Merge branch 'main' into staging

.github/workflows/tests.yml

@@ -9,9 +9,6 @@ jobs:
   backend_tests:
     name: Backend Tests
     runs-on: 'ubuntu-latest'
-    strategy:
-      matrix:
-        ruby: ['3.3']
     services:
         postgres:
           image: postgres:13
@@ -30,7 +27,7 @@ jobs:
         uses: ruby/setup-ruby@v1
         with:
           bundler-cache: true
-          ruby-version: ${{ matrix.ruby }}
+          ruby-version: '3.3'
           working-directory: ./server
 
       - name: Setup DB

client/src/app/components/genes/my-gene-info/my-gene-info.service.ts

@@ -13,8 +13,8 @@ export class MyGeneInfoService {
       pharmgkb: 'https://www.pharmgkb.org/pathway/',
       humancyc: 'http://humancyc.org/HUMAN/NEW-IMAGE?type=PATHWAY&object=',
       smpdb: 'http://www.smpdb.ca/view/',
-      pid: 'http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=',
       wikipathways: 'http://wikipathways.org/index.php/Pathway:',
+      pid: null,
       netpath: null,
       biocarta: null,
       inoh: null,

client/yarn.lock

@@ -4049,21 +4049,21 @@ bl@^4.0.3, bl@^4.1.0:
     inherits "^2.0.4"
     readable-stream "^3.4.0"
 
-[email protected].1:
-  version "1.20.1"
-  resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.1.tgz#b1812a8912c195cd371a3ee5e66faa2338a5c668"
-  integrity sha512-jWi7abTbYwajOytWCQc37VulmWiRae5RyTpaCyDcS5/lMdtwSz5lOpDE67srw/HYe35f1z3fDQw+3txg7gNtWw==
+[email protected].2:
+  version "1.20.2"
+  resolved "https://registry.yarnpkg.com/body-parser/-/body-parser-1.20.2.tgz#6feb0e21c4724d06de7ff38da36dad4f57a747fd"
+  integrity sha512-ml9pReCu3M61kGlqoTm2umSXTlRTuGTx0bfYj+uIUKKYycG5NtSbeetV3faSU6R7ajOPw0g/J1PvK4qNy7s5bA==
   dependencies:
     bytes "3.1.2"
-    content-type "~1.0.4"
+    content-type "~1.0.5"
     debug "2.6.9"
     depd "2.0.0"
     destroy "1.2.0"
     http-errors "2.0.0"
     iconv-lite "0.4.24"
     on-finished "2.4.1"
     qs "6.11.0"
-    raw-body "2.5.1"
+    raw-body "2.5.2"
     type-is "~1.6.18"
     unpipe "1.0.0"
 
@@ -4671,6 +4671,11 @@ content-type@~1.0.4:
   resolved "https://registry.yarnpkg.com/content-type/-/content-type-1.0.4.tgz#e138cc75e040c727b1966fe5e5f8c9aee256fe3b"
   integrity sha512-hIP3EEPs8tB9AT1L+NUqtwOAps4mk2Zob89MWXMHjHWg9milF/j4osnnQLXBCBFBk/tvIG/tUc9mOUJiPBhPXA==
 
+content-type@~1.0.5:
+  version "1.0.5"
+  resolved "https://registry.yarnpkg.com/content-type/-/content-type-1.0.5.tgz#8b773162656d1d1086784c8f23a54ce6d73d7918"
+  integrity sha512-nTjqfcBFEipKdXCv4YDQWCfmcLZKm81ldF0pAopTvyrFGVbcR6P/VAAd5G7N+0tTr8QqiU0tFadD6FK4NtJwOA==
+
 convert-source-map@^1.5.1, convert-source-map@^1.7.0:
   version "1.9.0"
   resolved "https://registry.yarnpkg.com/convert-source-map/-/convert-source-map-1.9.0.tgz#7faae62353fb4213366d0ca98358d22e8368b05f"
@@ -4686,10 +4691,10 @@ [email protected]:
   resolved "https://registry.yarnpkg.com/cookie-signature/-/cookie-signature-1.0.6.tgz#e303a882b342cc3ee8ca513a79999734dab3ae2c"
   integrity sha512-QADzlaHc8icV8I7vbaJXJwod9HWYp8uCqf1xa4OfNu1T7JVxQIrUgOWtHdNDtPiywmFbiS12VjotIXLrKM3orQ==
 
