From 3a7598ca3aca3aee69a895a98ae0c94d5b33bfe3 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Tue, 12 May 2026 07:03:16 +0000 Subject: [PATCH 01/17] Schlegel Fig 1: resolve remaining area overlaps Static audit after the previous follow-up still flagged three pairwise rect overlaps on Schlegel Fig 1: AL x ORN 30x20 px overlap (AL covered the ORN cell drawing). AL x ALLN 15x5 px overlap (ALLN y2 reached into AL y1). mPN x LHN 5x20 px overlap (LHN x2 reached into mPN x1). These were missed by the previous TL/centre/BR hit-test because the overlap sits in the body of the rect, not at probed corners. Two changes: 1. Reorder the AL/ALLN/ORN cluster so the cell-type rects come before the region rect. AL is a brain region; ORN and ALLN are cell-type drawings positioned inside the AL region in the schematic, so their rects necessarily overlap the AL rect. Per HTML5, the first matching in tree order wins, so putting cell types before the region makes the visible cells route to their own term while the rest of AL still routes to AL. 2. Trim ALLN.y2 from 260 -> 254 (one below AL.y1=255) so the small geometric overlap with AL is gone. Trim LHN.x2 from 85 -> 79 (one below mPN.x1=80) for the same reason, and reorder LHN before mPN. After this commit static audit reports a single residual geometric overlap (ORN x AL, 30x20 px); it is intentional, resolved by ordering, and documents the cell-inside-region layout faithfully. --- .../Olfactory system neuroanatomy/_index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/content/en/docs/Anatomy Diagrams/Olfactory system neuroanatomy/_index.md b/content/en/docs/Anatomy Diagrams/Olfactory system neuroanatomy/_index.md index f8b254f..b2610fe 100644 --- a/content/en/docs/Anatomy Diagrams/Olfactory system neuroanatomy/_index.md +++ b/content/en/docs/Anatomy Diagrams/Olfactory system neuroanatomy/_index.md @@ -9,15 +9,15 @@ description: > - - + + + - From 115a32814dfb8d02648d4aa04788a16a4c3d713a Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Tue, 12 May 2026 21:00:34 +0000 Subject: [PATCH 02/17] Anatomy diagrams: cover label text below cell drawings OCR pass with Tesseract on each natural-resolution figure surfaced visible text labels that sit just below the cell-drawing rects and were therefore unclickable. Two changes: 1. Hulse Fig 1 (panel C): the AB(R) / AB(L) text labels are at displayed y~736-751 in panel C, well below the existing rects at y=590-625 that cover the AB region drawings. Add two new rects at the label positions, linking the text labels to the same per-side asymmetrical body classes (FBbt_00051240 right, FBbt_00051239 left). 2. Aso 2014a Fig 10 (panels D, E, F): the existing MBON panel rects end at y=770, but the panel labels ('MBON-y3 (1)', 'MBON-y3b'1 (1)', 'MBON-y2a'1 (2)', 'MBON-y1pedc>a/B (1)') sit at displayed y~842-934. Extend each bottom-row panel rect's y2 to cover the text label below the cell drawing: MBON-y3 y2 770 -> 890 MBON-y3b'1 y2 770 -> 890 MBON-y2a'1 y2 770 -> 940 MBON-y1pedc>a/B y2 770 -> 940 Static audit after these changes: zero new overlaps (Hulse 28 areas, Aso unchanged at 45). The Schlegel ORN x AL geometric overlap from the previous commit remains intentional and ordered. --- .../Anatomy of the central complex/_index.md | 2 ++ .../Compartmentalization of mushroom body lobes/_index.md | 8 ++++---- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/content/en/docs/Anatomy Diagrams/Anatomy of the central complex/_index.md b/content/en/docs/Anatomy Diagrams/Anatomy of the central complex/_index.md index bbbeb58..2acd341 100644 --- a/content/en/docs/Anatomy Diagrams/Anatomy of the central complex/_index.md +++ b/content/en/docs/Anatomy Diagrams/Anatomy of the central complex/_index.md @@ -28,6 +28,8 @@ description: > + + diff --git a/content/en/docs/Anatomy Diagrams/Compartmentalization of mushroom body lobes/_index.md b/content/en/docs/Anatomy Diagrams/Compartmentalization of mushroom body lobes/_index.md index 55f0326..c420854 100644 --- a/content/en/docs/Anatomy Diagrams/Compartmentalization of mushroom body lobes/_index.md +++ b/content/en/docs/Anatomy Diagrams/Compartmentalization of mushroom body lobes/_index.md @@ -15,10 +15,10 @@ description: > - - - - + + + + From 79a8574be10bd7bf627f8696c541103ae54a2a68 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Wed, 20 May 2026 05:06:10 +0100 Subject: [PATCH 03/17] config: flip anonymizeIP to true to signal intent for GA4 --- config.toml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/config.toml b/config.toml index e79ca49..e768e80 100644 --- a/config.toml +++ b/config.toml @@ -109,7 +109,10 @@ section = ["HTML", "print", "RSS"] [privacy.disqus] disable = false [privacy.googleAnalytics] - anonymizeIP = false + # anonymizeIP is a no-op for GA4 (Universal Analytics-era flag) but is set + # to true here to signal intent — GA4 itself transiently uses the IP for + # geolocation only and does not store it. See content/en/about/cookies.md. + anonymizeIP = true disable = false respectDoNotTrack = true useSessionStorage = true From b3ba48f7af582025dc5eaa95a4814ae7ef8ecba1 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Wed, 20 May 2026 05:06:25 +0100 Subject: [PATCH 04/17] =?UTF-8?q?Add=20/about/cookies/=20=E2=80=94=20list?= =?UTF-8?q?=20cookies=20set=20by=20VFB,=20opt-out,=20DPF=20transfer=20note?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- content/en/about/cookies.md | 54 +++++++++++++++++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 content/en/about/cookies.md diff --git a/content/en/about/cookies.md b/content/en/about/cookies.md new file mode 100644 index 0000000..d7111a3 --- /dev/null +++ b/content/en/about/cookies.md @@ -0,0 +1,54 @@ +--- +title: "Cookies" +linkTitle: "Cookies" +weight: 21 +--- + +## Cookies we use on Virtual Fly Brain + +**Last updated: May 2026** + +This page lists the cookies set by [www.virtualflybrain.org](https://www.virtualflybrain.org) and the related Virtual Fly Brain (VFB) services. It complements the [Privacy Notice](/about/privacy/). + +### What is a cookie? + +A cookie is a small text file that a website saves on your device when you visit. Cookies let a site recognise your browser between requests and on return visits. + +### Strictly necessary cookies + +These cookies are required for the website and applications to work and cannot be turned off through any opt-out mechanism without breaking core features. + +| Name | Set by | Purpose | Expires | +|------|--------|---------|---------| +| `JSESSIONID` | Geppetto (`v2.virtualflybrain.org` and variants) | Maintains your application session in the 3D web client — currently selected neurons, layer visibility and camera state. | End of browser session | + +### Performance cookies + +These cookies help us understand how visitors use Virtual Fly Brain so we can improve content, navigation and the underlying data integrations. The data is aggregated and is not used to identify individual users. + +#### Google Analytics 4 + +We use Google Analytics 4 (GA4), a web analytics service provided by Google LLC. GA4 receives your IP address transiently for geolocation purposes, derives an approximate location (city/country level), and discards the raw IP — it is not stored against your analytics record. The data we see is aggregated counts, paths through the site, and broad geographic distribution. + +| Name | Purpose | Expires | +|------|---------|---------| +| `_ga` | Distinguishes browsers across visits. | 2 years from your most recent visit | +| `_ga_K7DDZVVXM7` | Maintains GA4 session state for the VFB property. | 2 years from your most recent visit | + +For details of Google's processing, see [Google's Privacy & Terms](https://policies.google.com/privacy). + +International transfer note: Google may process GA4 data on servers in the United States. The transfer is covered by the EU-U.S. Data Privacy Framework (Commission Implementing Decision (EU) 2023/1795); Google is certified under the framework. The UK extension to the framework applies for UK-origin data. + +### How to opt out + +You can opt out of Google Analytics on every site you visit by installing Google's [Analytics Opt-out browser add-on](https://tools.google.com/dlpage/gaoptout). You can also clear or block individual cookies via your browser's settings; doing so will not prevent you from using the public VFB services, but the Geppetto session cookie above is needed for the 3D viewer. + +### Other cookies set by sites we link to + +Pages elsewhere on virtualflybrain.org may embed content from third-party services (for example, YouTube or X/Twitter). Those embeds may set their own cookies; please refer to the third party's own cookie or privacy policy for details. We do not set non-essential third-party cookies of our own beyond Google Analytics. + +### Contact + +Questions about cookies on this site: . + +Wider University data-protection enquiries: [University of Edinburgh Data Protection Officer](mailto:dpo@ed.ac.uk). From 13708483cec52d51a598888c679748fd4a6eb59f Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Wed, 20 May 2026 05:06:36 +0100 Subject: [PATCH 05/17] =?UTF-8?q?Add=20/about/accessibility/=20=E2=80=94?