Production Update June 17 2024 (#409)

* Bump mysql2 from 3.9.7 to 3.9.8 in /test-node (#404) Bumps [mysql2](https://github.com/sidorares/node-mysql2) from 3.9.7 to 3.9.8. - [Release notes](https://github.com/sidorares/node-mysql2/releases) - [Changelog](https://github.com/sidorares/node-mysql2/blob/master/Changelog.md) - [Commits](sidorares/node-mysql2@v3.9.7...v3.9.8) --- updated-dependencies: - dependency-name: mysql2 dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Allow gnomad fields to display as empty if missing (#405) * Replace set-output the correct way (?) (#406) * Trim newlines from ssh agent eval string (#407) * Bump braces from 3.0.2 to 3.0.3 in /server (#408) Bumps [braces](https://github.com/micromatch/braces) from 3.0.2 to 3.0.3. - [Changelog](https://github.com/micromatch/braces/blob/master/CHANGELOG.md) - [Commits](micromatch/braces@3.0.2...3.0.3) --- updated-dependencies: - dependency-name: braces dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
ccmbioinfo · Jun 17, 2024 · 84d1670 · 84d1670
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commit 84d1670
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Showing 8 changed files with 30 additions and 26 deletions.
diff --git a/.github/workflows/node-prod.yml b/.github/workflows/node-prod.yml
@@ -92,12 +92,14 @@ jobs:
         #
         # https://docs.docker.com/engine/context/working-with-contexts/
         # This avoids passing an -H parameter to every Docker CLI call.
+        #
+        # We use `tr` to trim newlines. GITHUB_OUTPUT doesn't like multi-line strings
         run: |
-          SSH_AGENT_EVAL=$(ssh-agent -s)
+          SSH_AGENT_EVAL=$(ssh-agent -s | tr '\012\015' ' '; echo)
           eval "$SSH_AGENT_EVAL"
           ssh-add - <<< "${{ secrets.DEPLOY_PRIVATE_KEY }}"
-          echo "::set-output name=ssh-agent-eval::$SSH_AGENT_EVAL"
-          echo "::set-output name=ssh-agent-pid::$SSH_AGENT_PID"
+          echo "ssh-agent-eval=$SSH_AGENT_EVAL" >> $GITHUB_OUTPUT
+          echo "ssh-agent-pid=$SSH_AGENT_PID" >> $GITHUB_OUTPUT
           mkdir -p ~/.ssh
           echo "${{ secrets.DEPLOY_HOST_KEY }}" > ~/.ssh/known_hosts
           chmod -R g-rwx,o-rwx ~/.ssh

diff --git a/.github/workflows/node.yml b/.github/workflows/node.yml
@@ -137,12 +137,14 @@ jobs:
         #
         # https://docs.docker.com/engine/context/working-with-contexts/
         # This avoids passing an -H parameter to every Docker CLI call.
+        #
+        # We use `tr` to trim newlines. GITHUB_OUTPUT doesn't like multi-line strings
         run: |
-          SSH_AGENT_EVAL=$(ssh-agent -s)
+          SSH_AGENT_EVAL=$(ssh-agent -s | tr '\012\015' ' '; echo)
           eval "$SSH_AGENT_EVAL"
           ssh-add - <<< "${{ secrets.DEPLOY_PRIVATE_KEY }}"
-          echo "::set-output name=ssh-agent-eval::$SSH_AGENT_EVAL"
-          echo "::set-output name=ssh-agent-pid::$SSH_AGENT_PID"
+          echo "ssh-agent-eval=$SSH_AGENT_EVAL" >> $GITHUB_OUTPUT
+          echo "ssh-agent-pid=$SSH_AGENT_PID" >> $GITHUB_OUTPUT
           mkdir -p ~/.ssh
           echo "${{ secrets.DEPLOY_HOST_KEY }}" > ~/.ssh/known_hosts
           chmod -R g-rwx,o-rwx ~/.ssh

diff --git a/.github/workflows/react-prod.yml b/.github/workflows/react-prod.yml
@@ -38,7 +38,7 @@ jobs:
           node-version: 16
       - name: Get yarn cache directory path
         id: yarn-cache-dir-path
-        run: echo "dir=$(yarn cache dir)" >> "$GITHUB_OUTPUT"
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
       - uses: actions/cache@v4
         id: yarn-cache
         with:
@@ -75,7 +75,7 @@ jobs:
           node-version: 16
       - name: Get yarn cache path
         id: yarn-cache-path
-        run: echo "dir=$(yarn cache dir)" >> "$GITHUB_OUTPUT"
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
       - uses: actions/cache@v4
         id: restore
         with:

diff --git a/.github/workflows/react.yml b/.github/workflows/react.yml
@@ -27,7 +27,7 @@ jobs:
           node-version: 16
       - name: Get yarn cache directory path
         id: yarn-cache-dir-path
-        run: echo "dir=$(yarn cache dir)" >> "$GITHUB_OUTPUT"
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
       - uses: actions/cache@v4
         id: yarn-cache
         with:
@@ -64,7 +64,7 @@ jobs:
           node-version: 16
       - name: Get yarn cache path
         id: yarn-cache-path
-        run: echo "dir=$(yarn cache dir)" >> "$GITHUB_OUTPUT"
+        run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT
       - uses: actions/cache@v4
         id: restore
         with:

