/* ---------------------------------------------------------------------- */ /* Phage Annotation Server -- hand-written CSS, no build step, no CDN. */ /* Self-hosted only (PLAN.md 6.4.3), so this file is the entire visual */ /* design system: tokens, layout primitives, and every component below. */ /* */ /* Brand palette, sampled from the pharokka / phold logos: */ /* teal #008AA6 black #000000 cream #F8F0E3 */ /* white #FFFFFF grey #767676 / #B1B1B1 */ /* --color-brand-teal is the literal logo hex -- used decoratively (icons, */ /* borders, dots, badges with dark text on it). --color-primary is a */ /* slightly darkened teal used anywhere text sits directly on/as it, so */ /* body-text-sized links and button labels clear WCAG AA (4.5:1) rather */ /* than the logo teal's ~4:1 against white/cream. See PLAN.md 6.4.3. */ /* ---------------------------------------------------------------------- */ :root { /* -- color tokens (light) --------------------------------------------- */ --color-bg: #ffffff; --color-surface: #ffffff; --color-surface-muted: #f8f0e3; --color-border: #ddd2ba; --color-text: #16130e; --color-text-muted: #6a6a6a; --color-brand-teal: #008aa6; --color-primary: #00738a; --color-primary-hover: #005f73; --color-primary-contrast: #ffffff; --color-accent-soft: #dcf0f3; --color-danger: #b3261e; --color-danger-soft: #fbe9e7; --color-success: #00738a; --color-success-soft: #dcf0f3; --color-focus-ring: #008aa6; --color-link: #00738a; /* -- scale -------------------------------------------------------------- */ --space-1: 0.25rem; --space-2: 0.5rem; --space-3: 0.75rem; --space-4: 1rem; --space-5: 1.5rem; --space-6: 2rem; --space-7: 3rem; --space-8: 4rem; --radius-sm: 6px; --radius-md: 10px; --radius-lg: 16px; --shadow-card: 0 1px 2px rgba(20, 16, 10, 0.05), 0 8px 24px rgba(20, 16, 10, 0.08); --max-width: 72rem; --max-width-prose: 42rem; --font-sans: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Helvetica, Arial, sans-serif, "Apple Color Emoji", "Segoe UI Emoji"; --font-mono: ui-monospace, SFMono-Regular, Menlo, Consolas, "Liberation Mono", monospace; } @media (prefers-color-scheme: dark) { :root { --color-bg: #000000; --color-surface: #121212; --color-surface-muted: #1c1c1c; --color-border: #333333; --color-text: #f8f0e3; --color-text-muted: #b1b1b1; --color-brand-teal: #00a6c6; --color-primary: #00a6c6; --color-primary-hover: #33bcd8; --color-primary-contrast: #000000; --color-accent-soft: rgba(0, 166, 198, 0.16); --color-danger: #ff6b62; --color-danger-soft: #3a1e1c; --color-success: #00a6c6; --color-success-soft: rgba(0, 166, 198, 0.16); --color-focus-ring: #00a6c6; --color-link: #35c2e0; --shadow-card: 0 1px 2px rgba(0, 0, 0, 0.5), 0 8px 24px rgba(0, 0, 0, 0.55); } } /* Manual theme override hooks -- web/static/js/theme-toggle.js sets * data-theme on for an explicit user choice, and * web/static/js/theme-init.js re-applies a *stored* choice before first * paint (avoiding a flash of the wrong theme). These need the FULL variable * set, not just `color-scheme`: an attribute selector has higher * specificity than a bare `:root` (including the one inside the * `prefers-color-scheme` media query above), so explicitly repeating each * theme's values here is what lets an explicit choice correctly override * the OS setting in either direction -- e.g. "light" chosen while the OS * prefers dark, or vice versa. Keep in sync with the two blocks above by * construction: same hex values, just reachable a different way. */ :root[data-theme="dark"] { color-scheme: dark; --color-bg: #000000; --color-surface: #121212; --color-surface-muted: #1c1c1c; --color-border: #333333; --color-text: #f8f0e3; --color-text-muted: #b1b1b1; --color-brand-teal: #00a6c6; --color-primary: #00a6c6; --color-primary-hover: #33bcd8; --color-primary-contrast: #000000; --color-accent-soft: rgba(0, 166, 198, 0.16); --color-danger: #ff6b62; --color-danger-soft: #3a1e1c; --color-success: #00a6c6; --color-success-soft: rgba(0, 166, 198, 0.16); --color-focus-ring: #00a6c6; --color-link: #35c2e0; --shadow-card: 0 1px 2px rgba(0, 0, 0, 0.5), 0 8px 24px rgba(0, 0, 0, 0.55); } :root[data-theme="light"] { color-scheme: light; --color-bg: #ffffff; --color-surface: #ffffff; --color-surface-muted: #f8f0e3; --color-border: #ddd2ba; --color-text: #16130e; --color-text-muted: #6a6a6a; --color-brand-teal: #008aa6; --color-primary: #00738a; --color-primary-hover: #005f73; --color-primary-contrast: #ffffff; --color-accent-soft: #dcf0f3; --color-danger: #b3261e; --color-danger-soft: #fbe9e7; --color-success: #00738a; --color-success-soft: #dcf0f3; --color-focus-ring: #008aa6; --color-link: #00738a; --shadow-card: 0 1px 2px rgba(20, 16, 10, 0.05), 0 8px 24px rgba(20, 16, 10, 0.08); } /* ---------------------------------------------------------------------- */ /* Reset */ /* ---------------------------------------------------------------------- */ *, *::before, *::after { box-sizing: border-box; } html { color-scheme: light dark; -webkit-text-size-adjust: 100%; } body { margin: 0; font-family: var(--font-sans); font-size: 16px; line-height: 1.55; color: var(--color-text); background: var(--color-bg); } h1, h2, h3, h4 { line-height: 1.25; margin: 0 0 var(--space-4); } h1 { font-size: 2rem; } h2 { font-size: 1.3rem; margin-top: var(--space-6); } h3 { font-size: 1.1rem; } p { margin: 0 0 var(--space-4); } a { color: var(--color-link); } img, svg { max-width: 100%; display: block; } ul, ol { padding-left: 1.25rem; } code { font-family: var(--font-mono); background: var(--color-surface-muted); border-radius: 4px; padding: 0.1em 0.4em; font-size: 0.9em; } button { font: inherit; } /* Component classes below (e.g. .button) set their own `display`, which is * equal-specificity with the UA stylesheet's `[hidden] { display: none }` * and would otherwise win the cascade by source order -- silently breaking * the plain HTML `hidden` attribute used throughout for JS-free, no-flash * server-rendered show/hide (tabs, status-page action buttons). Force it * to always win instead of chasing `.foo[hidden]` overrides per component. */ [hidden] { display: none !important; } :focus-visible { outline: 2px solid var(--color-focus-ring); outline-offset: 2px; border-radius: 4px; } .visually-hidden { position: absolute; width: 1px; height: 1px; padding: 0; margin: -1px; overflow: hidden; clip: rect(0, 0, 0, 0); white-space: nowrap; border: 0; } .skip-link { position: absolute; left: var(--space-4); top: -3rem; background: var(--color-primary); color: var(--color-primary-contrast); padding: var(--space-2) var(--space-4); border-radius: var(--radius-sm); z-index: 100; transition: top 0.15s ease; } .skip-link:focus { top: var(--space-4); } /* ---------------------------------------------------------------------- */ /* Layout primitives */ /* ---------------------------------------------------------------------- */ .container { max-width: var(--max-width); margin-inline: auto; padding-inline: var(--space-5); } .card { background: var(--color-surface); border: 1px solid var(--color-border); border-radius: var(--radius-lg); box-shadow: var(--shadow-card); padding: var(--space-6); margin-bottom: var(--space-6); } .table-scroll { overflow-x: auto; border: 1px solid var(--color-border); border-radius: var(--radius-md); } /* ---------------------------------------------------------------------- */ /* Header / nav */ /* ---------------------------------------------------------------------- */ .site-header { border-bottom: 3px solid var(--color-brand-teal); background: var(--color-surface); position: sticky; top: 0; z-index: 10; } .site-header__bar { display: flex; align-items: center; justify-content: space-between; flex-wrap: wrap; gap: var(--space-3); padding-block: var(--space-4); } .site-header__brand { display: inline-flex; align-items: center; gap: 0.5em; font-weight: 800; /* Was 1.15rem -- read as small next to the rest of the page (hero h1 is * 2.4rem). Bumped for prominence; the icon before it is sized in `em` so * it scales along with the text automatically. Kept a notch smaller on * narrow screens (below) purely so five nav links + the theme toggle * keep their existing single-row layout at common tablet widths -- * mobile already wraps the nav to its own row by design (flex-wrap on * .site-header__bar), so this isn't about fitting everything on one line * there, just not overflowing/wrapping the brand text itself. */ font-size: 1.5rem; letter-spacing: -0.01em; color: var(--color-text); text-decoration: none; white-space: nowrap; } @media (max-width: 30rem) { .site-header__brand { font-size: 1.25rem; } } .site-header__brand::before { content: ""; display: inline-block; width: 0.8em; height: 0.8em; border-radius: 3px; background: var(--color-brand-teal); } .site-nav { display: flex; align-items: center; gap: var(--space-5); } .site-nav a { color: var(--color-text-muted); text-decoration: none; font-weight: 500; padding-block: var(--space-1); border-bottom: 2px solid transparent; } .site-nav a:hover { color: var(--color-text); } .site-nav a[aria-current="page"] { color: var(--color-primary); border-bottom-color: var(--color-primary); } /* ---------------------------------------------------------------------- */ /* Theme toggle (site header) */ /* ---------------------------------------------------------------------- */ .theme-toggle { display: inline-flex; align-items: center; justify-content: center; width: 2.25rem; height: 2.25rem; padding: 0; border: 1px solid var(--color-border); border-radius: var(--radius-sm); background: var(--color-surface); color: var(--color-text); cursor: pointer; flex: none; } .theme-toggle:hover { border-color: var(--color-primary); color: var(--color-primary); } /* Icon shown depends on the *effective* theme, resolved with no JS * dependency wherever possible so there's no icon flash to match the (JS- * free) page-background behaviour: `prefers-color-scheme` picks the OS- * default icon, and an explicit `data-theme` on (stamped before * paint by theme-init.js when a choice was previously stored) always wins * over it. `theme-toggle.js` additionally stamps `data-theme` on the button * itself so this stays correct immediately after a click, before any * ``-level attribute would otherwise be re-read. */ .theme-toggle__icon--moon { display: none; } @media (prefers-color-scheme: dark) { .theme-toggle__icon--sun { display: none; } .theme-toggle__icon--moon { display: block; } } :root[data-theme="dark"] .theme-toggle__icon--sun, .theme-toggle[data-theme="dark"] .theme-toggle__icon--sun { display: none; } :root[data-theme="dark"] .theme-toggle__icon--moon, .theme-toggle[data-theme="dark"] .theme-toggle__icon--moon { display: block; } :root[data-theme="light"] .theme-toggle__icon--sun, .theme-toggle[data-theme="light"] .theme-toggle__icon--sun { display: block; } :root[data-theme="light"] .theme-toggle__icon--moon, .theme-toggle[data-theme="light"] .theme-toggle__icon--moon { display: none; } /* ---------------------------------------------------------------------- */ /* Footer */ /* ---------------------------------------------------------------------- */ .site-footer { border-top: 3px solid var(--color-brand-teal); margin-top: var(--space-8); padding-block: var(--space-6); color: var(--color-text-muted); font-size: 0.9rem; } .site-footer__meta { margin-bottom: 0; } .site-footer__links { display: flex; flex-wrap: wrap; gap: var(--space-2) var(--space-4); margin: 0 0 var(--space-3); padding: 0; list-style: none; } .site-footer__links a { color: var(--color-text-muted); font-weight: 600; text-decoration: none; } .site-footer__links a:hover { color: var(--color-primary); text-decoration: underline; } /* Lightly obfuscated mailto -- see web/static/js/obfuscated-mail.js. The * holds a human-readable placeholder for no-JS / scraper contexts; * JS swaps it for a real mailto: link once the DOM is ready. */ .obfuscated-email { color: var(--color-text-muted); font-weight: 600; } a.obfuscated-email { text-decoration: underline; } a.obfuscated-email:hover { color: var(--color-primary); } /* ---------------------------------------------------------------------- */ /* Hero + submit form (the primary action -- PLAN.md 6.4.3) */ /* ---------------------------------------------------------------------- */ .hero { display: grid; gap: var(--space-6); padding-block: var(--space-7) var(--space-5); } @media (min-width: 900px) { .hero { grid-template-columns: 1fr 1fr; align-items: start; padding-block: var(--space-8) var(--space-6); } } .hero__intro h1 { font-size: 2.4rem; } .hero__lede { font-size: 1.1rem; color: var(--color-text-muted); max-width: 38rem; } /* Fills the space below the intro text in the hero's left column with the * pipeline logo strip (moved here from further down the page -- see * `.brand-logos` below, which this reuses rather than duplicating). */ .hero__pipeline { margin-top: var(--space-6); } .hero__pipeline-note { margin: 0 0 var(--space-3); font-size: 0.95rem; font-weight: 600; color: var(--color-text-muted); } .upload-form { margin-bottom: 0; } .field { margin-bottom: var(--space-5); } .field label { display: block; font-weight: 600; margin-bottom: var(--space-2); } .field__optional { font-weight: 400; color: var(--color-text-muted); } .field__hint { margin: var(--space-2) 0 0; font-size: 0.875rem; color: var(--color-text-muted); } .field input[type="text"], .field input[type="email"], .field input[type="number"], .field input[type="file"], .field select { width: 100%; padding: var(--space-3); font-size: 1rem; border: 1px solid var(--color-border); border-radius: var(--radius-sm); background: var(--color-surface); color: var(--color-text); } .field input[type="file"] { padding: var(--space-2); } .field--checkbox { display: flex; align-items: flex-start; gap: var(--space-3); } .field--checkbox input { margin-top: 0.3em; width: 1.1em; height: 1.1em; } .field--checkbox label { margin-bottom: 0; font-weight: 500; } .field label code, .field--checkbox label code { font-size: 0.8em; font-weight: 400; color: var(--color-text-muted); } /* ---------------------------------------------------------------------- */ /* Advanced options (submit form) */ /* ---------------------------------------------------------------------- */ .advanced-options { margin: var(--space-2) 0 var(--space-5); border: 1px solid var(--color-border); border-radius: var(--radius-md); padding: var(--space-4) var(--space-5); background: var(--color-surface-muted); } .advanced-options summary { cursor: pointer; font-weight: 700; padding-block: var(--space-1); } .advanced-options[open] summary { margin-bottom: var(--space-3); } .advanced-options__intro { margin-top: 0; } .advanced-group { padding-top: var(--space-4); margin-top: var(--space-4); border-top: 1px dashed var(--color-border); } .advanced-group:first-of-type { padding-top: 0; margin-top: 0; border-top: none; } .advanced-group__title { margin: 0 0 var(--space-3); font-size: 0.95rem; text-transform: uppercase; letter-spacing: 0.03em; color: var(--color-text-muted); } /* ---------------------------------------------------------------------- */ /* Buttons */ /* ---------------------------------------------------------------------- */ .button { display: inline-flex; align-items: center; justify-content: center; gap: var(--space-2); padding: 0.7rem 1.3rem; border-radius: var(--radius-sm); font-weight: 600; text-decoration: none; border: 1px solid transparent; cursor: pointer; transition: background-color 0.12s ease, border-color 0.12s ease, color 0.12s ease; } .button--primary { background: var(--color-primary); color: var(--color-primary-contrast); } .button--primary:hover { background: var(--color-primary-hover); } .button--secondary { background: transparent; border-color: var(--color-border); color: var(--color-text); } .button--secondary:hover { border-color: var(--color-primary); color: var(--color-primary); } .button--block { width: 100%; } .button[disabled] { opacity: 0.6; cursor: not-allowed; } /* ---------------------------------------------------------------------- */ /* Alerts */ /* ---------------------------------------------------------------------- */ .alert { border-radius: var(--radius-md); padding: var(--space-4); margin-bottom: var(--space-4); border: 1px solid transparent; } .alert--error { background: var(--color-danger-soft); border-color: var(--color-danger); color: var(--color-danger); } /* Caution callout -- used on /licenses and /terms to flag the commercially * restricted databases (CARD, VFDB). Uses the brand teal rather than a new * warning hue: it must read as "important, read this", not as an error, and * introducing a fourth accent colour would dilute the palette. Border-led so * it stays legible in both themes without a bespoke background per theme. */ .alert--warn { background: var(--color-accent-soft); border-color: var(--color-primary); color: var(--color-text); border-left-width: 4px; } .alert--warn p:last-child { margin-bottom: 0; } /* Intro paragraph on prose pages (terms, licences). Slightly larger and * muted -- a summary the reader can stop at if the detail below isn't * relevant to them. */ .lede { font-size: 1.1rem; line-height: 1.6; color: var(--color-text-muted); margin-bottom: var(--space-5); } /* ---------------------------------------------------------------------- */ /* Pipeline explainer (index page) */ /* ---------------------------------------------------------------------- */ .pipeline-explainer { padding-block: var(--space-6); border-top: 1px solid var(--color-border); } .steps { list-style: none; padding: 0; display: grid; gap: var(--space-5); counter-reset: step; } @media (min-width: 700px) { .steps { grid-template-columns: repeat(3, 1fr); } } .steps > li { counter-increment: step; background: var(--color-surface); border: 1px solid var(--color-border); border-radius: var(--radius-md); padding: var(--space-5); position: relative; padding-top: var(--space-6); } .steps > li::before { content: counter(step); position: absolute; top: -0.6rem; left: var(--space-5); background: var(--color-primary); color: var(--color-primary-contrast); width: 1.6rem; height: 1.6rem; border-radius: 50%; display: flex; align-items: center; justify-content: center; font-size: 0.85rem; font-weight: 700; } .steps p { margin: var(--space-2) 0 0; color: var(--color-text-muted); } .pipeline-explainer__note { color: var(--color-text-muted); } /* ---------------------------------------------------------------------- */ /* Brand logos -- pharokka -> phold -> phynteny (index + about pages) */ /* ---------------------------------------------------------------------- */ .brand-logos { display: flex; flex-wrap: wrap; align-items: center; justify-content: center; gap: var(--space-4); padding-block: var(--space-5); } .brand-logo-tile { display: flex; flex-direction: column; align-items: center; gap: var(--space-2); padding: var(--space-4) var(--space-5); background: var(--color-surface); border: 1px solid var(--color-border); border-radius: var(--radius-md); text-decoration: none; color: var(--color-text); transition: border-color 0.12s ease, box-shadow 0.12s ease, transform 0.12s ease; } .brand-logo-tile:hover, .brand-logo-tile:focus-visible { border-color: var(--color-brand-teal); box-shadow: var(--shadow-card); transform: translateY(-2px); } .brand-logo-tile__mark { /* Cream chip behind every logo -- makes pharokka/phold's transparent * artwork read as an intentional tile, and stops phynteny's own white * background from floating awkwardly on a dark-mode card. */ display: flex; align-items: center; justify-content: center; width: 5.5rem; height: 5.5rem; background: #f8f0e3; border-radius: var(--radius-md); padding: var(--space-2); } .brand-logo-tile__mark img { max-width: 100%; max-height: 100%; width: auto; height: auto; } .brand-logo-tile__name { font-weight: 700; } .brand-logos__arrow { color: var(--color-brand-teal); font-size: 1.5rem; font-weight: 700; align-self: center; } @media (max-width: 640px) { .brand-logos__arrow { transform: rotate(90deg); } } /* Smaller footprint for the hero's narrower column (`.hero__pipeline` * above) -- same component, just sized to fit next to the submit form * instead of spanning the full page width. Left-aligned to match the rest * of the hero copy; still wraps and rotates its arrows on narrow viewports * via the shared rules above. */ /* Hero pipeline: a VERTICAL chain, one full-width row per tool. * * The hero's left column is tall -- it sits beside the entire upload form -- * so a horizontal strip of small tiles left a large empty area beneath it. * Stacking the three tools with big marks fills that column and reads more * clearly as an ordered pipeline. */ .brand-logos--compact { display: flex; flex-direction: column; align-items: stretch; gap: var(--space-2); padding-block: 0; } .brand-logos--compact .brand-logo-tile { display: flex; flex-direction: row; align-items: center; justify-content: flex-start; gap: var(--space-4); width: 100%; padding: var(--space-3) var(--space-4); } /* The three logos have very different aspect ratios: pharokka is a square * roundel (~1:1) while phold (512x135, ~3.8:1) and phynteny are wide * wordmarks. A fixed square chip shrank the wordmarks to roughly a sixth of * the available height, which read as "faint" rather than "small". So the * chip is a fixed HEIGHT with flexible width, and each image is contained * within it -- every logo then renders as large as its own shape allows. */ .brand-logos--compact .brand-logo-tile__mark { width: auto; min-width: 6rem; max-width: 14rem; height: 6rem; flex: none; padding: var(--space-2) var(--space-3); } .brand-logos--compact .brand-logo-tile__mark img { max-width: 100%; max-height: 100%; width: auto; height: auto; object-fit: contain; } .brand-logos--compact .brand-logo-tile__name { /* Was 1.2rem. See the @media block below for the (also-bumped) narrow- * viewport value. */ font-size: 1.35rem; font-weight: 700; } /* The markup uses right-arrow glyphs; rotating them keeps one template that * works in both orientations rather than duplicating the entity. */ .brand-logos--compact .brand-logos__arrow { align-self: center; transform: rotate(90deg); font-size: 1.35rem; line-height: 1; color: var(--color-text-muted); } @media (max-width: 32rem) { .brand-logos--compact .brand-logo-tile__mark { width: 4.5rem; height: 4.5rem; } .brand-logos--compact .brand-logo-tile__name { font-size: 1.1rem; /* was 1rem */ } } /* ---------------------------------------------------------------------- */ /* Stage tracker (status page headline feature) */ /* ---------------------------------------------------------------------- */ .stage-tracker { list-style: none; display: flex; padding: 0; margin: var(--space-6) 0; gap: 0; } .stage-tracker__step { flex: 1; display: flex; flex-direction: column; align-items: center; text-align: center; position: relative; padding-top: var(--space-2); } .stage-tracker__step:not(:first-child)::before { content: ""; position: absolute; top: 0.95rem; left: -50%; width: 100%; height: 3px; background: var(--color-border); z-index: 0; } .stage-tracker__step[data-state="done"]:not(:first-child)::before, .stage-tracker__step[data-state="active"]:not(:first-child)::before { background: var(--color-primary); } .stage-tracker__dot { width: 1.9rem; height: 1.9rem; border-radius: 50%; background: var(--color-surface); border: 3px solid var(--color-border); z-index: 1; display: flex; align-items: center; justify-content: center; } .stage-tracker__step[data-state="pending"] .stage-tracker__dot { border-color: var(--color-border); } .stage-tracker__step[data-state="active"] .stage-tracker__dot { border-color: var(--color-primary); background: var(--color-accent-soft); animation: pulse 1.6s ease-in-out infinite; } .stage-tracker__step[data-state="done"] .stage-tracker__dot { border-color: var(--color-success); background: var(--color-success); } .stage-tracker__step[data-state="done"] .stage-tracker__dot::after { content: "\2713"; color: var(--color-primary-contrast); font-size: 0.95rem; font-weight: 700; } .stage-tracker__step[data-state="error"] .stage-tracker__dot { border-color: var(--color-danger); background: var(--color-danger-soft); } .stage-tracker__step[data-state="error"] .stage-tracker__dot::after { content: "!"; color: var(--color-danger); font-weight: 700; } .stage-tracker__label { margin-top: var(--space-2); font-size: 0.9rem; font-weight: 600; color: var(--color-text-muted); } .stage-tracker__step[data-state="active"] .stage-tracker__label, .stage-tracker__step[data-state="done"] .stage-tracker__label { color: var(--color-text); } @keyframes pulse { 0%, 100% { box-shadow: 0 0 0 0 rgba(31, 111, 92, 0.35); } 50% { box-shadow: 0 0 0 6px rgba(31, 111, 92, 0); } } .status-region { display: flex; flex-wrap: wrap; justify-content: space-between; gap: var(--space-3); padding: var(--space-4); background: var(--color-surface-muted); border-radius: var(--radius-md); margin-bottom: var(--space-5); } .status-region p { margin: 0; } .status-region__state { font-weight: 600; } .status-card__share { color: var(--color-text-muted); font-size: 0.9rem; } /* ---------------------------------------------------------------------- */ /* Submission summary / definition lists */ /* ---------------------------------------------------------------------- */ .submission-summary { margin-top: var(--space-6); border-top: 1px solid var(--color-border); padding-top: var(--space-4); } .submission-summary summary { cursor: pointer; font-weight: 600; } dl { display: grid; grid-template-columns: max-content 1fr; gap: var(--space-2) var(--space-4); margin: var(--space-4) 0; } dl dt { color: var(--color-text-muted); } dl dd { margin: 0; } .results-summary { display: grid; grid-template-columns: max-content 1fr; gap: var(--space-2) var(--space-5); margin: var(--space-4) 0 var(--space-6); font-size: 0.95rem; } /* Non-default advanced options used for a job (job.html / results.html) -- * a reproducibility summary, so a completed run's exact command-line * deltas are visible without downloading the log. */ .advanced-options-summary { margin: 0; padding-left: 1.1rem; font-size: 0.9em; } .advanced-options-summary li { margin-bottom: 0.2em; } .advanced-options-summary code { font-size: 0.9em; } /* ---------------------------------------------------------------------- */ /* Tables (id-map, per-CDS data tables) */ /* ---------------------------------------------------------------------- */ table { border-collapse: collapse; width: 100%; font-size: 0.9rem; } th, td { padding: var(--space-2) var(--space-3); text-align: left; border-bottom: 1px solid var(--color-border); white-space: nowrap; } thead th { position: sticky; top: 0; background: var(--color-surface-muted); font-weight: 700; } tbody tr:hover { background: var(--color-surface-muted); } .id-map-table td:first-child { font-family: var(--font-mono); } .data-table .th-sort { background: none; border: none; font: inherit; font-weight: 700; cursor: pointer; padding: 0; display: inline-flex; align-items: center; gap: 0.3em; color: inherit; } .data-table .th-sort::after { content: "\2195"; opacity: 0.35; font-size: 0.8em; } .data-table .th-sort[data-sort-dir="asc"]::after { content: "\2191"; opacity: 1; } .data-table .th-sort[data-sort-dir="desc"]::after { content: "\2193"; opacity: 1; } .data-table-toolbar { display: flex; flex-wrap: wrap; align-items: center; justify-content: space-between; gap: var(--space-3); margin-bottom: var(--space-3); } .table-filter { padding: var(--space-2) var(--space-3); border: 1px solid var(--color-border); border-radius: var(--radius-sm); min-width: 16rem; max-width: 100%; background: var(--color-surface); color: var(--color-text); } .data-table-toolbar__meta { font-size: 0.85rem; color: var(--color-text-muted); } .data-table tbody tr[hidden] { display: none; } /* ---------------------------------------------------------------------- */ /* Tabs (results page) */ /* ---------------------------------------------------------------------- */ .tabs__list { display: flex; gap: var(--space-2); border-bottom: 1px solid var(--color-border); margin-bottom: var(--space-5); flex-wrap: wrap; } .tabs__tab { background: none; border: none; border-bottom: 3px solid transparent; padding: var(--space-3) var(--space-2); margin-bottom: -1px; font-weight: 600; color: var(--color-text-muted); cursor: pointer; } .tabs__tab:hover { color: var(--color-text); } .tabs__tab.is-active { color: var(--color-primary); border-bottom-color: var(--color-primary); } .tabs__badge { font-size: 0.7rem; font-weight: 700; text-transform: uppercase; letter-spacing: 0.03em; background: var(--color-accent-soft); color: var(--color-primary); padding: 0.15em 0.5em; border-radius: 999px; vertical-align: middle; } .tabs__panel[hidden] { display: none; } .results-header { display: flex; flex-wrap: wrap; align-items: center; justify-content: space-between; gap: var(--space-3); } .results-header__actions { display: flex; gap: var(--space-3); flex-wrap: wrap; } .file-list { list-style: none; padding: 0; margin: var(--space-3) 0 var(--space-5); } .file-list li { display: flex; justify-content: space-between; gap: var(--space-3); padding: var(--space-2) 0; border-bottom: 1px dashed var(--color-border); } .file-list__size { color: var(--color-text-muted); font-size: 0.85rem; white-space: nowrap; } .empty-note { color: var(--color-text-muted); font-style: italic; } .genome-browser-placeholder { border: 2px dashed var(--color-border); border-radius: var(--radius-md); padding: var(--space-6); text-align: center; color: var(--color-text-muted); margin-block: var(--space-6); } /* ---------------------------------------------------------------------- */ /* Prose pages (about / help) + error page */ /* ---------------------------------------------------------------------- */ .prose { max-width: var(--max-width-prose); } /* Citations page needs room for side-by-side heading + logo + copy button; * the default prose measure is too narrow for the BibTeX blocks. */ .prose--wide { max-width: var(--max-width); } .prose h2 { border-top: 1px solid var(--color-border); padding-top: var(--space-5); } .prose h2:first-of-type { border-top: none; padding-top: 0; } .prose dt { font-weight: 600; color: var(--color-text); margin-top: var(--space-3); } .prose dd { margin: var(--space-1) 0 0; color: var(--color-text-muted); } .error-card { max-width: 34rem; margin-inline: auto; text-align: center; margin-top: var(--space-7); } /* ---------------------------------------------------------------------- */ /* Citations page (/cite) */ /* ---------------------------------------------------------------------- */ .citation-card { border: 1px solid var(--color-border); border-radius: var(--radius-md); padding: var(--space-5); margin-bottom: var(--space-5); } .citation-card__heading { display: flex; flex-wrap: wrap; align-items: center; gap: var(--space-3); margin-bottom: var(--space-2); } .citation-card__heading h3 { margin: 0; } .citation-card__logo { width: 2.25rem; height: 2.25rem; object-fit: contain; background: #f8f0e3; border-radius: var(--radius-sm); padding: 0.2rem; } .citation-card__text { margin: 0 0 var(--space-3); } .citation-card__bibtex { position: relative; } .citation-card__bibtex pre { margin: 0; padding: var(--space-3); padding-right: 6.5rem; background: var(--color-surface-muted); border: 1px solid var(--color-border); border-radius: var(--radius-sm); overflow-x: auto; font-family: var(--font-mono); font-size: 0.82rem; line-height: 1.5; } .citation-card__copy { position: absolute; top: var(--space-2); right: var(--space-2); padding: 0.35rem 0.7rem; font-size: 0.8rem; } .citation-protocol { background: var(--color-accent-soft); border: 1px solid var(--color-brand-teal); } /* ---------------------------------------------------------------------- */ /* My jobs (/my-jobs) -- client-side job history, localStorage only */ /* ---------------------------------------------------------------------- */ .my-jobs-header { display: flex; flex-wrap: wrap; align-items: center; justify-content: space-between; gap: var(--space-3); margin-bottom: var(--space-2); } .my-jobs-list { list-style: none; padding: 0; margin: var(--space-5) 0 0; display: grid; gap: var(--space-3); } .my-job-row { display: flex; flex-wrap: wrap; align-items: center; justify-content: space-between; gap: var(--space-3); padding: var(--space-4); border: 1px solid var(--color-border); border-radius: var(--radius-md); background: var(--color-surface); } .my-job-row__main { min-width: 0; } .my-job-row__filename { font-weight: 600; overflow-wrap: anywhere; } .my-job-row__meta { margin: 0.2rem 0 0; font-size: 0.85rem; color: var(--color-text-muted); } .my-job-row__meta code { font-size: 0.85em; } .my-job-row__actions { display: flex; align-items: center; gap: var(--space-3); flex-wrap: wrap; } .job-state-badge { display: inline-flex; align-items: center; gap: 0.4em; font-size: 0.78rem; font-weight: 700; text-transform: uppercase; letter-spacing: 0.03em; padding: 0.25em 0.7em; border-radius: 999px; background: var(--color-surface-muted); color: var(--color-text-muted); border: 1px solid var(--color-border); } .job-state-badge[data-state="completed"] { background: var(--color-success-soft); color: var(--color-success); border-color: var(--color-success); } .job-state-badge[data-state="running"], .job-state-badge[data-state="queued"] { background: var(--color-accent-soft); color: var(--color-primary); border-color: var(--color-primary); } .job-state-badge[data-state="failed"] { background: var(--color-danger-soft); color: var(--color-danger); border-color: var(--color-danger); } .job-state-badge[data-state="expired"] { background: var(--color-surface-muted); color: var(--color-text-muted); } .my-jobs-empty { color: var(--color-text-muted); font-style: italic; padding-block: var(--space-4); } .button--small { padding: 0.4rem 0.8rem; font-size: 0.85rem; } .button--danger-text { background: transparent; border: 1px solid var(--color-border); color: var(--color-danger); } .button--danger-text:hover { border-color: var(--color-danger); background: var(--color-danger-soft); } /* ---------------------------------------------------------------------- */ /* Funder acknowledgement (front page) */ /* ---------------------------------------------------------------------- */ /* Deliberately understated: this is a credit, not a call to action, so it * sits below the pipeline explainer in muted type rather than competing * with the submit form. Bordered-top rather than boxed so it reads as a * closing note on the page. */ .acknowledgement { margin-top: var(--space-7); padding-top: var(--space-5); border-top: 1px solid var(--color-border); max-width: var(--max-width-prose); } .acknowledgement__heading { font-size: 0.85rem; font-weight: 600; text-transform: uppercase; letter-spacing: 0.06em; color: var(--color-text-muted); margin: 0 0 var(--space-2); } .acknowledgement__body { font-size: 0.95rem; color: var(--color-text-muted); margin: 0; } /* Failed-job explanation. The plain-English hint leads; the raw tool error is * kept but demoted to supporting detail -- never hidden, since a real bug has * to stay reportable. */ .job-error__hint { font-weight: 600; } .job-error__detail { font-size: 0.9rem; color: var(--color-text-muted); } .job-error__detail code { word-break: break-word; }