-cookie@0.5.0:
-  version "0.5.0"
-  resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.5.0.tgz#d1f5d71adec6558c58f389987c366aa47e994f8b"
-  integrity sha512-YZ3GUyn/o8gfKJlnlX7g7xq4gyO6OSuhGPKaaGssGB2qgDUS0gPgtTvoyZLTt9Ab6dC4hfc9dV5arkvc/OCmrw==
+cookie@0.6.0:
+  version "0.6.0"
+  resolved "https://registry.yarnpkg.com/cookie/-/cookie-0.6.0.tgz#2798b04b071b0ecbff0dbb62a505a8efa4e19051"
+  integrity sha512-U71cyTamuh1CRNCfpGY6to28lxvNwPG4Guz/EVjgf3Jmzv0vlDp1atT9eS5dDjMYHucpHbWns6Lwf3BKz6svdw==
 
 cookie@~0.4.1:
   version "0.4.2"
@@ -5545,16 +5550,16 @@ exponential-backoff@^3.1.1:
   integrity sha512-dX7e/LHVJ6W3DE1MHWi9S1EYzDESENfLrYohG2G++ovZrYOkm4Knwa0mc1cn84xJOR4KEU0WSchhLbd0UklbHw==
 
 express@^4.17.3:
-  version "4.18.2"
-  resolved "https://registry.yarnpkg.com/express/-/express-4.18.2.tgz#3fabe08296e930c796c19e3c516979386ba9fd59"
-  integrity sha512-5/PsL6iGPdfQ/lKM1UuielYgv3BUoJfz1aUwU9vHZ+J7gyvwdQXFEBIEIaxeGf0GIcreATNyBExtalisDbuMqQ==
+  version "4.19.2"
+  resolved "https://registry.yarnpkg.com/express/-/express-4.19.2.tgz#e25437827a3aa7f2a827bc8171bbbb664a356465"
+  integrity sha512-5T6nhjsT+EOMzuck8JjBHARTHfMht0POzlA60WV2pMD3gyXw2LZnZ+ueGdNxG+0calOJcWKbpFcuzLZ91YWq9Q==
   dependencies:
     accepts "~1.3.8"
     array-flatten "1.1.1"
-    body-parser "1.20.1"
+    body-parser "1.20.2"
     content-disposition "0.5.4"
     content-type "~1.0.4"
-    cookie "0.5.0"
+    cookie "0.6.0"
     cookie-signature "1.0.6"
     debug "2.6.9"
     depd "2.0.0"
@@ -7460,6 +7465,11 @@ minipass@^4.0.0:
   dependencies:
     yallist "^4.0.0"
 
+minipass@^5.0.0:
+  version "5.0.0"
+  resolved "https://registry.yarnpkg.com/minipass/-/minipass-5.0.0.tgz#3e9788ffb90b694a5d0ec94479a45b5d8738133d"
+  integrity sha512-3FnjYuehv9k6ovOEbyOswadCDPX1piCfhV8ncmYtHOjuPwylVWsghTLo7rabjC3Rx5xD4HDx8Wm1xnMF7S5qFQ==
+
 "minipass@^5.0.0 || ^6.0.2 || ^7.0.0":
   version "7.0.2"
   resolved "https://registry.yarnpkg.com/minipass/-/minipass-7.0.2.tgz#58a82b7d81c7010da5bd4b2c0c85ac4b4ec5131e"
@@ -7538,11 +7548,6 @@ [email protected]:
   resolved "https://registry.yarnpkg.com/mute-stream/-/mute-stream-1.0.0.tgz#e31bd9fe62f0aed23520aa4324ea6671531e013e"
   integrity sha512-avsJQhyd+680gKXyG/sQc0nXaC6rBkPOfyHYcFb9+hdkqQkR9bdnkJ0AMZhke0oesPqIO+mFFJ+IdBc7mst4IA==
 
-nanoid@^3.3.4:
-  version "3.3.4"
-  resolved "https://registry.yarnpkg.com/nanoid/-/nanoid-3.3.4.tgz#730b67e3cd09e2deacf03c027c81c9d9dbc5e8ab"
-  integrity sha512-MqBkQh/OHTS2egovRtLk45wEyNXwF+cokD+1YPf9u5VfJiRdAiRwB2froX5Co9Rh20xs4siNPm8naNotSD6RBw==
-
 nanoid@^3.3.6:
   version "3.3.6"
   resolved "https://registry.yarnpkg.com/nanoid/-/nanoid-3.3.6.tgz#443380c856d6e9f9824267d960b4236ad583ea4c"
@@ -8306,32 +8311,14 @@ [email protected]:
     picocolors "^1.0.0"
     source-map-js "^1.0.2"
 
-postcss@^8.2.14:
-  version "8.4.21"
-  resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.21.tgz#c639b719a57efc3187b13a1d765675485f4134f4"
-  integrity sha512-tP7u/Sn/dVxK2NnruI4H9BG+x+Wxz6oeZ1cJ8P6G/PZY0IKk4k/63TDsQf2kQq3+qoJeLm2kIBUNlZe3zgb4Zg==
-  dependencies:
-    nanoid "^3.3.4"
-    picocolors "^1.0.0"
-    source-map-js "^1.0.2"
-
-postcss@^8.4.21, postcss@^8.4.23:
-  version "8.4.26"
-  resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.26.tgz#1bc62ab19f8e1e5463d98cf74af39702a00a9e94"
-  integrity sha512-jrXHFF8iTloAenySjM/ob3gSj7pCu0Ji49hnjqzsgSRa50hkWCKD0HQ+gMNJkW38jBI68MpAAg7ZWwHwX8NMMw==
-  dependencies:
-    nanoid "^3.3.6"
-    picocolors "^1.0.0"
-    source-map-js "^1.0.2"
-
-postcss@^8.4.27:
-  version "8.4.33"
-  resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.33.tgz#1378e859c9f69bf6f638b990a0212f43e2aaa742"
-  integrity sha512-Kkpbhhdjw2qQs2O2DGX+8m5OVqEcbB9HRBvuYM9pgrjEFUg30A9LmXNlTAUj4S9kgtGyrMbTzVjH7E+s5Re2yg==
+postcss@^8.2.14, postcss@^8.4.21, postcss@^8.4.23, postcss@^8.4.27:
+  version "8.4.38"
+  resolved "https://registry.yarnpkg.com/postcss/-/postcss-8.4.38.tgz#b387d533baf2054288e337066d81c6bee9db9e0e"
+  integrity sha512-Wglpdk03BSfXkHoQa3b/oulrotAkwrlLDRSOb9D0bN86FdRyE9lppSp33aHNPgBa0JKCoB+drFLZkQoRRYae5A==
   dependencies:
     nanoid "^3.3.7"
     picocolors "^1.0.0"
-    source-map-js "^1.0.2"
+    source-map-js "^1.2.0"
 
 prettier@^1.19.1:
   version "1.19.1"
@@ -8454,17 +8441,7 @@ range-parser@^1.2.1, range-parser@~1.2.0, range-parser@~1.2.1:
   resolved "https://registry.yarnpkg.com/range-parser/-/range-parser-1.2.1.tgz#3cf37023d199e1c24d1a55b84800c2f3e6468031"
   integrity sha512-Hrgsx+orqoygnmhFbKaHE6c296J+HTAQXoxEF6gNupROmmGJRoyzfG3ccAveqCBrwr/2yxQ5BVd/GTl5agOwSg==
 
-[email protected]:
-  version "2.5.1"
-  resolved "https://registry.yarnpkg.com/raw-body/-/raw-body-2.5.1.tgz#fe1b1628b181b700215e5fd42389f98b71392857"
-  integrity sha512-qqJBtEyVgS0ZmPGdCFPWJ3FreoqvG4MVQln/kCgF7Olq95IbOp0/BWyMwbdtn4VTvkM8Y7khCQ2Xgk/tcrCXig==
-  dependencies:
-    bytes "3.1.2"
-    http-errors "2.0.0"
-    iconv-lite "0.4.24"
-    unpipe "1.0.0"
-
-raw-body@^2.3.2:
+[email protected], raw-body@^2.3.2:
   version "2.5.2"
   resolved "https://registry.yarnpkg.com/raw-body/-/raw-body-2.5.2.tgz#99febd83b90e08975087e8f1f9419a149366b68a"
   integrity sha512-8zGqypfENjCIqGhgXToC8aB2r7YrBX+AQAfIPs/Mlk+BtPTztOvTS01NRW/3Eh60J+a48lt8qsCzirQ6loCVfA==
@@ -9229,6 +9206,11 @@ socks@^2.7.1:
   resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.0.2.tgz#adbc361d9c62df380125e7f161f71c826f1e490c"
   integrity sha512-R0XvVJ9WusLiqTCEiGCmICCMplcCkIwwR11mOSD9CR5u+IXYdiseeEuXCVAjS54zqwkLcPNnmU4OeJ6tUrWhDw==
 
