AI prompt pipeline implemented

[idkcoder93]

This PR implements the OCR and data processing pipeline, including context windowing to improve LLM ingestion accuracy. It also adds an LLM endpoint for extracting patient data from processed documents.

Changes:

• Implemented OCR pipeline for document text extraction.
• Added data processing and normalization.
• Introduced context windowing for improved LLM context handling.
• Added patient data extraction endpoint.

---

Summary by cubic

Implements an OCR + PDF text caching pipeline with context windowing and a new /llm/export endpoint to return patient data for LLM processing. Adds an “AI Summary” link in Chart Notes to open the prompter for the current patient.

• New Features

  • Caches extracted PDF text in llm_document_text keyed by SHA-256; bulk loads per patient.
  • REST endpoint /llm/export returns demographics, meds, allergies, measurements, labs, documents, and notes as JSON.
  • OCR/text extraction via PDFBox with context windowing to improve downstream LLM ingestion.
  • Validates Ocean eReferral attachments belong to the current patient across documents, labs, eForms, and HRM.
  • Adds an “AI Summary” button in Chart Notes to open the prompter for the current patient.

• Migration

  • Run DB updates to create llm_document_text and add new codes:
    • NRTF measurement and diabetes flowsheet updates (OMD DE16.066).
    • OMA uninsured service fee codes for Ontario private billing (PC13.19).
  • No config changes required; LLMExtractorEndpoint is registered via Spring.

^{Written for commit c22f7fd. Summary will update on new commits.}

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[sourcery-ai]

Sorry @idkcoder93, your pull request is larger than the review limit of 150000 diff characters

[gemini-code-assist]

Code Review

This pull request introduces an AI-ready patient export feature, including a new REST endpoint (/llm/export), an extraction service (LLMExtractorService), and a two-layer caching mechanism (LlmDocumentTextService) for extracted PDF text. It also adds attachment validation for Ocean eReferrals, introduces the NRTF measurement type for diabetes flowsheet compliance, and refactors client-side drug profile filtering and Tickler restore actions. The review feedback highlights several robustness improvements, including converting a query parameter to a string to avoid type mismatches, adding defensive null checks for array parameters and note results, handling potential parsing exceptions for demographic numbers, and correcting a cache sentinel return value mismatch.

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[cubic-dev-ai]

5 issues found across 56 files

Confidence score: 2/5

• Multiple high-confidence, user-impacting issues are present (sev 6–7), including historical data misclassification in src/main/resources/oscar/oscarEncounter/oscarMeasurements/flowsheets/diabetesQueensFlowsheet.xml and invalid document payloads being accepted in src/main/java/ca/openosp/openo/documentManager/DocumentAttachmentManagerImpl.java, which makes this a high-risk merge.
• src/main/webapp/js/custom/ocean/conreq.js uses synchronous AJAX (async: false), which can block the browser UI during attachment validation and cause hung referral workflows.
• src/main/java/ca/openosp/openo/encounter/oceanEReferal/pageUtil/ERefer2Action.java can throw NumberFormatException for malformed demographicNo, and src/main/java/ca/openosp/openo/managers/LlmDocumentTextService.java returns "" instead of null on cache hits, creating request-failure and contract-consistency risks.
• Pay close attention to src/main/resources/oscar/oscarEncounter/oscarMeasurements/flowsheets/diabetesQueensFlowsheet.xml, src/main/java/ca/openosp/openo/documentManager/DocumentAttachmentManagerImpl.java, src/main/webapp/js/custom/ocean/conreq.js, src/main/java/ca/openosp/openo/encounter/oceanEReferal/pageUtil/ERefer2Action.java, src/main/java/ca/openosp/openo/managers/LlmDocumentTextService.java - they contain the highest-impact correctness, validation, and UX stability risks.

Prompt for AI agents (unresolved issues)

Check if these issues are valid — if so, understand the root cause of each and fix them. If appropriate, use sub-agents to investigate and fix each issue separately.


<file name="src/main/java/ca/openosp/openo/documentManager/DocumentAttachmentManagerImpl.java">

<violation number="1" location="src/main/java/ca/openosp/openo/documentManager/DocumentAttachmentManagerImpl.java:686">
P1: Malformed or unknown document tokens are silently skipped in validateDocumentsBelongToPatient, allowing invalid payloads to incorrectly return true.</violation>
</file>

<file name="src/main/webapp/js/custom/ocean/conreq.js">

<violation number="1" location="src/main/webapp/js/custom/ocean/conreq.js:41">
P1: Synchronous AJAX (`async: false`) blocks the UI thread during attachment validation, risking frozen/hung referral interactions.</violation>
</file>

<file name="src/main/java/ca/openosp/openo/encounter/oceanEReferal/pageUtil/ERefer2Action.java">

<violation number="1" location="src/main/java/ca/openosp/openo/encounter/oceanEReferal/pageUtil/ERefer2Action.java:126">
P2: Handle invalid `demographicNo` values before parsing; a malformed request can currently throw `NumberFormatException` and fail the request.</violation>
</file>

<sub>Reply with feedback, questions, or to request a fix.

Re-trigger cubic</sub>

[cubic-dev-ai]

P1: Malformed or unknown document tokens are silently skipped in validateDocumentsBelongToPatient, allowing invalid payloads to incorrectly return true.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/main/java/ca/openosp/openo/documentManager/DocumentAttachmentManagerImpl.java, line 686:

<comment>Malformed or unknown document tokens are silently skipped in validateDocumentsBelongToPatient, allowing invalid payloads to incorrectly return true.</comment>

<file context>
@@ -663,4 +669,48 @@ public void flattenPDFFormFields(Path pdfPath) throws PDFGenerationException {
+            char type = doc.charAt(0);
+            try {
+                int id = Integer.parseInt(doc.substring(1));
+                switch (type) {
+                    case 'D': docIds.add(id); break;
+                    case 'L': labIds.add(id); break;
</file context>

Suggested change

	switch (type) {
	case 'D': docIds.add(id); break;
	case 'L': labIds.add(id); break;
	case 'E': eformIds.add(id); break;
	case 'H': hrmIds.add(id); break;
	switch (type) {
	case 'D': docIds.add(id); break;
	case 'L': labIds.add(id); break;
	case 'E': eformIds.add(id); break;
	case 'H': hrmIds.add(id); break;
	default: return false;
	}

[cubic-dev-ai]

P1: Synchronous AJAX (async: false) blocks the UI thread during attachment validation, risking frozen/hung referral interactions.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/main/webapp/js/custom/ocean/conreq.js, line 41:

<comment>Synchronous AJAX (`async: false`) blocks the UI thread during attachment validation, risking frozen/hung referral interactions.</comment>

<file context>
@@ -34,20 +34,38 @@ jQuery(document).ready(function () {
+    let valid = false;
+    jQuery.ajax({
+        type: 'POST',
+        async: false,
+        url: document.getElementById("contextPath").value + '/oscarEncounter/eRefer.do',
+        data: "demographicNo=" + demographicNo + "&method=validateDocuments&" + jQuery.param({documents: docs}, true),
</file context>

[cubic-dev-ai]

P2: Handle invalid demographicNo values before parsing; a malformed request can currently throw NumberFormatException and fail the request.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. At src/main/java/ca/openosp/openo/encounter/oceanEReferal/pageUtil/ERefer2Action.java, line 126:

<comment>Handle invalid `demographicNo` values before parsing; a malformed request can currently throw `NumberFormatException` and fail the request.</comment>

<file context>
@@ -92,11 +94,40 @@ public String execute() {
+            writeResponse(true);
+            return;
+        }
+        boolean valid = documentAttachmentManager.validateDocumentsBelongToPatient(
+                loggedInInfo, Integer.parseInt(demographicNo), documents);
+        writeResponse(valid);
</file context>

Suggested change

	boolean valid = documentAttachmentManager.validateDocumentsBelongToPatient(
	loggedInInfo, Integer.parseInt(demographicNo), documents);
	writeResponse(valid);
	try {
	int demoNo = Integer.parseInt(demographicNo);
	boolean valid = documentAttachmentManager.validateDocumentsBelongToPatient(
	loggedInInfo, demoNo, documents);
	writeResponse(valid);
	} catch (NumberFormatException e) {
	writeResponse(false);
	}

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