSearchFormattedResults(searchResults) {
     return searchResults.map(r => {
         return {
             key: r.id,
-            biosamples: (r.phenopackets || []).flatMap((p) => p.biosamples),
-            diseases: r.phenopackets[0].diseases, //TO FIX, multiple phenopackets possible
-            experiments: (r.phenopackets || []).flatMap((p) =>
-                (p.biosamples || []).flatMap((b) => b?.experiments ? [b.experiments] : [])
-            ),
-            phenotypic_features: r.phenopackets[0].phenotypic_features || [], //TO FIX, as above
             individual: {
-                age: r.age,
-                created: r.created,
-                date_of_birth: r.date_of_birth,
                 id: r.id,
-                karyotypic_sex: r.karyotypic_sex,
-                taxonomy: r.taxonomy,
-                updated: r.updated,
+                alternate_ids: r.alternate_ids
             },
+            biosamples: r.biosamples,
+            experiments: r.num_experiments
         };
     });
 }

From 41ca8c3f4072f4b9588883226cc82057713aab51 Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Thu, 8 Sep 2022 09:04:19 -0400
Subject: [PATCH 20/23] better log

Using `+` was casting the object to a string, that is [Object object].
Using `,` allows to log the object and its properties
---
 src/components/explorer/ExplorerDatasetSearch.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/components/explorer/ExplorerDatasetSearch.js b/src/components/explorer/ExplorerDatasetSearch.js
index 3f1d138d9..9c4f9d8cf 100644
--- a/src/components/explorer/ExplorerDatasetSearch.js
+++ b/src/components/explorer/ExplorerDatasetSearch.js
@@ -117,7 +117,7 @@ class ExplorerDatasetSearch extends Component {
             ? (this.state.currentPage * this.state.pageSize) - this.state.pageSize + 1
             : 0;
 
-        console.log("search results: " + this.props.searchResults);
+        console.log("search results: ", this.props.searchResults);
 
         return <>
             <Typography.Title level={4}>Explore Dataset {selectedDataset.title}</Typography.Title>

From d70e38936fe569f0e5576346689c389e354efccb Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Thu, 8 Sep 2022 09:37:50 -0400
Subject: [PATCH 21/23] consistent bento_search_result, DRY code

---
 src/modules/explorer/reducers.js | 18 +-----------------
 src/propTypes.js                 | 10 ++++++----
 2 files changed, 7 insertions(+), 21 deletions(-)

diff --git a/src/modules/explorer/reducers.js b/src/modules/explorer/reducers.js
index ee77c0214..4c6b97558 100644
--- a/src/modules/explorer/reducers.js
+++ b/src/modules/explorer/reducers.js
@@ -178,7 +178,7 @@ export const explorer = (
                     ...state.searchResultsByDatasetID,
                     [action.datasetID]: {
                         results: freeTextResults(action.data),
-                        searchFormattedResults: freeTextSearchFormattedResults(action.data.results),
+                        searchFormattedResults: tableSearchResults(action.data),
                     },
                 },
             };
@@ -239,19 +239,3 @@ function freeTextResults(_searchResults) {
         }
     };
 }
-
-// produces searchFormattedResults (input for results table and other components)
-// free-text equivalent to tableSearchResults() above
-function freeTextSearchFormattedResults(searchResults) {
-    return searchResults.map(r => {
-        return {
-            key: r.id,
-            individual: {
-                id: r.id,
-                alternate_ids: r.alternate_ids
-            },
-            biosamples: r.biosamples,
-            experiments: r.num_experiments
-        };
-    });
-}
diff --git a/src/propTypes.js b/src/propTypes.js
index abd02f88f..cb96d075b 100644
--- a/src/propTypes.js
+++ b/src/propTypes.js
@@ -361,10 +361,12 @@ export const explorerSearchResultsPropTypesShape = PropTypes.shape({
     }),
     searchFormattedResults: PropTypes.arrayOf(PropTypes.shape({
         key: PropTypes.string.isRequired,
-        individual: individualPropTypesShape,
-        biosamples: PropTypes.arrayOf(biosamplePropTypesShape),
-        diseases: PropTypes.arrayOf(diseasePropTypesShape),
-        experiments: PropTypes.arrayOf(experimentPropTypesShape),  // TODO
+        individual: PropTypes.shape({
+            id: PropTypes.string.isRequired,
+            alternate_ids: PropTypes.arrayOf(PropTypes.string)
+        }),
+        biosamples: PropTypes.arrayOf(PropTypes.string),
+        experiments: PropTypes.number
     })),
 });
 

From 2af6e5e6d864cf7eedafe9b6bc8efb549a819b16 Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Thu, 8 Sep 2022 11:25:30 -0400
Subject: [PATCH 22/23] remove console.log

---
 src/components/explorer/SearchTracksModal.js | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/components/explorer/SearchTracksModal.js b/src/components/explorer/SearchTracksModal.js
index 881c72ac3..ece710b15 100644
--- a/src/components/explorer/SearchTracksModal.js
+++ b/src/components/explorer/SearchTracksModal.js
@@ -6,8 +6,6 @@ import {explorerSearchResultsPropTypesShape} from "../../propTypes";
 import GenomeBrowser from "./GenomeBrowser";
 
 const SearchTracksModal = ({searchResults, ...props}) => {
-    console.log("searchResults", searchResults);
-
     const variants = searchResults.results.results.variant || [];
 
     // TODO: Display some basic statistics about n. of variants/tracks/etc.

From 0353906f3f0bc370ab8fd06f0465de55644217d3 Mon Sep 17 00:00:00 2001
From: Paul Pillot <paul.pillot@mcgill.ca>
Date: Thu, 8 Sep 2022 11:33:15 -0400
Subject: [PATCH 23/23] Disable View Summary for now

This feature is computing statistics from the whole
set of phenopackets expectd from results.
As the new bento_search_results format is slimmer,
the properties for computing stats are missing.
This feature should be replaced by a call to Katsu for the
required properties.
---
 src/components/explorer/ExplorerDatasetSearch.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/components/explorer/ExplorerDatasetSearch.js b/src/components/explorer/ExplorerDatasetSearch.js
index 9c4f9d8cf..ddfbc0a46 100644
--- a/src/components/explorer/ExplorerDatasetSearch.js
+++ b/src/components/explorer/ExplorerDatasetSearch.js
@@ -142,9 +142,9 @@ class ExplorerDatasetSearch extends Component {
                                 onClick={() => this.setState({tracksModalVisible: true})}
                                 disabled={true}>
                             Visualize Tracks</Button> */}
-                        <Button icon="bar-chart"
+                        {/* <Button icon="bar-chart"
                                 style={{marginRight: "8px"}}
-                                onClick={() => this.setState({summaryModalVisible: true})}>View Summary</Button>
+                        onClick={() => this.setState({summaryModalVisible: true})}>View Summary</Button> */}
                         <Spin spinning={this.props.isFetchingDownload} style={{display: "inline-block !important"}}>
                             <Button icon="export" style={{marginRight: "8px"}}
                                     disabled={this.props.isFetchingDownload}