+source-map-js@^1.2.0:
+  version "1.2.0"
+  resolved "https://registry.yarnpkg.com/source-map-js/-/source-map-js-1.2.0.tgz#16b809c162517b5b8c3e7dcd315a2a5c2612b2af"
+  integrity sha512-itJW8lvSA0TXEphiRoawsCksnlf8SyvmFzIhltqAHluXd88pkCd+cXJVHTDwdCr0IzwptSm035IHQktUu1QUMg==
+
 [email protected]:
   version "4.0.1"
   resolved "https://registry.yarnpkg.com/source-map-loader/-/source-map-loader-4.0.1.tgz#72f00d05f5d1f90f80974eda781cbd7107c125f2"
@@ -9586,13 +9568,13 @@ tar-stream@~2.2.0:
     readable-stream "^3.1.1"
 
 tar@^6.1.11, tar@^6.1.2:
-  version "6.1.13"
-  resolved "https://registry.yarnpkg.com/tar/-/tar-6.1.13.tgz#46e22529000f612180601a6fe0680e7da508847b"
-  integrity sha512-jdIBIN6LTIe2jqzay/2vtYLlBHa3JF42ot3h1dW8Q0PaAG4v8rm0cvpVePtau5C6OKXGGcgO9q2AMNSWxiLqKw==
+  version "6.2.1"
+  resolved "https://registry.yarnpkg.com/tar/-/tar-6.2.1.tgz#717549c541bc3c2af15751bea94b1dd068d4b03a"
+  integrity sha512-DZ4yORTwrbTj/7MZYq2w+/ZFdI6OZ/f9SFHR+71gIVUZhOQPHzVCLpvRnPgyaMpfWxxk/4ONva3GQSyNIKRv6A==
   dependencies:
     chownr "^2.0.0"
     fs-minipass "^2.0.0"
-    minipass "^4.0.0"
+    minipass "^5.0.0"
     minizlib "^2.1.1"
     mkdirp "^1.0.3"
     yallist "^4.0.0"
@@ -10136,9 +10118,9 @@ [email protected]:
     schema-utils "^4.0.0"
 
 webpack-dev-middleware@^5.3.1:
-  version "5.3.3"
-  resolved "https://registry.yarnpkg.com/webpack-dev-middleware/-/webpack-dev-middleware-5.3.3.tgz#efae67c2793908e7311f1d9b06f2a08dcc97e51f"
-  integrity sha512-hj5CYrY0bZLB+eTO+x/j67Pkrquiy7kWepMHmUMoPsmcUaeEnQJqFzHJOyxgWlq746/wUuA64p9ta34Kyb01pA==
+  version "5.3.4"
+  resolved "https://registry.yarnpkg.com/webpack-dev-middleware/-/webpack-dev-middleware-5.3.4.tgz#eb7b39281cbce10e104eb2b8bf2b63fce49a3517"
+  integrity sha512-BVdTqhhs+0IfoeAf7EoH5WE+exCmqGerHfDM0IL096Px60Tq2Mn9MAbnaGUe6HiMa41KMCYF19gyzZmBcq/o4Q==
   dependencies:
     colorette "^2.0.10"
     memfs "^3.4.3"

server/db/migrate/20240416154605_update_feature_browse_table_rows_to_version_4.rb

@@ -0,0 +1,8 @@
+class UpdateFeatureBrowseTableRowsToVersion4 < ActiveRecord::Migration[7.1]
+  def change
+    update_view :feature_browse_table_rows,
+      version: 4,
+      revert_to_version: 3,
+      materialized: true
+  end
+end

server/db/migrate/20240416175953_update_variant_browse_table_rows_to_version_16.rb

@@ -0,0 +1,8 @@
+class UpdateVariantBrowseTableRowsToVersion16 < ActiveRecord::Migration[7.1]
+  def change
+    update_view :variant_browse_table_rows,
+      version: 16,
+      revert_to_version: 15,
+      materialized: true
+  end
+end