diff --git a/react/src/utils/tableHelpers.ts b/react/src/utils/tableHelpers.ts
@@ -55,9 +55,9 @@ const addAdditionalFieldsAndFormatNulls = (
     uniqueId,
     cdna: results.cdna || 'NA',
     aaChange: results.aaChange || 'NA',
-    af: results.af || 0,
-    ac: results.ac || 0,
-    gnomadHom: results.gnomadHom || 0,
+    af: results.af,
+    ac: results.ac,
+    gnomadHom: results.gnomadHom,
     // gnomadHet: results.gnomadHet || 0,
     maleCount: 0,
     geneName: !!results.geneName ? results.geneName! : 'Not Specified',

diff --git a/server/yarn.lock b/server/yarn.lock
@@ -2712,11 +2712,11 @@ brace-expansion@^1.1.7:
     concat-map "0.0.1"
 
 braces@^3.0.2, braces@~3.0.2:
-  version "3.0.2"
-  resolved "https://registry.yarnpkg.com/braces/-/braces-3.0.2.tgz#3454e1a462ee8d599e236df336cd9ea4f8afe107"
-  integrity sha512-b8um+L1RzM3WDSzvhm6gIz1yfTbBt6YTlcEKAvsmqCZZFw46z626lVj9j1yEPW33H5H+lBQpZMP1k8l+78Ha0A==
+  version "3.0.3"
+  resolved "https://registry.yarnpkg.com/braces/-/braces-3.0.3.tgz#490332f40919452272d55a8480adc0c441358789"
+  integrity sha512-yQbXgO/OSZVD2IsiLlro+7Hf6Q18EJrKSEsdoMzKePKXct3gvD8oLcOQdIzGupr5Fj+EDe8gO/lxc1BzfMpxvA==
   dependencies:
-    fill-range "^7.0.1"
+    fill-range "^7.1.1"
 
 brorand@^1.1.0:
   version "1.1.0"
@@ -3759,10 +3759,10 @@ file-uri-to-path@^2.0.0:
   resolved "https://registry.yarnpkg.com/file-uri-to-path/-/file-uri-to-path-2.0.0.tgz#7b415aeba227d575851e0a5b0c640d7656403fba"
   integrity sha512-hjPFI8oE/2iQPVe4gbrJ73Pp+Xfub2+WI2LlXDbsaJBwT5wuMh35WNWVYYTpnz895shtwfyutMFLFywpQAFdLg==
 
-fill-range@^7.0.1:
-  version "7.0.1"
-  resolved "https://registry.yarnpkg.com/fill-range/-/fill-range-7.0.1.tgz#1919a6a7c75fe38b2c7c77e5198535da9acdda40"
-  integrity sha512-qOo9F+dMUmC2Lcb4BbVvnKJxTPjCm+RRpe4gDuGrzkL7mEVl/djYSu2OdQ2Pa302N4oqkSg9ir6jaLWJ2USVpQ==
+fill-range@^7.1.1:
+  version "7.1.1"
+  resolved "https://registry.yarnpkg.com/fill-range/-/fill-range-7.1.1.tgz#44265d3cac07e3ea7dc247516380643754a05292"
+  integrity sha512-YsGpe3WHLK8ZYi4tWDg2Jy3ebRz2rXowDxnld4bkQB00cc/1Zw9AWnC0i9ztDJitivtQvaI9KaLyKrc+hBW0yg==
   dependencies:
     to-regex-range "^5.0.1"
 

diff --git a/test-node/package.json b/test-node/package.json
@@ -13,7 +13,7 @@
     "express": "^4.19.2",
     "express-jwt": "^6.1.0",
     "jwks-rsa": "^2.0.4",
-    "mysql2": "^3.9.7"
+    "mysql2": "^3.9.8"
   },
   "devDependencies": {
     "@tsconfig/node16": "^1.0.2",

diff --git a/test-node/yarn.lock b/test-node/yarn.lock
@@ -1652,10 +1652,10 @@ [email protected], ms@^2.1.1:
   resolved "https://registry.yarnpkg.com/ms/-/ms-2.1.3.tgz#574c8138ce1d2b5861f0b44579dbadd60c6615b2"
   integrity sha512-6FlzubTLZG3J2a/NVCAleEhjzq5oxgHyaCU9yYXvcLsvoVaHJq/s5xXI6/XXP6tz7R9xAOtHnSO/tXtF3WRTlA==
 
-mysql2@^3.9.7:
-  version "3.9.7"
-  resolved "https://registry.yarnpkg.com/mysql2/-/mysql2-3.9.7.tgz#843755daf65b5ef08afe545fe14b8fb62824741a"
-  integrity sha512-KnJT8vYRcNAZv73uf9zpXqNbvBG7DJrs+1nACsjZP1HMJ1TgXEy8wnNilXAn/5i57JizXKtrUtwDB7HxT9DDpw==
+mysql2@^3.9.8:
+  version "3.9.8"
+  resolved "https://registry.yarnpkg.com/mysql2/-/mysql2-3.9.8.tgz#fe8a0f975f2c495ed76ca988ddc5505801dc49ce"
+  integrity sha512-+5JKNjPuks1FNMoy9TYpl77f+5frbTklz7eb3XDwbpsERRLEeXiW2PDEkakYF50UuKU2qwfGnyXpKYvukv8mGA==
   dependencies:
     denque "^2.1.0"
     generate-function "^2.3.1"