[v5.5] Diagnostics UI: model/log viewer + ModelFile page + MathJax by lil-aditya · Pull Request #408 · EAPD-DRB/MUIOGO

lil-aditya · 2026-04-02T14:28:15Z

Closes: #391
Part of: #388
Requires: PR1 (guardrails) and PR2 (backend/runtime routes) to be merged

Summary

This PR ports the upstream MUIO v5.5 diagnostics UI into MUIOGO, including:

DataFile page model/log viewer flow
Standalone ModelFile page (#/ModelFile)
MathJax-based equation rendering
Scenario toggle-all control

Changes included

Added "View Model", "View Log", and "Equations" controls to DataFile page
Integrated safe frontend calls to:
- /readModelFile
- /readLogFile
Added standalone ModelFile page with equation parsing + rendering
Integrated MathJax (scoped to equations page only)
Added scenario toggle-all control (preserves locked SC_0)

Compatibility + Safety

Frontend requests only fixed backend endpoints (no arbitrary path input)
Raw model/log text rendered using DOM text nodes (no innerHTML usage)
MathJax applied only to equation view (not logs or raw text)
Toggle-all excludes disabled scenarios and preserves SC_0

Narrow upstream adaptations

The upstream UI was followed by default, with minimal, targeted changes:

Switched from eager preload → on-demand fetch for model/log text
Replaced HTML-string rendering with safe DOM-based rendering
Fixed routing to use SPA hash format (#/ModelFile)
Adjusted toggle-all behavior to respect MUIOGO constraints

Files touched (frontend scope)

WebAPP/App/Controller/DataFile.js
WebAPP/App/Controller/ModelFile.js
WebAPP/App/View/DataFile.html
WebAPP/App/View/ModelFile.html
WebAPP/Classes/Html.Class.js
WebAPP/Classes/Osemosys.Class.js
WebAPP/Routes/Routes.Class.js
WebAPP/index.html

Validation

git diff --check passed (no whitespace/syntax issues)
ES modules import cleanly (Node-based check)
Equation parser validated (67 equations extracted from model file)
Route wiring verified at code level

Known limitations

PR3 depends on PR2 backend routes (readModelFile, readLogFile)

End-to-end UI validation is expected in CI / reviewer environment.

Out of scope

Backend/runtime logic (PR2 [Task] Pull the safe backend/runtime changes from MUIO v5.5 #390)
Result metadata and rendering (PR4 [Task] Fix result metadata and shadow-price rendering from MUIO v5.5 #392)
Any non-diagnostics UI changes

Notes

This PR intentionally keeps changes minimal and aligned with upstream v5.5 UI behavior, while enforcing MUIOGO’s safety constraints for path handling and rendering.

…s.json

lil-aditya · 2026-04-02T14:30:40Z

This PR is based on the PR2 branch since upstream main did not yet include PR2 in this checkout.
Happy to rebase if needed once PR2 is merged.

Copilot

Pull request overview

Ports the upstream v5.5 diagnostics UI into MUIOGO by adding model/log viewers, a standalone ModelFile equations page, and supporting backend routes/guardrails for safe diagnostics reads.

Changes:

Added DataFile-page controls and modals for viewing the fixed-path model/log text, plus a scenario toggle-all control.
Introduced a standalone #/ModelFile page that parses GMPL constraints and typesets them with MathJax.
Added backend fixed-path routes (/readModelFile, /readLogFile), runtime logging location changes, and a smoke/clean-base verification harness + CI workflow.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
WebAPP/SOLVERs/model.v.5.4.txt	Minor formatting tweaks in solver model text; used by equations extraction/rendering.
WebAPP/Routes/Routes.Class.js	Adds SPA route for `#/ModelFile`.
WebAPP/index.html	Adds MathJax configuration + CDN script include.
WebAPP/Classes/Osemosys.Class.js	Adds frontend helpers for `readModelFile` / `readLogFile` via fetch.
WebAPP/Classes/Html.Class.js	Adds safe plain-text rendering helpers for model/log/data text.
WebAPP/App/View/ModelFile.html	New equations page layout + styles.
WebAPP/App/View/DataFile.html	Adds EQUATIONS / VIEW MODEL / VIEW LOG controls, toggle-all button, and model/log modals.
WebAPP/App/Controller/ModelFile.js	New controller: extracts objective/constraints and typesets with MathJax.
WebAPP/App/Controller/DataFile.js	Adds modal text viewer helper and scenario toggle-all behavior.
API/Routes/DataFile/DataFileRoute.py	Adds fixed-path read endpoints and improves logging around runs.
API/Classes/Base/Config.py	Introduces runtime/log directory configuration and solver model path constant.
API/app.py	Adds rotating file logging setup and warning capture.
API/Classes/Case/OsemosysClass.py	Refactors path bookkeeping (results/view/resData paths) and solver model file reference.
API/Classes/Case/DataFileClass.py	Refactors case run creation/update/cleanup to use instance paths and preserve viewDefinitions.
tests_smoke/test_smoke_app.py	Adds stdlib unittest smoke coverage for app import and fixed routes.
scripts/verify_clean_base.py	Adds “clean-base” verification script (git state, conflict markers, py_compile, smoke tests).
docs/dev/upstream_sync_playbook.md	Documents upstream sync order, overlap surface, rejected patterns, and verification command.
CONTRIBUTING.md	Adds clean-base verification guidance and pointers to the playbook.
.github/workflows/smoke.yml	Runs clean-base verification in CI on pull requests.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-04-02T14:32:15Z

WebAPP/SOLVERs/model.v.5.4.txt

-
-
-# Energy balance – include only pairs that exist (others implicitly 0)
+# Energy balance � include only pairs that exist (others implicitly 0)


The comment line contains a replacement character ("�"), which suggests an encoding/typography corruption (likely meant to be an en dash). Since this file is solver input, please replace it with plain ASCII (e.g., "-"), or ensure the intended character is preserved reliably.

