Add Supplemental File Guidelines page#2398
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Important Review skippedAuto reviews are disabled on this repository. Please check the settings in the CodeRabbit UI or the You can disable this status message by setting the WalkthroughA new "Supplemental File Guidelines" feature was introduced, including a dedicated page, navigation updates, access control, and acceptance tests. Guide and help pages were updated for content and style consistency, and CSS for definition lists was enhanced with new classes and styles. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant WebApp
participant SiteController
participant ViewRenderer
User->>WebApp: Navigate to /site/supplementalFileGuide
WebApp->>SiteController: Calls actionSupplementalFileGuide()
SiteController->>ViewRenderer: Render 'supplementafileguide' view
ViewRenderer-->>User: Display Supplemental File Guidelines page
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Actionable comments posted: 0
🧹 Nitpick comments (1)
protected/views/site/supplementafileguide.php (1)
7-10: Fix the breadcrumb array formatting.The array formatting is broken across lines in an inconsistent way, making it hard to read.
- $this->widget('TitleBreadcrumb', ['pageTitle' => 'GigaDB - - Supplemental File Guidelines', 'breadcrumbItems' => [['label' => 'Home', - 'href' => '/'], ['isActive' => true, 'label' => 'Supplemental File - Guidelines', ]]]); ?> + $this->widget('TitleBreadcrumb', [ + 'pageTitle' => 'GigaDB - Supplemental File Guidelines', + 'breadcrumbItems' => [ + ['label' => 'Home', 'href' => '/'], + ['isActive' => true, 'label' => 'Supplemental File Guidelines'] + ] + ]); ?>
📜 Review details
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📒 Files selected for processing (11)
CHANGELOG.md(1 hunks)less/modules/definition-lists.less(1 hunks)playwright/paths.js(1 hunks)protected/components/GuideNavigation.php(2 hunks)protected/controllers/SiteController.php(2 hunks)protected/views/guide/_guideNavigationView.php(1 hunks)protected/views/site/faq.php(1 hunks)protected/views/site/guide.php(2 hunks)protected/views/site/help.php(8 hunks)protected/views/site/supplementafileguide.php(1 hunks)tests/acceptance/StaticContentNavigation.feature(1 hunks)
🧰 Additional context used
📓 Path-based instructions (4)
`**/*`: - Focus on code smells, logic errors, edge cases, missing test cases, se...
**/*: - Focus on code smells, logic errors, edge cases, missing test cases, security flaws and serious issues
- Avoid commenting on minor issues such as linting, formatting and style issues
- Never commit secrets, PII, passwords or API keys—use env-vars and .env files.
- Flag any file >300 lines or function >30 lines and suggest refactoring.
- Every new feature or bug-fix must arrive with automated tests; warn if none are touched.
- If the PR includes changes to the UI, the style guide should be updated too; warn if not.
⚙️ Source: CodeRabbit Configuration File
List of files the instruction was applied to:
protected/controllers/SiteController.phpCHANGELOG.mdprotected/views/site/faq.phptests/acceptance/StaticContentNavigation.featureprotected/components/GuideNavigation.phpprotected/views/guide/_guideNavigationView.phpprotected/views/site/help.phpplaywright/paths.jsprotected/views/site/supplementafileguide.phpprotected/views/site/guide.phpless/modules/definition-lists.less
`**/*.php`: - HTML follows web accessibility WCAG 2 standards
**/*.php: - HTML follows web accessibility WCAG 2 standards
⚙️ Source: CodeRabbit Configuration File
List of files the instruction was applied to:
protected/controllers/SiteController.phpprotected/views/site/faq.phpprotected/components/GuideNavigation.phpprotected/views/guide/_guideNavigationView.phpprotected/views/site/help.phpprotected/views/site/supplementafileguide.phpprotected/views/site/guide.php
`**/*.js`: - New JavaScript must live in `giga/app/client/js/` (not in `protecte...
**/*.js: - New JavaScript must live ingiga/app/client/js/(not inprotected/js/).
- Write ES-module code (
import…export) only—no global scripts.- Functions needing >2 logical params must take a single options object.
- Rely on jQuery 3 or Vue for DOM work; avoid direct DOM APIs unless impossible.
- No Console.log
⚙️ Source: CodeRabbit Configuration File
List of files the instruction was applied to:
playwright/paths.js
`**/*.less`: - Follow SMACSS: - Base: Default element styles - Layout: `.l-*...
**/*.less: - Follow SMACSS:
- Base: Default element styles
- Layout:
.l-*classes for page skeleton- Modules:
.my-module-*for reusable components- State:
.is-*for UI states- Theme:
.theme-*for theme overrides- Never hard-code colors, always use color variables defined in
less/base/variables.less.- Desktop-first: media queries for mobile styles.
- Limit nesting to three levels; favour flat selectors for maintainability.
⚙️ Source: CodeRabbit Configuration File
List of files the instruction was applied to:
less/modules/definition-lists.less
🧠 Learnings (4)
📓 Common learnings
Learnt from: rija
PR: gigascience/gigadb-website#2157
File: CHANGELOG.md:7-7
Timestamp: 2025-05-26T17:52:49.544Z
Learning: In the GigaDB project, textual changes to website content should be categorized as "Feat" (feature) entries in the CHANGELOG.md, not as "Docs" (documentation) entries, even when the changes involve updating guidance or instructional text on web pages.
Learnt from: alli83
PR: gigascience/gigadb-website#2301
File: protected/views/user/_form.php:179-187
Timestamp: 2025-05-23T02:02:48.284Z
Learning: The PR "Fix 561 separate admin user page from non admin user page" focuses specifically on separating admin user pages from non-admin user pages, removing terms and captcha requirements on update and change password pages, and adding token generation for activation links. Issues outside this scope should be addressed in separate PRs.
CHANGELOG.md (1)
Learnt from: rija
PR: gigascience/gigadb-website#2157
File: CHANGELOG.md:7-7
Timestamp: 2025-05-26T17:52:49.544Z
Learning: In the GigaDB project, textual changes to website content should be categorized as "Feat" (feature) entries in the CHANGELOG.md, not as "Docs" (documentation) entries, even when the changes involve updating guidance or instructional text on web pages.
protected/views/site/supplementafileguide.php (1)
Learnt from: rija
PR: gigascience/gigadb-website#2157
File: CHANGELOG.md:7-7
Timestamp: 2025-05-26T17:52:49.544Z
Learning: In the GigaDB project, textual changes to website content should be categorized as "Feat" (feature) entries in the CHANGELOG.md, not as "Docs" (documentation) entries, even when the changes involve updating guidance or instructional text on web pages.
protected/views/site/guide.php (1)
Learnt from: rija
PR: gigascience/gigadb-website#2157
File: CHANGELOG.md:7-7
Timestamp: 2025-05-26T17:52:49.544Z
Learning: In the GigaDB project, textual changes to website content should be categorized as "Feat" (feature) entries in the CHANGELOG.md, not as "Docs" (documentation) entries, even when the changes involve updating guidance or instructional text on web pages.
🔇 Additional comments (17)
CHANGELOG.md (1)
7-8: LGTM! Proper categorization and format.The changelog entry correctly categorizes this as a "Feat" entry, which aligns with the established pattern for textual website content changes.
protected/views/site/faq.php (1)
499-499: LGTM! Consistent styling enhancement.Adding the
inline-listclass aligns with the coordinated styling improvements across definition lists in the application.playwright/paths.js (1)
33-33: LGTM! Proper accessibility testing integration.The new path correctly adds the supplemental file guidelines page to the accessibility testing suite.
protected/components/GuideNavigation.php (1)
26-26: LGTM! Consistent pattern implementation.The new
$isActiveSupplementalFileGuidevariable follows the exact same pattern as the existing$isActiveGeneralvariable, maintaining consistency in the navigation logic.Also applies to: 40-42
tests/acceptance/StaticContentNavigation.feature (1)
173-176: LGTM! Proper test coverage for new feature.The acceptance test correctly verifies the presence of the supplemental file guidelines link with appropriate tagging and follows established patterns in the feature file.
protected/controllers/SiteController.php (2)
39-39: LGTM!Access control properly updated to include the new action.
247-249: No view name typo—render call matches the existing file
The fileprotected/views/site/supplementafileguide.phpexists with the same spelling, so the render call is correct as written. No changes needed.Likely an incorrect or invalid review comment.
protected/views/site/help.php (1)
41-41: LGTM!Consistent application of
inline-listclass to all definition lists for improved styling consistency.Also applies to: 124-124, 215-215, 317-317, 667-667, 688-688, 731-731, 780-780
protected/views/guide/_guideNavigationView.php (1)
3-3: LGTM!Navigation logic correctly implements mutual exclusivity for active states and follows established patterns for the new supplemental file guidelines tab.
Also applies to: 12-15
protected/views/site/guide.php (3)
27-27: Good generalization of the GigaDB description.Removing the specific mention of China National GeneBank makes the description more universally applicable.
31-44: Excellent addition of supplemental files context.This new section provides valuable guidance on how GigaScience Press handles supplemental files differently from traditional publishers. The explanation is clear and the link to the new guidelines page is well-placed.
136-136: Good typographical correction.Replacing curly quotes with straight quotes improves consistency and readability.
protected/views/site/supplementafileguide.php (2)
23-183: Excellent use of semantic HTML and accessibility features.The definition list structure is appropriate for this content, and the accessibility features (aria-labels, proper footnote implementation) follow WCAG guidelines well.
185-192: Good footnote implementation.The footnote with back-reference link provides good accessibility and user experience.
less/modules/definition-lists.less (3)
1-25: Good refactoring to use specific class selector.Changing from generic
dltodl.inline-listprevents unintended style application and follows good CSS practices. The use of color variables is also commendable.
16-20: Nice addition of the separator modifier.The
.separator-nonemodifier provides good flexibility for different use cases.
28-44: Well-designed definition list styles.The new
.definition-liststyles provide good visual hierarchy with appropriate spacing and the left border visual cue.
1 participant
Pull request for issue: #2330
How to test?
How have functionalities been implemented?
Any issues with implementation?
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Any changes to automated tests?
Added one acceptance test to expect the presence of a link to the new page
Any changes to documentation?
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Any technical debt repayment?
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Any improvements to CI/CD pipeline?
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Summary by CodeRabbit