From e3da29f3e96102c1498a05712a9f7a21d8bc8767 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Fri, 17 May 2024 08:49:41 -0400 Subject: [PATCH 001/159] Adjust SECURITY.md to reflect that we call yearly releases LTS, actual practice is the same. --- SECURITY.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/SECURITY.md b/SECURITY.md index 2b30ab9b1106..c1dcb56f30e9 100644 --- a/SECURITY.md +++ b/SECURITY.md @@ -16,8 +16,7 @@ The following branches or releases receive security support: - Development on the `dev` branch, hosted on GitHub, which will become the next release of Galaxy - Releases within the past 12 months. - - E.g. 16.04 will receive support until 2017-04. As the month changes to 2017-05 it will become unsupported. -- There are currently no plans for Long Term Support (LTS) releases. + - E.g. 24.0 will receive support for a full year, at which point 25.0 will be available. For unsupported branches: From 46c247d3f90ffc04a0b7f5bfac3efcabddce3887 Mon Sep 17 00:00:00 2001 From: guerler Date: Sun, 7 Apr 2024 07:49:54 +0300 Subject: [PATCH 002/159] Remove masthead icons --- client/src/components/Masthead/Masthead.vue | 9 +- client/src/entry/analysis/menu.js | 150 +------------------- 2 files changed, 5 insertions(+), 154 deletions(-) diff --git a/client/src/components/Masthead/Masthead.vue b/client/src/components/Masthead/Masthead.vue index 0390029c3951..3b4ff0f44269 100644 --- a/client/src/components/Masthead/Masthead.vue +++ b/client/src/components/Masthead/Masthead.vue @@ -14,8 +14,6 @@ import MastheadItem from "./MastheadItem"; import QuotaMeter from "./QuotaMeter"; import { getActiveTab } from "./utilities"; -import NotificationsBell from "@/components/Notifications/NotificationsBell.vue"; - const { isAnonymous } = storeToRefs(useUserStore()); const route = useRoute(); @@ -138,13 +136,8 @@ onMounted(() => { :active-tab="activeTab" @open-url="emit('open-url', $event)" /> - - - + - diff --git a/client/src/entry/analysis/menu.js b/client/src/entry/analysis/menu.js index ec1de4f190af..7d5f0adbe8a4 100644 --- a/client/src/entry/analysis/menu.js +++ b/client/src/entry/analysis/menu.js @@ -18,124 +18,12 @@ export function fetchMenu(options = {}) { target: "_top", }); - // - // Workflow tab. - // - menu.push({ - id: "workflow", - title: _l("Workflow"), - tooltip: _l("Chain tools into workflows"), - disabled: !Galaxy.user.id, - url: "/workflows/list", - }); - - // - // Visualization tab. - // - if (Galaxy.config.visualizations_visible) { - menu.push({ - id: "visualization", - title: _l("Visualize"), - tooltip: _l("Visualize datasets"), - disabled: !Galaxy.user.id, - url: "/visualizations", - }); - } - - // - // 'Data' tab. - // - if (Galaxy.user.id) { - menu.push({ - id: "resources", - title: _l("Data"), - url: "javascript:void(0)", - tooltip: _l("Access resources"), - menu: [ - { - title: _l("Data Libraries"), - url: "/libraries", - }, - { - title: _l("Datasets"), - url: "/datasets/list", - }, - { - title: _l("Histories"), - url: "/histories/list", - }, - { - title: _l("Pages"), - url: "/pages/list", - }, - { - title: _l("Visualizations"), - url: "/visualizations/list", - }, - { - title: _l("Workflows"), - url: "/workflows/list", - }, - { - title: _l("Workflow Invocations"), - url: "/workflows/invocations", - }, - ], - }); - } else { - menu.push({ - id: "resources", - title: _l("Data"), - url: "javascript:void(0)", - tooltip: _l("Access published resources"), - menu: [ - { - title: _l("Data Libraries"), - url: "/libraries", - }, - { - title: _l("Histories"), - url: "/histories/list_published", - }, - { - title: _l("Pages"), - url: "/pages/list_published", - }, - { - title: _l("Visualizations"), - url: "/visualizations/list_published", - }, - { - title: _l("Workflows"), - url: "/workflows/list_published", - }, - ], - }); - } - - // - // Admin. - // - if (Galaxy.user.get("is_admin")) { - menu.push({ - id: "admin", - title: _l("Admin"), - url: "/admin", - tooltip: _l("Administer this Galaxy"), - cls: "admin-only", - onclick: () => { - const userStore = useUserStore(); - userStore.toggleSideBar("admin"); - }, - }); - } - // // Help tab. // const helpTab = { id: "help", - title: _l("Help"), + icon: "fa-question", url: "javascript:void(0)", tooltip: _l("Support, contact, and community"), menu: [ @@ -213,42 +101,12 @@ export function fetchMenu(options = {}) { } else { userTab = { id: "user", - title: _l("User"), + icon: "fa-sign-out-alt", cls: "loggedin-only", - url: "javascript:void(0)", - tooltip: _l("Account and saved data"), - menu: [ - { - title: `${_l("Signed in as")} ${ - Galaxy.user.get("username") ? Galaxy.user.get("username") : Galaxy.user.get("email") - }`, - disabled: true, - }, - { divider: true }, - ], - }; - if (Galaxy.config.interactivetools_enable) { - userTab.menu.push({ - title: _l("Active Interactive Tools"), - url: "/interactivetool_entry_points/list", - }); - } - if (Galaxy.config.enable_notification_system) { - userTab.menu.push({ - title: _l("Notifications"), - url: "/user/notifications", - }); - } - userTab.menu.push({ divider: true }); - userTab.menu.push({ - title: _l("Preferences"), - url: "/user", - }); - userTab.menu.push({ - title: _l("Sign Out"), onclick: userLogout, hidden: Galaxy.config.single_user, - }); + tooltip: _l("Logout"), + }; } menu.push(userTab); return menu; From 9cbb3182a25106750dba9139ae489a642f11c870 Mon Sep 17 00:00:00 2001 From: guerler Date: Sun, 7 Apr 2024 08:17:02 +0300 Subject: [PATCH 003/159] Adjust masthead size --- client/src/components/Masthead/Masthead.vue | 15 ++++++++------- client/src/style/scss/theme/blue.scss | 2 +- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/client/src/components/Masthead/Masthead.vue b/client/src/components/Masthead/Masthead.vue index 3b4ff0f44269..cc6680c58158 100644 --- a/client/src/components/Masthead/Masthead.vue +++ b/client/src/components/Masthead/Masthead.vue @@ -103,7 +103,7 @@ onMounted(() => { @@ -177,12 +177,12 @@ onMounted(() => { color: var(--masthead-text-hover); } &.nav-icon { - font-size: 1.3em; + font-size: 1em; .nav-note { position: absolute; - left: 1.9rem; - top: 1.9rem; - font-size: 0.6rem; + left: 1.4rem; + top: 1.4rem; + font-size: 0.4rem; font-weight: bold; } } @@ -194,11 +194,12 @@ onMounted(() => { } .navbar-brand { cursor: pointer; + line-height: $masthead-height; img { filter: $text-shadow; display: inline; border: none; - height: 2.3rem; + height: 2rem; } } .navbar-text { @@ -206,7 +207,7 @@ onMounted(() => { font-weight: bold; font-family: Verdana, sans-serif; font-size: 1rem; - line-height: 2rem; + line-height: $masthead-height; color: var(--masthead-text-color); } } diff --git a/client/src/style/scss/theme/blue.scss b/client/src/style/scss/theme/blue.scss index 24c9f4972e8a..bd34431a210b 100644 --- a/client/src/style/scss/theme/blue.scss +++ b/client/src/style/scss/theme/blue.scss @@ -110,7 +110,7 @@ $input-color-placeholder: $text-muted; $body-bg: $white; // Masthead -$masthead-height: 3rem; +$masthead-height: 2.5rem; // Side panels $panel-bg-color: $brand-light; From 97cc442d9cadd06a68a70aa034838b52994de6f6 Mon Sep 17 00:00:00 2001 From: guerler Date: Mon, 20 May 2024 11:26:47 +0300 Subject: [PATCH 004/159] Remove masthead dropdown handler, only allow regular tabs --- .../src/components/Masthead/MastheadItem.vue | 33 ------------------- 1 file changed, 33 deletions(-) diff --git a/client/src/components/Masthead/MastheadItem.vue b/client/src/components/Masthead/MastheadItem.vue index 889526e01ffa..43d28f9d675f 100644 --- a/client/src/components/Masthead/MastheadItem.vue +++ b/client/src/components/Masthead/MastheadItem.vue @@ -27,7 +27,6 @@ const props = defineProps({ }); /* computed */ -const menu = computed(() => props.tab.menu); const popoverNote = computed( () => `Please log in or register to use this feature.` ); @@ -71,7 +70,6 @@ function open(tab, event) { From 43c12261e7165ab7af7d4c16fc3c60c7ab8d1ad8 Mon Sep 17 00:00:00 2001 From: guerler Date: Mon, 20 May 2024 11:28:02 +0300 Subject: [PATCH 005/159] Remove unused imports from masthead item component --- client/src/components/Masthead/MastheadItem.vue | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/client/src/components/Masthead/MastheadItem.vue b/client/src/components/Masthead/MastheadItem.vue index 43d28f9d675f..d73887928908 100644 --- a/client/src/components/Masthead/MastheadItem.vue +++ b/client/src/components/Masthead/MastheadItem.vue @@ -1,14 +1,13 @@