= =?UTF-8?q?=20WCAG=202.2=20AA=20statement,=203D-viewer=20limitations=20doc?= =?UTF-8?q?umented?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- content/en/about/accessibility.md | 87 +++++++++++++++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 content/en/about/accessibility.md diff --git a/content/en/about/accessibility.md b/content/en/about/accessibility.md new file mode 100644 index 0000000..63ec793 --- /dev/null +++ b/content/en/about/accessibility.md @@ -0,0 +1,87 @@ +--- +title: "Accessibility Statement" +linkTitle: "Accessibility" +weight: 22 +--- + +## Accessibility statement for Virtual Fly Brain + +Website accessibility statement in line with the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. + +This statement applies to the public Virtual Fly Brain (VFB) services hosted at [www.virtualflybrain.org](https://www.virtualflybrain.org) and its sub-domains. VFB is run by the [University of Edinburgh's School of Informatics](https://www.inf.ed.ac.uk/) as a research data integration platform for *Drosophila melanogaster* neurobiology. + +We want as many people as possible to be able to use this website. Where the underlying content is inherently visual (3D image stacks, neuron skeletons and connectivity diagrams) we recognise that some features cannot be made fully accessible without losing scientific meaning, and we have documented those limitations below. + +### Using this website + +Across the site you should be able to: + +- Change colours, contrast levels and font size using your browser settings on the documentation pages +- Use the documentation pages without encountering flashing, scrolling or moving content +- Listen to most of the documentation pages with a screen reader (JAWS, NVDA, VoiceOver) +- Navigate the documentation pages by keyboard alone +- Resize text up to 200% on the documentation pages without loss of content + +The 3D web client (Geppetto-based) and the embedded CATMAID connectome viewers have known accessibility limitations — see below. + +### Customising the website + +[AbilityNet — My Computer My Way](https://mcmw.abilitynet.org.uk/) has advice on making your device easier to use if you have a disability. + +University of Edinburgh staff and students can use the free [SensusAccess document conversion service](https://www.ed.ac.uk/information-services/computing/computing-infrastructure/disability-information/sensusaccess) for converting accessible PDFs, captions and large print. + +### How accessible this website is + +We know parts of the website are not fully accessible: + +- The Geppetto 3D web client (`v2.virtualflybrain.org` and variants) is built around WebGL and a 3D scene-graph. Keyboard navigation of the scene is limited; screen-reader access to the neuron meshes is not currently meaningful. +- The CATMAID connectome viewers (`*.catmaid.virtualflybrain.org`) are embedded third-party software whose interface is optimised for mouse and keyboard interaction at high zoom levels. We do not control its accessibility behaviour. +- Some neuroanatomical diagrams use colour to encode region or cell-type identity. We are progressively adding `aria-label` and image-map fallbacks; some legacy diagrams still rely on colour alone. +- Some embedded scientific figures from external publications retain their original styling, including small text size and low colour contrast. +- Not all image alternative text fully describes the underlying scientific content. + +### Feedback and contact information + +If you need information from this site in a different format, or you encounter an accessibility problem we have not listed: + +- Email: [support@virtualflybrain.org](mailto:support@virtualflybrain.org) +- GitHub: file an issue at [github.com/VirtualFlyBrain/VFB2/issues](https://github.com/VirtualFlyBrain/VFB2/issues) + +We will respond within five working days. + +### Enforcement procedure + +The Equality and Human Rights Commission (EHRC) is responsible for enforcing the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. If you are not satisfied with how we respond to your complaint, you can contact the [Equality Advisory and Support Service (EASS)](https://www.equalityadvisoryservice.com/). + +### Technical information about this website's accessibility + +The University of Edinburgh is committed to making its websites and applications accessible in line with the regulations. This website is partially compliant with the [Web Content Accessibility Guidelines (WCAG) 2.2 AA standard](https://www.w3.org/TR/WCAG22/), with the non-compliances listed below. + +#### Non-compliance with the accessibility regulations + +The following items do not currently comply with WCAG 2.2 AA success criteria: + +- **1.1.1 Non-text content.** Not all neuron images and anatomical diagrams have meaningful alternative text. We are adding alt text and image-map labels on an ongoing basis. +- **1.3.1 Info and relationships, 1.3.2 Meaningful sequence.** Some legacy figure pages do not present content in a programmatically determined reading order. +- **1.4.1 Use of colour.** Some neuroanatomical schematics use colour as the sole means of distinguishing regions or cell types. +- **1.4.3 Contrast (minimum).** Some embedded figures from external publications use low-contrast labels we cannot modify. +- **2.1.1 Keyboard.** The Geppetto 3D viewer cannot be navigated by keyboard alone for full feature parity with mouse interaction. +- **4.1.2 Name, role, value.** The 3D viewer's scene-graph elements (neurons, brain regions) are not exposed to assistive technology as named, role-tagged elements. + +#### Content that is not within the scope of the accessibility regulations + +- **Third-party scientific content.** PDFs and figures imported from peer-reviewed publications retain their original formatting and are republished under their original licences. We do not modify them. +- **Older content (pre-September 2018).** Some legacy pages and PDFs pre-date the regulations and are kept for reference; we will replace them with accessible HTML where reasonable. + +### What we are doing to improve accessibility + +- Adding `aria-label` and image-map fallbacks to anatomical schematics — ongoing through 2026. +- Documenting alternative routes to the same information (text search, the [VFB_connect Python API](https://github.com/VirtualFlyBrain/VFB_connect), and the [VFB MCP server](https://virtualflybrain.org/blog/2026/02/07/introducing-the-vfb-model-context-protocol-mcp-tool/)) so users who cannot use the 3D viewer can still access the underlying data programmatically. +- Reviewing and improving alternative text for image content. +- Following the [University of Edinburgh accessibility guidance](https://www.ed.ac.uk/about/website/accessibility) for the documentation site framework (Hugo + Docsy). + +### Preparation of this statement + +This statement was prepared in May 2026. It has not yet been independently audited; an internal review will be carried out before the firewall-hole review cycle. + +This article was published on 2026-05-19. From 0387592addb8801f61e4ae44c62aa0bc2add4af4 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Wed, 20 May 2026 05:07:05 +0100 Subject: [PATCH 06/17] Privacy notice: replace Privacy Shield (invalidated 2020) with DPF, correct IP language, link to cookies page Privacy Shield was invalidated by CJEU Schrems II (July 2020) and replaced by the EU-U.S. Data Privacy Framework in July 2023 (Commission Implementing Decision (EU) 2023/1795). The 'IP address (anonymized)' line was incorrect for GA4, which transiently uses IP for geolocation and discards it rather than anonymising in the GA-UA sense. Server-log paragraph added to declare that container logs are ephemeral and not persisted. --- content/en/about/privacy.md | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/content/en/about/privacy.md b/content/en/about/privacy.md index 21bcdb1..2733a77 100644 --- a/content/en/about/privacy.md +++ b/content/en/about/privacy.md @@ -6,22 +6,23 @@ weight: 20 ## Virtual Fly Brain Privacy Notice -**Last updated: February 2026** +**Last updated: May 2026** The Virtual Fly Brain (VFB) project is committed to protecting your privacy and keeping you informed about how your personal information is used. This privacy notice explains how we collect, use, and protect your personal data when you visit our website. ### What information do we collect? -We collect information about your visit to our website through Google Analytics, a web analytics service provided by Google, Inc. This includes: +**Website analytics (Google Analytics 4).** We use Google Analytics 4 to understand how the site is used. When you visit a page, your IP address is sent to Google for the purpose of deriving an approximate geographic location, and is then discarded; the raw IP is not stored against your analytics record. The data we receive is aggregated and includes: -- Your IP address (anonymized) +- Approximate geographic location (city/country level) - Browser type and version - Operating system - Referring website - Pages visited and time spent on each page -- Geographic location (country/city level only) -We do not collect any personally identifiable information such as names, email addresses, or contact details unless you voluntarily provide them (for example, through our contact forms or feedback mechanisms). +**Web-server logs.** Our front-end load balancers and application containers produce request logs that include your IP address. These logs are short-lived and operational only — they are not persisted beyond the lifetime of the running container and are lost on restart. + +We do not collect personally identifiable information such as names, email addresses or contact details unless you voluntarily provide them through our contact forms, feedback links or community channels. ### How do we use this information? @@ -33,11 +34,11 @@ The information collected helps us: - Analyze website traffic patterns - Support our research by understanding user interests in neuroanatomical data -### Cookies and Website Privacy +### Cookies -We use Google Analytics cookies to collect this information. These are small text files stored on your device. You can control cookies through your browser settings, and you can opt out of Google Analytics tracking by visiting [Google Analytics Opt-out](https://tools.google.com/dlpage/gaoptout). +Google Analytics 4 sets cookies on your browser to distinguish your visits. The Geppetto 3D web client sets a session cookie to maintain application state during a visit. A full list of cookies set by Virtual Fly Brain, with their purposes and expiry, is on the [Cookies page](/about/cookies/), which also explains how to opt out of Google Analytics. -For more information about Google's privacy practices, please see [Google's Privacy Policy](https://policies.google.com/privacy). +For Google's processing details see [Google's Privacy & Terms](https://policies.google.com/privacy). ### Legal Basis for Processing @@ -48,7 +49,9 @@ Our processing of your personal data is based on: ### Data Sharing and Disclosure -We do not sell, rent, or trade your personal information. Information collected by Google Analytics may be processed by Google on servers located in the United States. Google is committed to complying with the EU-U.S. Privacy Shield framework. +We do not sell, rent or trade your personal information. + +Analytics data collected by Google Analytics may be processed by Google on servers located in the United States. International transfers are covered by the EU-U.S. Data Privacy Framework (Commission Implementing Decision (EU) 2023/1795); Google is [certified under the framework](https://www.dataprivacyframework.gov/list). The UK extension to the framework applies for UK-origin data. ### Data Retention From f58bdd3b12e017dd9db3c131b4cea15665814883 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Wed, 20 May 2026 13:42:19 +0100 Subject: [PATCH 07/17] accessibility: drop UoE-only SensusAccess line; AbilityNet covers worldwide users VFB has a worldwide user base of Drosophila researchers; the SensusAccess document conversion service is only available to UoE staff and students and so is unhelpful to most. The AbilityNet 'My Computer My Way' link above already covers generic browser/OS accessibility customisation for any user. --- content/en/about/accessibility.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/content/en/about/accessibility.md b/content/en/about/accessibility.md index 63ec793..a29f08c 100644 --- a/content/en/about/accessibility.md +++ b/content/en/about/accessibility.md @@ -28,8 +28,6 @@ The 3D web client (Geppetto-based) and the embedded CATMAID connectome viewers h [AbilityNet — My Computer My Way](https://mcmw.abilitynet.org.uk/) has advice on making your device easier to use if you have a disability. -University of Edinburgh staff and students can use the free [SensusAccess document conversion service](https://www.ed.ac.uk/information-services/computing/computing-infrastructure/disability-information/sensusaccess) for converting accessible PDFs, captions and large print. - ### How accessible this website is We know parts of the website are not fully accessible: From ddf64c4a6cafdcc5dcf656876a5d900819cd45aa Mon Sep 17 00:00:00 2001 From: Clare72 Date: Mon, 25 May 2026 16:58:34 +0100 Subject: [PATCH 08/17] Update accessibility.md --- content/en/about/accessibility.md | 59 +++++++++++++------------------ 1 file changed, 24 insertions(+), 35 deletions(-) diff --git a/content/en/about/accessibility.md b/content/en/about/accessibility.md index a29f08c..08e2708 100644 --- a/content/en/about/accessibility.md +++ b/content/en/about/accessibility.md @@ -10,6 +10,8 @@ Website accessibility statement in line with the Public Sector Bodies (Websites This statement applies to the public Virtual Fly Brain (VFB) services hosted at [www.virtualflybrain.org](https://www.virtualflybrain.org) and its sub-domains. VFB is run by the [University of Edinburgh's School of Informatics](https://www.inf.ed.ac.uk/) as a research data integration platform for *Drosophila melanogaster* neurobiology. +The University of Edinburgh is committed to making its websites and applications accessible in line with the regulations. This website is partially compliant with the [Web Content Accessibility Guidelines (WCAG) 2.2 AA standard](https://www.w3.org/TR/WCAG22/), with the non-compliances listed below. + We want as many people as possible to be able to use this website. Where the underlying content is inherently visual (3D image stacks, neuron skeletons and connectivity diagrams) we recognise that some features cannot be made fully accessible without losing scientific meaning, and we have documented those limitations below. ### Using this website @@ -28,38 +30,11 @@ The 3D web client (Geppetto-based) and the embedded CATMAID connectome viewers h [AbilityNet — My Computer My Way](https://mcmw.abilitynet.org.uk/) has advice on making your device easier to use if you have a disability. -### How accessible this website is - -We know parts of the website are not fully accessible: - -- The Geppetto 3D web client (`v2.virtualflybrain.org` and variants) is built around WebGL and a 3D scene-graph. Keyboard navigation of the scene is limited; screen-reader access to the neuron meshes is not currently meaningful. -- The CATMAID connectome viewers (`*.catmaid.virtualflybrain.org`) are embedded third-party software whose interface is optimised for mouse and keyboard interaction at high zoom levels. We do not control its accessibility behaviour. -- Some neuroanatomical diagrams use colour to encode region or cell-type identity. We are progressively adding `aria-label` and image-map fallbacks; some legacy diagrams still rely on colour alone. -- Some embedded scientific figures from external publications retain their original styling, including small text size and low colour contrast. -- Not all image alternative text fully describes the underlying scientific content. - -### Feedback and contact information - -If you need information from this site in a different format, or you encounter an accessibility problem we have not listed: - -- Email: [support@virtualflybrain.org](mailto:support@virtualflybrain.org) -- GitHub: file an issue at [github.com/VirtualFlyBrain/VFB2/issues](https://github.com/VirtualFlyBrain/VFB2/issues) - -We will respond within five working days. - -### Enforcement procedure - -The Equality and Human Rights Commission (EHRC) is responsible for enforcing the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. If you are not satisfied with how we respond to your complaint, you can contact the [Equality Advisory and Support Service (EASS)](https://www.equalityadvisoryservice.com/). - -### Technical information about this website's accessibility - -The University of Edinburgh is committed to making its websites and applications accessible in line with the regulations. This website is partially compliant with the [Web Content Accessibility Guidelines (WCAG) 2.2 AA standard](https://www.w3.org/TR/WCAG22/), with the non-compliances listed below. +### Known accessibility issues -#### Non-compliance with the accessibility regulations +#### Non-compliance with WCAG 2.2 AA criteria -The following items do not currently comply with WCAG 2.2 AA success criteria: - -- **1.1.1 Non-text content.** Not all neuron images and anatomical diagrams have meaningful alternative text. We are adding alt text and image-map labels on an ongoing basis. +- **1.1.1 Non-text content.** Not all neuron images and anatomical diagrams have meaningful alternative text. - **1.3.1 Info and relationships, 1.3.2 Meaningful sequence.** Some legacy figure pages do not present content in a programmatically determined reading order. - **1.4.1 Use of colour.** Some neuroanatomical schematics use colour as the sole means of distinguishing regions or cell types. - **1.4.3 Contrast (minimum).** Some embedded figures from external publications use low-contrast labels we cannot modify. @@ -68,18 +43,32 @@ The following items do not currently comply with WCAG 2.2 AA success criteria: #### Content that is not within the scope of the accessibility regulations -- **Third-party scientific content.** PDFs and figures imported from peer-reviewed publications retain their original formatting and are republished under their original licences. We do not modify them. +- **Third-party scientific content.** PDFs and figures imported from peer-reviewed publications retain their original formatting, including small text size and low colour contrast, and are republished under their original licences. We do not modify them. +- **The CATMAID connectome viewers (`*.catmaid.virtualflybrain.org`)** are embedded third-party software whose interface is optimised for mouse and keyboard interaction at high zoom levels. We do not control its accessibility behaviour. - **Older content (pre-September 2018).** Some legacy pages and PDFs pre-date the regulations and are kept for reference; we will replace them with accessible HTML where reasonable. -### What we are doing to improve accessibility +#### Ongoing improvements -- Adding `aria-label` and image-map fallbacks to anatomical schematics — ongoing through 2026. +- Adding `aria-label` and image-map fallbacks to anatomical schematics. - Documenting alternative routes to the same information (text search, the [VFB_connect Python API](https://github.com/VirtualFlyBrain/VFB_connect), and the [VFB MCP server](https://virtualflybrain.org/blog/2026/02/07/introducing-the-vfb-model-context-protocol-mcp-tool/)) so users who cannot use the 3D viewer can still access the underlying data programmatically. - Reviewing and improving alternative text for image content. -- Following the [University of Edinburgh accessibility guidance](https://www.ed.ac.uk/about/website/accessibility) for the documentation site framework (Hugo + Docsy). +- Following the [University of Edinburgh accessibility guidance](https://www.ed.ac.uk/about/website/accessibility) for the documentation site framework. + +### Feedback and contact information + +If you need information from this site in a different format, or you encounter an accessibility problem we have not listed: + +- Email: [support@virtualflybrain.org](mailto:support@virtualflybrain.org) +- GitHub: file an issue at [github.com/VirtualFlyBrain/VFB2/issues](https://github.com/VirtualFlyBrain/VFB2/issues) + +We will respond within five working days. + +### Enforcement procedure + +The Equality and Human Rights Commission (EHRC) is responsible for enforcing the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018. If you are not satisfied with how we respond to your complaint, you can contact the [Equality Advisory and Support Service (EASS)](https://www.equalityadvisoryservice.com/). ### Preparation of this statement -This statement was prepared in May 2026. It has not yet been independently audited; an internal review will be carried out before the firewall-hole review cycle. +This statement was prepared in May 2026, it has not been independently audited. This article was published on 2026-05-19. From a2cec33d8222517b6d7678e3dc3da33c9deef3f3 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Mon, 25 May 2026 17:08:52 +0100 Subject: [PATCH 09/17] minor edits to cookies and privacy --- content/en/about/cookies.md | 2 +- content/en/about/privacy.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/content/en/about/cookies.md b/content/en/about/cookies.md index d7111a3..357181f 100644 --- a/content/en/about/cookies.md +++ b/content/en/about/cookies.md @@ -4,7 +4,7 @@ linkTitle: "Cookies" weight: 21 --- -## Cookies we use on Virtual Fly Brain +## Cookies used by Virtual Fly Brain **Last updated: May 2026** diff --git a/content/en/about/privacy.md b/content/en/about/privacy.md index 2733a77..de4b3cb 100644 --- a/content/en/about/privacy.md +++ b/content/en/about/privacy.md @@ -32,7 +32,7 @@ The information collected helps us: - Improve the user experience and content - Identify technical issues - Analyze website traffic patterns -- Support our research by understanding user interests in neuroanatomical data +- Understand user interests in our neuroanatomical data ### Cookies From 15d16a0d9bbfa8b3d1e560a01bb5c1c75363dcae Mon Sep 17 00:00:00 2001 From: jenkins Date: Thu, 4 Jun 2026 05:22:01 +0000 Subject: [PATCH 10/17] Updating contributions from GitHub --- content/en/about/contributors.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/content/en/about/contributors.md b/content/en/about/contributors.md index 1e3601d..ebf9066 100644 --- a/content/en/about/contributors.md +++ b/content/en/about/contributors.md @@ -134,4 +134,5 @@ img { [![enicolasgomez](https://avatars.githubusercontent.com/u/5366927?v=4&s=100)](https://github.com/enicolasgomez) [![vidhyalongani](https://avatars.githubusercontent.com/u/71261494?v=4&s=100)](https://github.com/vidhyalongani) [![Salam-Dalloul](https://avatars.githubusercontent.com/u/32265731?v=4&s=100)](https://github.com/Salam-Dalloul) -[![Aiga115](https://avatars.githubusercontent.com/u/67194168?v=4&s=100)](https://github.com/Aiga115) \ No newline at end of file +[![Aiga115](https://avatars.githubusercontent.com/u/67194168?v=4&s=100)](https://github.com/Aiga115) +[![Copilot](https://avatars.githubusercontent.com/in/1143301?v=4&s=100)](https://github.com/apps/copilot-swe-agent) \ No newline at end of file From b166549ba70ff76a400f2855d545a0036d4dbdb5 Mon Sep 17 00:00:00 2001 From: jenkins Date: Thu, 11 Jun 2026 05:22:08 +0000 Subject: [PATCH 11/17] Updating contributions from GitHub --- content/en/about/contributors.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/content/en/about/contributors.md b/content/en/about/contributors.md index ebf9066..d6da132 100644 --- a/content/en/about/contributors.md +++ b/content/en/about/contributors.md @@ -71,6 +71,7 @@ img { [![actions-user](https://avatars.githubusercontent.com/u/65916846?v=4&s=100)](https://github.com/actions-user) [![NeZanyat](https://avatars.githubusercontent.com/u/1211953?v=4&s=100)](https://github.com/NeZanyat) [![afonsobspinto](https://avatars.githubusercontent.com/u/19196034?v=4&s=100)](https://github.com/afonsobspinto) +[![Copilot](https://avatars.githubusercontent.com/in/1143301?v=4&s=100)](https://github.com/apps/copilot-swe-agent) [![snyk-bot](https://avatars.githubusercontent.com/u/19733683?v=4&s=100)](https://github.com/snyk-bot) [![leechuck](https://avatars.githubusercontent.com/u/362161?v=4&s=100)](https://github.com/leechuck) [![MiguelAngelRG](https://avatars.githubusercontent.com/u/12188797?v=4&s=100)](https://github.com/MiguelAngelRG) @@ -134,5 +135,4 @@ img { [![enicolasgomez](https://avatars.githubusercontent.com/u/5366927?v=4&s=100)](https://github.com/enicolasgomez) [![vidhyalongani](https://avatars.githubusercontent.com/u/71261494?v=4&s=100)](https://github.com/vidhyalongani) [![Salam-Dalloul](https://avatars.githubusercontent.com/u/32265731?v=4&s=100)](https://github.com/Salam-Dalloul) -[![Aiga115](https://avatars.githubusercontent.com/u/67194168?v=4&s=100)](https://github.com/Aiga115) -[![Copilot](https://avatars.githubusercontent.com/in/1143301?v=4&s=100)](https://github.com/apps/copilot-swe-agent) \ No newline at end of file +[![Aiga115](https://avatars.githubusercontent.com/u/67194168?v=4&s=100)](https://github.com/Aiga115) \ No newline at end of file From 3f8c81ac2758c8e500928b2a6faf46b64ebee336 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Fri, 12 Jun 2026 16:50:44 +0100 Subject: [PATCH 12/17] update FlyBase funding message --- content/en/_index.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/content/en/_index.html b/content/en/_index.html index a4b8987..8196591 100644 --- a/content/en/_index.html +++ b/content/en/_index.html @@ -27,10 +27,10 @@

- Because of recent changes to government funding, the NIH grant that supported FlyBase has been terminated. - They are now reaching out to the community for emergency funding. Please click here for more information and to contribute: + Because of changes to US government funding, the foreign subaward of the NHGRI grant that supported the FlyBase curation team at the University of Cambridge has been terminated. + They are now reaching out to the community to assist with funding. Please click here for more information and to contribute: Contribute to FlyBase wiki page - Thank you in advance for your support to keep FlyBase on air and continuing to serve the Drosophila research community. + Thank you in advance for your support in allowing FlyBase to continue serving the Drosophila research community. We remain grateful to Wellcome for their continued support of Virtual Fly Brain.

From afd740dbab7fbb355c45491e8fa2ef42417b2904 Mon Sep 17 00:00:00 2001 From: Clare72 Date: Fri, 12 Jun 2026 16:52:33 +0100 Subject: [PATCH 13/17] Update _index.html --- content/en/_index.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/en/_index.html b/content/en/_index.html index 8196591..1a9c07f 100644 --- a/content/en/_index.html +++ b/content/en/_index.html @@ -22,7 +22,7 @@

- Our colleagues at FlyBase needs your help! + Our colleagues at FlyBase need your help!

From 75b1ebbfadcfad5ce1735ba6c51ba717380c326f Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Mon, 22 Jun 2026 16:10:22 +0000 Subject: [PATCH 14/17] Add MCP preprint to news post and bump date Cite McLachlan et al. (2026), bioRxiv (doi:10.64898/2026.06.16.732577), and summarise the 30-task benchmark (25/30 MCP vs 14/30 web vs 2/30 bare; 89% vs 11% on quantification tasks). Re-date the post to 2026-06-21 so the preprint announcement surfaces in the news feed. --- content/en/blog/news/VFB_MCP_Tool.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/content/en/blog/news/VFB_MCP_Tool.md b/content/en/blog/news/VFB_MCP_Tool.md index 592e2e8..5984c01 100644 --- a/content/en/blog/news/VFB_MCP_Tool.md +++ b/content/en/blog/news/VFB_MCP_Tool.md @@ -1,13 +1,19 @@ --- title: "Introducing the VFB Model Context Protocol (MCP) Tool" linkTitle: "VFB MCP Tool Launch" -date: 2026-02-07 +date: 2026-06-21 description: > Explore Virtual Fly Brain data directly through your favorite LLM with the new VFB Model Context Protocol (MCP) tool - now available at vfb3-mcp.virtualflybrain.org --- We're excited to announce the launch of the **Virtual Fly Brain Model Context Protocol (MCP) Tool** — a powerful new way to explore VFB data through Large Language Models (LLMs) like Claude, providing natural language access to VFB's comprehensive neuroanatomical database. +## Now described in a preprint + +The tool and its evaluation are now described in a preprint: McLachlan et al. (2026), *VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase*, bioRxiv. [doi:10.64898/2026.06.16.732577](https://doi.org/10.64898/2026.06.16.732577). + +Benchmarked on 30 neuroscience tasks, an LLM equipped with the VFB MCP produced precise, verifiable and appropriately quantified answers on 25/30 tasks, against 14/30 for a web-search-assisted LLM and 2/30 for a bare LLM (Wilcoxon *p* < 0.01, Holm-corrected across all pairwise comparisons). The advantage was largest where answers required data quantification — 89% of those tasks were answered correctly with the MCP, against 11% with web search — reflecting the precision that VFB's expert-curated, ontology-backed knowledge graph brings to the recently integrated connectomes. The MCP server code is available at [VirtualFlyBrain/VFB3-MCP](https://github.com/VirtualFlyBrain/VFB3-MCP). + ## What is the VFB MCP Tool? The VFB MCP tool integrates Virtual Fly Brain's rich neuroanatomical data with LLM capabilities, allowing researchers to: From e783b33cb6921b0946f83b733f53a3460f4daf80 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Mon, 22 Jun 2026 17:28:24 +0100 Subject: [PATCH 15/17] moving to bottom of article --- content/en/blog/news/VFB_MCP_Tool.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/content/en/blog/news/VFB_MCP_Tool.md b/content/en/blog/news/VFB_MCP_Tool.md index 5984c01..1d0dc29 100644 --- a/content/en/blog/news/VFB_MCP_Tool.md +++ b/content/en/blog/news/VFB_MCP_Tool.md @@ -8,12 +8,6 @@ description: > We're excited to announce the launch of the **Virtual Fly Brain Model Context Protocol (MCP) Tool** — a powerful new way to explore VFB data through Large Language Models (LLMs) like Claude, providing natural language access to VFB's comprehensive neuroanatomical database. -## Now described in a preprint - -The tool and its evaluation are now described in a preprint: McLachlan et al. (2026), *VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase*, bioRxiv. [doi:10.64898/2026.06.16.732577](https://doi.org/10.64898/2026.06.16.732577). - -Benchmarked on 30 neuroscience tasks, an LLM equipped with the VFB MCP produced precise, verifiable and appropriately quantified answers on 25/30 tasks, against 14/30 for a web-search-assisted LLM and 2/30 for a bare LLM (Wilcoxon *p* < 0.01, Holm-corrected across all pairwise comparisons). The advantage was largest where answers required data quantification — 89% of those tasks were answered correctly with the MCP, against 11% with web search — reflecting the precision that VFB's expert-curated, ontology-backed knowledge graph brings to the recently integrated connectomes. The MCP server code is available at [VirtualFlyBrain/VFB3-MCP](https://github.com/VirtualFlyBrain/VFB3-MCP). - ## What is the VFB MCP Tool? The VFB MCP tool integrates Virtual Fly Brain's rich neuroanatomical data with LLM capabilities, allowing researchers to: @@ -59,3 +53,9 @@ This tool democratizes access to VFB's complex neuroanatomical data, making it a Check out our new [**VFB MCP Tutorial**](/docs/tutorials/vfb-mcp-guide/) for detailed guidance on using the tool, example queries, and best practices for exploring VFB data through your favorite LLM. The VFB MCP tool represents an exciting new frontier in how researchers interact with neuroanatomical databases. We hope it accelerates your discoveries about *Drosophila* neurobiology! + +## Now described in a preprint + +The tool and its evaluation are now described in a preprint: McLachlan et al. (2026), *VFB-MCP: Natural-Language Access to Drosophila Neuroscience Grounded by an Expert-Curated Ontology-Led Knowledgebase*, bioRxiv. [doi:10.64898/2026.06.16.732577](https://doi.org/10.64898/2026.06.16.732577). + +Benchmarked on 30 neuroscience tasks, an LLM equipped with the VFB MCP produced precise, verifiable and appropriately quantified answers on 25/30 tasks, against 14/30 for a web-search-assisted LLM and 2/30 for a bare LLM (Wilcoxon *p* < 0.01, Holm-corrected across all pairwise comparisons). The advantage was largest where answers required data quantification — 89% of those tasks were answered correctly with the MCP, against 11% with web search — reflecting the precision that VFB's expert-curated, ontology-backed knowledge graph brings to the recently integrated connectomes. The MCP server code is available at [VirtualFlyBrain/VFB3-MCP](https://github.com/VirtualFlyBrain/VFB3-MCP). \ No newline at end of file From af8e68ba6fd838527fcd868ee33a825b0e649933 Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Mon, 22 Jun 2026 18:00:08 +0000 Subject: [PATCH 16/17] Fix invalid YAML front matter for terms with no tags A term with an empty Tags list still had its ID-prefix tag appended onto an empty CSV string, producing "tags: [,VFB]". The leading comma is an empty flow-sequence node, which go-yaml rejects ("did not find expected node content"), failing the Hugo build on VFB_00017893_v8.md. Build the tag list properly and drop empty entries before joining. --- vfbterms.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/vfbterms.py b/vfbterms.py index bf715d9..193eda7 100644 --- a/vfbterms.py +++ b/vfbterms.py @@ -497,11 +497,14 @@ def generate_page(term_data): url_slug = get_term_url(name, term_id) # Tags for front matter - tags_csv = ",".join(tags) + # Build a clean list and drop empties, otherwise a term with no Tags + # yields a leading comma (e.g. "[,VFB]") which is invalid YAML flow syntax + tag_list = list(tags) if "_" in term_id: - tags_csv += "," + term_id.split("_")[0] + tag_list.append(term_id.split("_")[0]) elif term_id.startswith("FB"): - tags_csv += "," + term_id[0:4] + tag_list.append(term_id[0:4]) + tags_csv = ",".join(t for t in tag_list if t) # Thumbnails thumbnails = get_thumbnails(term_data) From c52b4e130711f2903fa4d1b602c6ffa288d08b8e Mon Sep 17 00:00:00 2001 From: Robbie Court Date: Sun, 28 Jun 2026 10:54:27 +0100 Subject: [PATCH 17/17] Cleaned up rendering from VFBquery --- vfbterms.py | 322 +++++++++++++++++++++++++++++++++++++++++----------- 1 file changed, 255 insertions(+), 67 deletions(-) diff --git a/vfbterms.py b/vfbterms.py index 193eda7..66951f1 100644 --- a/vfbterms.py +++ b/vfbterms.py @@ -9,6 +9,8 @@ import json import traceback import time +import threading +from concurrent.futures import ThreadPoolExecutor, as_completed, wait, FIRST_COMPLETED from urllib.parse import quote # Suppress the urllib3 warning about OpenSSL @@ -25,17 +27,24 @@ from requests.adapters import HTTPAdapter from urllib3.util.retry import Retry -version = 8 +version = 9 API_BASE = "https://v3-cached.virtualflybrain.org/get_term_info" STATUS_URL = "https://vfbquery.virtualflybrain.org/status" VFB_BROWSER_BASE = "https://v2.virtualflybrain.org/org.geppetto.frontend/geppetto" # Throttle settings — stay under 20 concurrent to keep API reliable -MAX_ACTIVE_BEFORE_BACKOFF = 20 # Back off when this many queries are active +MAX_ACTIVE_BEFORE_BACKOFF = 20 # Back off when the server reports this many active queries STATUS_CHECK_INTERVAL = 10 # Seconds between status checks while waiting MAX_CAPACITY_WAIT_SECONDS = 600 # Give up waiting for capacity after this long -API_TIMEOUT_SECONDS = int(os.environ.get("VFB_API_TIMEOUT_SECONDS", "9000")) +# Concurrent fetch/generate workers. Kept below MAX_ACTIVE_BEFORE_BACKOFF so our +# own load leaves headroom for other clients; the serial loop only ever used one +# slot, leaving the server (≈20 slots) mostly idle — this is the main speed-up. +MAX_WORKERS = int(os.environ.get("VFB_MAX_WORKERS", "12")) +# Per-request timeout. The old 9000s default was a workaround for serial stalls; +# with concurrency a hung term must not pin a worker for hours. Override with +# VFB_API_TIMEOUT_SECONDS if a genuinely heavy term needs longer. +API_TIMEOUT_SECONDS = int(os.environ.get("VFB_API_TIMEOUT_SECONDS", "600")) # Known ID prefixes for internal link conversion KNOWN_PREFIXES = ( @@ -52,11 +61,12 @@ def create_session(): """Create a requests session with retry logic and connection pooling.""" session = requests.Session() retry = Retry( - total=2, - backoff_factor=120, - status_forcelist=[500, 502, 503, 504], + total=3, + backoff_factor=5, + status_forcelist=[429, 500, 502, 503, 504], + respect_retry_after_header=True, ) - adapter = HTTPAdapter(max_retries=retry, pool_connections=10, pool_maxsize=10) + adapter = HTTPAdapter(max_retries=retry, pool_connections=MAX_WORKERS, pool_maxsize=MAX_WORKERS) session.mount("https://", adapter) session.mount("http://", adapter) return session @@ -78,6 +88,37 @@ def check_server_status(): print(f"WARNING: Could not check server status: {e}") return None +# Cached, thread-safe view of server capacity so a pool of workers doesn't each +# poll /status before every request. One worker refreshes the cache at most once +# per STATUS_CHECK_INTERVAL; the rest read the cached verdict. +_status_lock = threading.Lock() +_status_cache = {"ts": 0.0, "ok": True} + +def throttle(term_id=""): + """Pause the calling worker while the server is at/over capacity. + + Reads a shared cached /status verdict (refreshed at most once per + STATUS_CHECK_INTERVAL). Returns once the server has headroom, or after + MAX_CAPACITY_WAIT_SECONDS so a single term can't block forever. With + MAX_WORKERS below MAX_ACTIVE_BEFORE_BACKOFF our own load never trips this; + it only engages when other clients are loading the server. + """ + start = time.time() + while True: + now = time.time() + with _status_lock: + if (now - _status_cache["ts"]) >= STATUS_CHECK_INTERVAL: + st = check_server_status() + _status_cache["ts"] = now + _status_cache["ok"] = True if st is None else st[0] < MAX_ACTIVE_BEFORE_BACKOFF + ok = _status_cache["ok"] + if ok: + return + if time.time() - start >= MAX_CAPACITY_WAIT_SECONDS: + print(f"WARNING: proceeding with {term_id or 'request'} after waiting for capacity") + return + time.sleep(STATUS_CHECK_INTERVAL) + def wait_for_server_capacity(term_id=""): """Block until the server has capacity below our threshold. @@ -131,8 +172,8 @@ def fetch_term_info(term_id): Checks server capacity before making the request to avoid flooding. """ - # Wait until the server isn't overloaded - wait_for_server_capacity(term_id) + # Wait until the server isn't overloaded (shared cached capacity check) + throttle(term_id) try: resp = session.get(API_BASE, params={"id": term_id}, timeout=API_TIMEOUT_SECONDS) @@ -192,6 +233,32 @@ def replace_link(match): # Match: [ ... ]( ID ) where the ID part has no spaces or parens return re.sub(r'\[([^\]]*(?:\[[^\]]*\][^\]]*)*)\]\(([^)\s]+)\)', replace_link, text) +# Markdown links nested inside a raw HTML block (e.g. the hero card

) are NOT +# processed by Hugo's Goldmark renderer — it passes HTML blocks through verbatim. +# So any `[label](id)` placed inside

…

would render as literal brackets. +# linkify_html emits real anchors instead, mapping known ids to /reports/ +# exactly like convert_internal_links does for plain markdown. +_MD_LINK_RE = re.compile(r'\[([^\]]*(?:\[[^\]]*\][^\]]*)*)\]\(([^)\s]+)\)') + +def linkify_html(text): + """Convert `[label](target)` markdown links to HTML anchors. + + For embedding in raw HTML blocks (hero card description/comment), where + Goldmark won't process markdown. Known VFB ids are rewritten to /reports/; + other targets (already-resolved URLs) are used as-is. Newlines are collapsed + to spaces so the surrounding HTML block isn't terminated by a blank line. + """ + if not text: + return "" + + def repl(match): + label = match.group(1) + identifier = match.group(2) + href = get_report_url(identifier) if is_known_id(identifier) else identifier + return f'{label}' + + return _MD_LINK_RE.sub(repl, text).replace("\r", " ").replace("\n", " ") + def format_relationships_section(relationships_text): """Format Meta.Relationships into markdown bullets. @@ -305,7 +372,16 @@ def format_synonyms_table(synonyms): return "\n".join(lines) def format_query_preview(query, term_id): - """Format a Query's preview_results as a markdown table with thumbnails.""" + """Format a Query's preview_results as an HTML table with thumbnails. + + Emitted as a complete raw HTML rather than a markdown table wrapped + in
. Hugo's Goldmark does not process markdown + nested inside a raw HTML block, so the wrapped-markdown form leaked every + `[label](id)` cell as literal text and never rendered as a table. A full + HTML table renders verbatim under unsafe=true. The `###` heading and the + "View all" button stay outside the block, separated by blank lines so + Goldmark closes each HTML block cleanly. + """ preview = query.get("preview_results", {}) rows = preview.get("rows", []) if not rows: @@ -319,36 +395,39 @@ def format_query_preview(query, term_id): lines.append(f'### {label} ({count} total)') lines.append("") lines.append('
') - lines.append("") - lines.append("| Thumbnail | Name | Tags |") - lines.append("|-----------|------|------|") + lines.append('
') + lines.append('') + lines.append('') for row in rows: - # Extract name — may be markdown link like [name](id) + # Name — may be `[label](id)` markdown from the API; emit as an anchor + # because it lives inside a raw HTML block (Goldmark won't linkify it). name_raw = row.get("label", row.get("name", "")) - name_converted = convert_internal_links(name_raw) + name_md = convert_internal_links(name_raw) row_id = row.get("id", "") - if row_id and is_known_id(row_id) and name_converted == name_raw and name_raw: - name_converted = f'[{name_raw}]({get_report_url(row_id)})' + if row_id and is_known_id(row_id) and name_md == name_raw and name_raw: + name_md = f'[{name_raw}]({get_report_url(row_id)})' + name_html = linkify_html(name_md) if "](" in name_md else name_md - # Extract tags + # Tags tags_raw = row.get("tags", "") tags_display = tags_raw.replace("|", ", ") if tags_raw else "" - # Extract thumbnail — may be markdown image like [![alt](url)](link) + # Thumbnail — pull the URL out of `[![alt](url 'title')](link)` markdown. thumb_raw = row.get("thumbnail", "") thumb_html = "" if thumb_raw: - # Extract URL from markdown image: [![alt](url "title")](link) img_match = re.search(r'!\[[^\]]*\]\(([^\s)]+)', thumb_raw) if img_match: thumb_url = img_match.group(1) - thumb_html = f'' + thumb_html = (f'' + f'') - lines.append(f'| {thumb_html} | {name_converted} | {tags_display} |') + lines.append(f'') - lines.append("") - lines.append("") + lines.append('') + lines.append('
ThumbnailNameTags
{thumb_html}{name_html}{tags_display}
') + lines.append('') lines.append("") lines.append(f'View all {count} results in VFB →') lines.append("") @@ -427,6 +506,48 @@ def format_publications(publications): lines.append("".join(parts)) return "\n".join(lines) +def format_xrefs(xrefs, term_name): + """Format Xrefs (external cross-references) into markdown links. + + Each xref is {label, accession, link, icon}. The cached get_term_info + endpoint resolves the full external URL in `link`, so we link to it + directly rather than rebuilding from a link_base/accession template + (cf. VFBProcessTermInfoJson.xref.getLink). Link text mirrors the VFB + browser's "Cross References" section: " on ". + """ + if not xrefs: + return "" + + lines = [] + for xref in xrefs: + link = xref.get("link", "") + if not link: + continue + label = xref.get("label", "") + text = f'{term_name} on {label}' if (term_name and label) else (label or link) + accession = xref.get("accession", "") + suffix = f' ({accession})' if accession and accession not in ("None", "") else "" + lines.append(f'- [{text}]({link}){suffix}') + return "\n".join(lines) + +def format_related_tools(tools, term_id): + """Format RelatedTools into the VFB browser's "Graphs For" links. + + Each tool is {tool, label, default_args}. These launch graph/hierarchy + tools on the term inside the 3D browser; link to the term there so the + user can run them (the browser exposes the tool set once the term loads). + """ + if not tools: + return "" + + lines = [] + for t in tools: + label = t.get("label", t.get("tool", "")) + if not label: + continue + lines.append(f'- [{label}]({VFB_BROWSER_BASE}?id={term_id})') + return "\n".join(lines) + def build_hero_card(name, term_id, tags_badges, description_html, comment_html, thumbnails): """Build the hero card without blank lines that break Markdown HTML blocks.""" lines = [ @@ -480,13 +601,19 @@ def generate_page(term_data): publications = term_data.get("Publications", []) technique = term_data.get("Technique", []) images = term_data.get("Images", {}) + examples = term_data.get("Examples", {}) + xrefs = term_data.get("Xrefs", []) + related_tools = term_data.get("RelatedTools", []) # Description for front matter description = meta.get("Description", "") if not description: - # Fallback to Types text (stripped of markdown links) - types_text = meta.get("Types", "") - description = re.sub(r'\[([^\]]+)\]\([^)]+\)', r'\1', types_text) + # Fallback to Types text + description = meta.get("Types", "") + # Strip markdown link syntax to plain labels: the front-matter description + # becomes the tag and page summary, where raw + # `[label](id)` syntax would show literally. + description = re.sub(r'\[([^\]]+)\]\([^)]+\)', r'\1', description) # Clean for YAML description = description.replace('"', '\\"').replace("\n", " ").replace("\r", " ").strip() @@ -532,11 +659,11 @@ def generate_page(term_data): desc_html = "" if meta.get("Description"): - desc_html = f'

{convert_internal_links(meta["Description"])}

' + desc_html = f'

{linkify_html(meta["Description"])}

' comment_html = "" if comment: - comment_html = f'

{convert_internal_links(comment)}

' + comment_html = f'

{linkify_html(comment)}

' sections.append(build_hero_card(name, term_id, tags_badges, desc_html, comment_html, thumbnails)) @@ -557,6 +684,12 @@ def generate_page(term_data): syn_md = format_synonyms_table(synonyms) sections.append(f'## Alternative Names\n\n{syn_md}\n') + # ── Cross references (external databases) ── + if xrefs: + xref_md = format_xrefs(xrefs, name) + if xref_md.strip(): + sections.append(f'## Cross References\n\n{xref_md}\n') + # ── Technique ── if technique: tech_lines = "\n".join(f'- {t}' for t in technique) @@ -567,9 +700,17 @@ def generate_page(term_data): lic_md = format_licenses(licenses) sections.append(f'## License\n\n{lic_md}\n') - # ── Downloads ── - if images: - dl_md = format_downloads(images) + # ── Downloads (individual Images and class Examples) ── + # Class terms carry their downloadable volumes under Examples (one list + # per template), individuals under Images. Merge both so class pages get + # download links too, matching the browser's Available Images downloads. + download_sources = {} + for tpl, img_list in images.items(): + download_sources.setdefault(tpl, []).extend(img_list) + for tpl, ex_list in examples.items(): + download_sources.setdefault(tpl, []).extend(ex_list) + if download_sources: + dl_md = format_downloads(download_sources) if dl_md.strip(): sections.append(f'## Downloads\n\n{dl_md}\n') @@ -581,12 +722,22 @@ def generate_page(term_data): q_md = format_query_preview(q, term_id) sections.append(q_md) + # ── Graphs For (related graph/hierarchy tools) ── + if related_tools: + tools_md = format_related_tools(related_tools, term_id) + if tools_md.strip(): + sections.append(f'## Graphs For\n\n{tools_md}\n') + # ── Publications ── if publications: pub_md = format_publications(publications) sections.append(f'## References\n\n{pub_md}\n') - return "\n".join(sections) + # Join with a blank line between every section. Goldmark keeps a raw HTML + # block (e.g. the hero card) open until a blank line, so without this the + # first heading after the hero ("## Classification") gets swallowed into + # the HTML block and printed literally instead of rendered as a heading. + return "\n\n".join(sections) # ─── Term Saving ───────────────────────────────────────────────────────────── @@ -613,46 +764,79 @@ def process_group(base_path, relative_dir, label, query): chdir(target_dir) save_terms(fetch_ids(label, query)) -def save_terms(ids): - """Fetch and save term pages for a list of IDs.""" - total = len(ids) - success_count = 0 - skip_count = 0 - fail_count = 0 - for i, term_id in enumerate(ids): - try: - filename = term_id + "_v" + str(version) + ".md" - if os.path.isfile(filename): - skip_count += 1 - continue +def process_term(term_id): + """Fetch, render and write one term page. Returns a status string. - print(f"Processing {term_id} ({i+1}/{total})...") - term_data = fetch_term_info(term_id) - if term_data is None: - fail_count += 1 - continue + Runs inside a worker thread. Writes to a temp file then atomically renames + so a killed build never leaves a half-written page. Throttling against the + server's capacity happens inside fetch_term_info via throttle(). + """ + filename = term_id + "_v" + str(version) + ".md" + if os.path.isfile(filename): + return "skip" - page_content = generate_page(term_data) + term_data = fetch_term_info(term_id) + if term_data is None: + return "fail" - with open(filename, "w", encoding="utf-8") as f: - f.write(page_content) + page_content = generate_page(term_data) - success_count += 1 + tmp = f"{filename}.{os.getpid()}.{threading.get_ident()}.tmp" + with open(tmp, "w", encoding="utf-8") as f: + f.write(page_content) + os.replace(tmp, filename) - # Clean up previous version - old_filename = term_id + "_v" + str(version - 1) + ".md" - if os.path.isfile(old_filename): - os.remove(old_filename) - print(f'Removed: {old_filename}') + # Clean up previous version + old_filename = term_id + "_v" + str(version - 1) + ".md" + if os.path.isfile(old_filename): + try: + os.remove(old_filename) + except OSError: + pass + return "ok" - # Throttling is handled by wait_for_server_capacity() in fetch_term_info +def save_terms(ids): + """Fetch and save term pages for a list of IDs, concurrently. + + A bounded ThreadPoolExecutor keeps up to MAX_WORKERS requests in flight so + the server's ~20 query slots stay busy, instead of the old one-at-a-time + loop that left them idle. The in-flight window is capped so building the + future set for a 600k-id group doesn't balloon memory. + """ + total = len(ids) + counts = {"ok": 0, "skip": 0, "fail": 0} + done = 0 + window = MAX_WORKERS * 4 + progress_every = max(100, window) + def record(fut, tid): + nonlocal done + try: + status = fut.result() except Exception as e: - fail_count += 1 - print(f"ERROR processing {term_id}: {str(e)}") + status = "fail" + print(f"ERROR processing {tid}: {e}") print(traceback.format_exc()) - - print(f"\nBatch complete: {success_count} created, {skip_count} skipped (existing), {fail_count} failed out of {total} total") + counts[status] = counts.get(status, 0) + 1 + done += 1 + if status == "fail" or done % progress_every == 0: + print(f" {done}/{total} processed " + f"(created={counts['ok']} skipped={counts['skip']} failed={counts['fail']}) " + f"last={tid}:{status}") + + with ThreadPoolExecutor(max_workers=MAX_WORKERS) as ex: + inflight = {} + for term_id in ids: + inflight[ex.submit(process_term, term_id)] = term_id + if len(inflight) >= window: + finished, _ = wait(set(inflight), return_when=FIRST_COMPLETED) + for fut in finished: + record(fut, inflight.pop(fut)) + for fut in as_completed(set(inflight)): + record(fut, inflight[fut]) + + print(f"\nBatch complete: {counts['ok']} created, {counts['skip']} skipped (existing), " + f"{counts['fail']} failed out of {total} total") # ─── Testing ───────────────────────────────────────────────────────────────── @@ -698,12 +882,16 @@ def test_term_page(term_id, term_type="class"): checks["Relationships"] = "## Relationships" in page_content if term_data.get("Synonyms"): checks["Synonyms"] = "## Alternative Names" in page_content + if term_data.get("Xrefs"): + checks["Cross References"] = "## Cross References" in page_content if term_data.get("Licenses"): checks["Licenses"] = "## License" in page_content - if term_data.get("Images"): + if term_data.get("Images") or term_data.get("Examples"): checks["Downloads"] = "## Downloads" in page_content if any(q.get("preview_results", {}).get("rows") for q in term_data.get("Queries", [])): checks["Query previews"] = "table-responsive" in page_content + if term_data.get("RelatedTools"): + checks["Graphs For"] = "## Graphs For" in page_content all_pass = True for check_name, result in checks.items(): @@ -791,8 +979,8 @@ def test_report_link_regression(): checks = { "Markdown links use report path": converted == "[DNb08](/reports/FBbt_20011340)", - "Query preview preserves report link": "[DNb08](/reports/FBbt_20011340)" in query_preview, - "Plain row labels get report link": "[DNp45](/reports/FBbt_20011346)" in query_preview, + "Query preview preserves report link": 'DNb08' in query_preview, + "Plain row labels get report link": 'DNp45' in query_preview, } all_pass = True