Suggested change

# Energy balance � include only pairs that exist (others implicitly 0)

# Energy balance - include only pairs that exist (others implicitly 0)

Copilot · 2026-04-02T14:32:15Z

WebAPP/index.html

+		<script>
+			window.MathJax = window.MathJax || {
+				tex: {
+					packages: { '[+]': ['ams'] },
+					inlineMath: [['\\(', '\\)']],


MathJax is being configured and loaded in the global entrypoint, which means every page load pulls MathJax even when the equations view isn't used. This also conflicts with the PR description claim that MathJax is scoped to the equation page only; consider loading/injecting MathJax only when the ModelFile route/view is entered.

Copilot · 2026-04-02T14:32:16Z

WebAPP/index.html

+		<!-- Swap this CDN src later if MathJax is vendored locally. -->
+		<script id="muiogo-mathjax-script" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" defer></script>


The MathJax CDN URL is not version-pinned ("mathjax@3"), so it can change underneath you. Pin to a specific version and consider adding an integrity/crossorigin policy (or vendoring locally) to reduce supply-chain risk.

Suggested change



<script id="muiogo-mathjax-script" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" defer></script>



<script id="muiogo-mathjax-script" src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-chtml.js" defer></script>

Copilot · 2026-04-02T14:32:16Z

WebAPP/App/Controller/ModelFile.js

+                equation.latex,
+                '\\end{align}',
+                `\\tag{${counter}}`,


The generated MathJax block puts \tag{} after \end{align}. In LaTeX/MathJax, \tag must be inside an ams math environment (e.g., within align/equation) or it may be ignored / throw a typeset error. Move the tag into the align environment (or use an environment that supports tagging as written).

Suggested change

equation.latex,

'\\end{align}',

`\\tag{${counter}}`,

`${equation.latex} \\tag{${counter}}`,

'\\end{align}',

Copilot · 2026-04-02T14:32:16Z

WebAPP/App/Controller/DataFile.js

            }else{
                Html.renderScOrder(model.scenarios);
            }
+            DataFile.syncScenarioToggleButton();


The toggle-all button label/icon is only synced when the modal opens and when toggle-all is clicked. If a user manually checks/unchecks individual scenario checkboxes, the toggle-all label can become stale. Add a change handler on '#osy-scOrder' checkbox inputs to call syncScenarioToggleButton() after any manual toggle.

Suggested change

DataFile.syncScenarioToggleButton();

DataFile.syncScenarioToggleButton();

// Keep toggle-all button state in sync when individual scenario checkboxes change

$("#osy-scOrder")

.off("change", "input[type='checkbox']")

.on("change", "input[type='checkbox']", function () {

DataFile.syncScenarioToggleButton();

});

lil-aditya added 6 commits April 2, 2026 11:09

chore: add clean-base verification and smoke harness

a036e1f

chore(v5.5): update solver model file

c2ff593

fix(results): resData bookkeeping cleanup and preserve viewDefinition…

c1e8428

…s.json

feat(api): add safe readModelFile/readLogFile routes and logging

5ff62c5

feat(ui): add standalone ModelFile page and MathJax rendering

18ebbd3

feat(ui): add DataFile diagnostics viewers and scenario toggle-all

e5e0915

Copilot AI review requested due to automatic review settings April 2, 2026 14:28

github-actions bot added the needs-intake-fix PR intake structure needs maintainer follow-up label Apr 2, 2026

Copilot started reviewing on behalf of lil-aditya April 2, 2026 14:28 View session

Copilot AI reviewed Apr 2, 2026

View reviewed changes

lil-aditya mentioned this pull request Apr 2, 2026

[Proposal/Architecture] Keep MUIOGO upstream-compatible by default #393

Open

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[v5.5] Diagnostics UI: model/log viewer + ModelFile page + MathJax#408

[v5.5] Diagnostics UI: model/log viewer + ModelFile page + MathJax#408
lil-aditya wants to merge 6 commits intoEAPD-DRB:mainfrom
lil-aditya:feat/v55-diagnostics-ui

lil-aditya commented Apr 2, 2026

Uh oh!

lil-aditya commented Apr 2, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Apr 2, 2026

Uh oh!

Copilot AI Apr 2, 2026

Uh oh!

Copilot AI Apr 2, 2026

Uh oh!

Copilot AI Apr 2, 2026

Uh oh!

Copilot AI Apr 2, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants



		# Energy balance – include only pairs that exist (others implicitly 0)
		# Energy balance � include only pairs that exist (others implicitly 0)

	# Energy balance � include only pairs that exist (others implicitly 0)
	# Energy balance - include only pairs that exist (others implicitly 0)

		<!-- Swap this CDN src later if MathJax is vendored locally. -->
		<script id="muiogo-mathjax-script" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-chtml.js" defer></script>

-            DataFile.syncScenarioToggleButton();
+            DataFile.syncScenarioToggleButton();
+            // Keep toggle-all button state in sync when individual scenario checkboxes change
+            $("#osy-scOrder")
+                .off("change", "input[type='checkbox']")
+                .on("change", "input[type='checkbox']", function () {
+                    DataFile.syncScenarioToggleButton();
+                });

Conversation

lil-aditya commented Apr 2, 2026

Summary

Changes included

Compatibility + Safety

Narrow upstream adaptations

Files touched (frontend scope)

Validation

Known limitations

Out of scope

Notes

Uh oh!

lil-aditya commented Apr 2, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Apr 2, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 2, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 2, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 2, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 2, 2026

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants