v0.4.1

What's Changed

Commit history since v0.4.0

• Remove originalResource from dataTrace by @smailliwcs in #736
• Bump development version by @smailliwcs in #738
• LNK-1547: Adding in basic versioning to metric entries in SQL databas… by @ajagann1 in #740
• Fix NullPointerException in aggregation by @smailliwcs in #741
• LNK-2334 by @MontaltoNick in #745
• LNK-2172: Remove dataTrace, aggregate and patientReport entries when re-generating report in MVP by @smailliwcs in #746
• Lnk 2116 logging improvements by @edward-miller-lcg in #744
• LNK-2298: Get report insights (metrics and errors) by invoking API endpoint by @smailliwcs in #747
• LNK-2322: Bring in latest changes from development branch to rc_0.4.1 branch by @sdmcgeown in #748 (note: this required the creation of a new tag: v0.4.1.1)

Full Changelog: v0.4.0...v0.4.1.1

Jira tickets closed since v0.4.0

Stories

• Remove originalResource from dataTrace table in MVP
• MVP logging improvements
• Store version number of report in metrics
• Get report insights (metrics and errors) by invoking API endpoint

Tasks

• Subject-List MeasureReport Profile Modification

Defects

• Remove dataTrace, aggregate and patientReport entries when re-generating report in MVP
• NPM Packages Failing to Load and Validate

v0.4.0

What's Changed

Commit History Since v0.3.1

Commit	Description
2463849	Fix NullPointerException in aggregation (#742)
1580f5c	Bump rc_0.4.0 version (#737)
e73c421	Merge pull request #734 from lantanagroup/remove-imrs-from-context
db6ceb9	Merge pull request #733 from lantanagroup/LNK-2177
7d07583	Remove IMRs from measure context
b041967	Fix unsafe publication
80117cc	Fix progress reporting
38a6f3b	Prevent simultaneous report generation
caaf0e3	Updating dependencies based on outstanding dependabot PR's (#732)
193fbe1	Merge branch 'LNK-2186' into development
912d9ef	Fixing broken unit test
268132d	Moving ValidationCategorizer to the validation package. (#721)
34e5084	Merge branch 'development' into LNK-2186
002681a	LNK-2187 Refactor MVP tenant and report summaries (#723)
ace3451	Merge pull request #724 from lantanagroup/fix-date-handling
a1a0776	Merge pull request #716 from lantanagroup/LNK-1871
78a8f6d	Merge pull request #722 from lantanagroup/LNK-1833
fd6c191	Reverted
3b0ba67	LNK-1871: Shifting engine initialization to a class variable instead of being done each time filterResourcesByPathList is called
5bb567b	LNK-1871: Moved fetching all structure definitions to a static initialization block per the PR.
349ae6a	Delegate date parsing to HAPI
ef2b0e8	Remove assumption of millisecond precision
1845269	LNK-1833: Move reporting plan configuration into ApiConfig
f58a740	Moving ValidationCategorizer to the validation package. Adding unit test to ensure unique category ids are specified. Updates categories to de-duplicate them, fixing the naming/guidance on at least one of them. Add text/html output for the validation category results endpoint that produces an HTML file that can be downloaded and opened in a browser, showing the categories and validation result details. Moving some logic for categorizing from the controller to ValidationCategorizer. Adding validation-results.html as output in the folder-based submission so that they can be automatically generated and included in the submission for review.
256ff48	Merge pull request #719 from lantanagroup/LNK-1387-add-columns-report-tbl
71b5e67	LNK-1871: One more.
5ac8f11	LNK-1871: Minor refactor
19277cd	LNK-1871: Some more PR updates and some cleanup in ApplyConceptMaps and FHIRHelper.
bbcc2f2	Creating app config that can be altered in each deployed environment (#720)
480581e	New endpoint to get both categories and results together (#717)
c9b5556	Merge pull request #718 from lantanagroup/LNK-2089
7259193	Add totalPatients and includedPatients
fe591a8	LNK-1871: Updated to include all the suggestions made on PR.  Added in some minor refactors.
ea1a9c2	Adding case statements for more message ids
7b3a905	LNK-1871: Some refactors to the FileSystemSender. Also, updates to annotate validation results with what file each issue listed in the results comes from when the not a Bundle flag is set in the sender configuration and saves said results to the same location as the rest of the bundle files.
bb792f2	LNK-1808: Actually adding in the data.
521df3d	LNK-1808: Adding back in data for mimetype value set
da76c87	Merge pull request #712 from lantanagroup/fix-terminology
e261133	Catching a minor error in the post census list process
05ad0dc	Merge pull request #704 from lantanagroup/IMPS-160
46a03f3	Merge pull request #713 from lantanagroup/fix-swagger-spec
e6e45ae	Merge pull request #714 from lantanagroup/fix-jackson-conflict
575dee2	Update auth.service.ts for Oauth removed /auth
e716020	Update Jackson to 2.16.1
2623ba8	Fix path for $deleteReportById
3a3d01d	Add timing-abbreviation cleanup
0449774	Remove duplicate code systems
f15bc22	Handle unknown tenant/measure (#711)
18ac853	Add endpoints for raw patient data retrieval (#710)
3b0bd38	Misc improvements to Device generation (#708)
0363ad5	Fix threading issues with in-process measure evaluation (#709)
3a563bc	Fix validation (#707)
61975c1	Merge pull request #705 from lantanagroup/fix-docker-build
26f6602	Merge pull request #706 from lantanagroup/LNK-1851-use-common-pool-reports
a6a390b	remove config property
2756897	Update ApiConfig.java
eb2ac9e	PR Updates
5475bdd	Convert to CommonPool and Patient Scoop progress tracking
615e73a	Bump parent image to Tomcat 10.1
c686349	Merge pull request #703 from lantanagroup/LNK-2037
1253a26	Merge pull request #701 from lantanagroup/LNK-1523
d36e4b1	Add in-process $evaluate endpoint
81bbd9a	Rename class
48458a0	LNK-1808: Adding in missing codesystems
befb1b9	small formatting tweaks.
f452f4f	small formatting tweaks.
1fa82e2	Review Refactors 3
75e3e90	Review Refactors 2
e33c048	Review Refactors
f65d608	LNK-1809 Improvements to issue FHIRPath expressions (#702)
2055998	Add ability to Metrics to get size data on reports, filtering with patientId, measureId, and/or reportId
286b12e	Refactor Location.type normalizers
5de4b7f	Remove duplicative logging
d059768	Move ad hoc code system URL to constant
654810b	Store original value for "fixed" period
f7c932c	Ignore unimplemented normalization methods
a00cccf	Fix unit test
1dc609e	Compile with Java 17
040ada6	Store FHIR client in report context
ca80b50	Remove narrative text from libraries
b21ba9b	Supply resource type for references
18543dc	Add measure def existence check
1799a09	Evaluate measures in-process
1f6a6cc	Defer Validator.init until first use
cff2344	Upgrade dependencies
c11e9bb	Remove Fortify rulepack
78ad84f	Merge pull request #699 from lantanagroup/frontend/develop
2843447	removing bugherd script
1dd4ad5	Merge pull request #698 from lantanagroup/LNK-2065
3bb4d14	Removing updateMeasures() as this concept no longer seems to be needed. We're no longer getting errors about "Canonical URL XXX exists, but cant be loaded", which was being caused by the measures not being available to the validation pipeline.
4f345df	Merge branch 'development' into LNK-2065
33d4971	Loading the extra terminology resources from resources again. Commenting out use of writeConformanceResourcesToFile(). Adding a few code-comments.
5b0718e	Using NPM packages load into the validation pipeline instead of individual profiles and terminology resources.
0aa9503	Merge pull request #696 from lantanagroup/LNK-1859
44c051f	Add Invalid_whitespace_non_identifier validation category, variant of Invalid_whitespace_(non-identifier).
5312e29	Merge pull request #694 from lantanagroup/frontend/develop
a36a0d4	updating form validation to handle errors better
efd9dec	Merge pull request #695 from lantanagroup/EncounterStatusTransformer
35720f8	Fix EncounterStatusTransformer
c7b3840	guarding auth against 403 errors
e94d48d	removing a log
eea4046	fixing metric card labels
e3418f5	removing these, not using anymore
4a064ea	setting api url relative to host
bfbd14a	fixing a normalizing mapping
ee26a53	Merge pull request #693 from lantanagroup/frontend/develop
08231e7	adding in environment files
06f522b	removing console logs
46f91d3	fixing normalization mapping on facility detail page
d6fd560	adjusting how we handle timestamps
bc58776	adding in tenant concept map data to bundle
e461208	updating census mock data on bundle summary
1b05b46	making mock data on system performance page match
013212c	changing normalization display on bundle details to 4 cols, not 3
002cdfe	fixing pagination on facilities table
367d893	Merge pull request #692 from lantanagroup/LNK-1828
5d5a510	LNK-1828: Add ability to debug patient data bundles that are passed into CQF-Ruler
ed9d43d	LNK-1828: Add ability to debug patient data bundles that are passed into CQF-Ruler
43a4a76	Lnk-1857 (#642)
2dc87a1	Merge pull request #691 from lantanagroup/frontend/develop
7543854	updating bundle details endpoint, trimming initial whitespace on measure strings
53c804f	Merge pull request #688 from lantanagroup/LNK-1524-validation-error
8e02522	LNK-1524: fix validation error
0d33d20	LNK-1524: fix validation error
e46fe85	Added "vendor" and "otherVendor" to tenant config to support the UI (#689)
079fde4	Lnk 1877 "type" Removed from Validation Category Endpoint Response (#676)
10a140c	LNK-1524: fix validation error
2dc93bf	Merge pull request #687 from lantanagroup/bundle-sorting
88b7e2f	Ensure bundle sorting retains all entries
aa5d68d	Merge pull request #686 from lantanagroup/patient-list-fix
1191e46	Fix POI creation in bulk acquisition
fbc0189	Merge pull request #684 from lantanagroup/LNK-1844
76074eb	Cleanup unused TenantId
6246381	Report Generation TIme Metrics
8eb7f13	Fix Metric Averaging logic for all metrics.
a8b31f4	Validation Issue Metric Logging and Incorporation into Metrics.
dbf3a05	Merge branch 'development' into LNK-1844
b39f61e	Defect fix in validation categorizer... It's comparing id to title when it should just be comparing id to id
7426398	Merge pull request #683 from lantanagroup/session-exhaustion
1b8793f	Share tenant data sources across requests
18a0ba2	Merge pull request #674 from lantanagroup/LNK-1825
b49162a	Merge pull...

v0.2.0

Epic

Progressive Query: NHSNLink can perform a progressive query (IP resources first, then query for SDE)

NHSNLink successfully pulls data from HCA's sandbox (Alpha)

Beta installation and configuration MM

Address errors found in the Fortify Scan from June 2023

Implement use of auditing capability in MVP

Build an MVP Terminology Service

Architecture

Architecture: Determine CQF Ruler failure outputs

Quantify the steps to bring BulkFHIR functionality for MVP

Progressive query-analyze the work necessary to incorporate a progressive querying approach into MVP

Evaluate feasibility and functionality associated with tagging a bundle at the patient encounter level per measure in MVP

Implications of a rolling 3-month pull

Analyze solutions for merging the same fhir resource when it exists in multiple measures

Create MVP Architecture Confluence Page

Review NHSN FHIR IG by Arch

Associate data queried and stored with the report criteria that the queries originate from

Create SRS drawings that describes MVP services

Deployment diagrams for CDC environment (Beta installs)

Create a Confluence page that summarizes MVP tenant settings

Create Confluence page for MVP Scheduling

Document validation assertions in MeasureEval

Activity diagram of MeasureDef and IG/Profile authorship and deployment

Develop stubs for API (REST interfaces) for MVP to support UI (Figma comps) requirements

Document MVP DB ERD

Review MVP Swagger and produce documentation as needed

Story

User Functionality for Viewing Reports (Pre and Post Submission)

Successfully sends a call out and accepts Monthly Reporting Plan details back via API in production

Integrate Link with MRP

Efficient Bundling of Two or More Measures

NHSNLink Deploy One Config Tool for Each Installation of Link

Test CDI and HOB Combined Measure (QA only)

Proof out query that uses bulk FHIR in EHR test environment

Test SAMS authentication in CDC Staging env

Deploy MM Beta to Stage

Debug the intermittent connectivity issues with CDC VMs for MM Beta

Data transfer to Lantana data analysts from MM Beta results

Understand current performance metrics in beta

Add remaining/new config fields to Configurator

Coordinate Incremental Testing with Leidos for API Connection

Create "dummy" facility within NHSN to test MRP

Modify the Config for the Alpha Installation at UMich to add in additional measures

Add dQM unique measure-versioning into Report

Create Location ConceptMap from Spreadsheet mapping

Beta (Prod) Manually create larger census patient list for UMich

Beta (Prod) Kickoff report generation manually via Postman for UMich

Beta (Prod) Watch logs and document interactions; debug integration issues for UMich

Beta (Prod) Execute $send endpoint on API to internal FHIR server for UMich

Validate measure report bundle

Validate FHIR structure using the FHIR Validator and NHSNMeasures IG on an Alpha Bundle

Update MVP Bundling functionality to align with updated output structure requirements

Bulk FHIR acquisition in MVP

Document BulkFHIR Findings

Link can successfully process a census of 250 patients

Link can successfully process a census of 500 patients

Link can successfully process a census of 1000 patients

Link can successfully process a census of 2500 patients

Improvements to build/deployment process for MVP in CDC on-prem environment

Test configuring OS Scheduler to execute CLI for refresh-patient-list

Test configuring OS Scheduler to execute CLI for generate-and-submit

Nebraska (Alpha): Establish connectivity to site sandbox

Identify the resources required for measure eval (hypo)

MGB (Alpha): Establish connectivity to site sandbox

Billings Clinic (Alpha): Establish connectivity to site sandbox

URMC (Alpha): Establish connectivity to site sandbox

Test Memory Overload in CQF-Ruler

Use SAMS authentication to query MRP endpoint

"Publish" The NHSN Measures

Develop appropriate tests for MRP Functionality

UMich(Beta): Configure NHSNLink Scheduler to execute CLI for refresh-patient-list every 3 hours

UMich (Beta) - Configure NHSNLink scheduler to execute CLI for generate-and-submit every day

UMich (Beta) - Configure OS scheduler to execute CLI for generate-and-submit once per week

UMich (Beta): Configure and Execute CLI for Refresh-patient-list

UMich (Beta) - Configure and execute CLI for generate-and-submit

UMich (Beta) - Send a measure bundle to staging ABS server in NHSN

URMC (Alpha): Data Seeding - Phase 1

Billings Clinic (Alpha): Data Seeding - Phase 1

Nebraska (Alpha): Data Seeding - Phase 1

Yale (Alpha): Establish connectivity to site sandbox

Yale (Alpha): Data Seeding - Phase 1

UNC (Alpha): Establish connectivity to site sandbox

HCA (Alpha): Establish connectivity to site sandbox

Ensure basic FHIR structure validation in Link

Update FHIR validation in Link to support validating USCore 3.1.1

Apply progressive query workflow to MVP Link

Validate 125-patient beta report bundle against the FHIR Validator

DevOps: Incorporate version number/and build number into each site's build

Add version/build number to report submission bundle

FHIR IG - Import updated version of NHSN Measure IG and incorporate changes into the NHSNLink codebase

MM Beta - Link can successfully process a census of 125 patients (CDI/HOB)

MM Beta - Link can successfully process a census of 125 patients (Multi-measure)

Add NHSN org ID to metadata in bundle

Metadata: Add date/timestamp per resource based on pull date/time

Full automation of census retrieval and use in Link is complete

MVP code base is all in the same branch

Set Up Link Stack for UNC Alpha testing

QA: Add test cases and/or regression testing to QA updates in Hypo measure

QA: Regression testing for Updated CQL Logic

MM (Beta): Re-pull 125-Patient Census Bundle and Validate against R4

QA Prep: MVP multi-measure testing for CDI/HOB and hypo

MM (Beta): Create and implement concept map for encounter.type

QA - Test approach/plan for automated census validation

Comment out the reference to the NHSN-specific IG in the validator

Enable FHIR Validator to check against NHSN Specific IG

Ability to set period's start date to same precision as end date

Install Multitenant MVP in the Billings/Multitenant Server in NHSN environment

Pull a new bundle using May's STU3 Patient List

BULK FHIR: Test use as patient census at UC Davis

Set up unit tests to ensure validation is accurate

Pull incremental beta bundles for MM hypo

Determine whether FHIR Validator is working

Pull STU3 patient list for May and for June for QA to use

Yale (Alpha): Repull alpha bundle

FHIR structure validation

MVP dev/test environments and pipeline cleanup

DevOps: Complete MM set up in Multi-tenant server

Enhanced unit testing on validation

QA FHIR Validation Code

Incorporation of FHIR validator in Link

QA- test FHIR Validator

QA- Load testing (MVP)

Update HAPI install

Document process for necessary valuesets for NHSNLink

Terminology server

DevOps: Deploy updated CQF Ruler in our environment

QA: Test updated version of CQF Ruler in our environment

DevOps: Deploy updated CQF Ruler in the CDC environment

QA: Test updated CQF Ruler in the CDC environment

QA: Side by side testing of updated CQF Ruler

MSSQL Setup for Windows Authentication

BULK FHIR: Populate census with patient IDs based on pt resources present in bulk FHIR response

Final export for June patient list

DevOps: Deploy MS SQL server to Dev environment (Lantana environment)

DevOps: Elevate to test MS SQL Server

QA: Generate several censuses to confirm results are the same (SQL Server)

QA: Regression testing for SQL Server

QA: Test to ensure scheduling functionality is working correctly (SQL Server and Mongo DB)

Hypo: Create Encounter.type concept map for YNHH

Deploy Link-MVP sqlserver branch to Lantana test environment for QA

Create databases in the Link-MVP test environment for the SQL Server update

Load dQM into EHR test

QA: RPS measure testing

DevOps: Create databases for DEV & Test environments in Azure MSSQL

Implement HAPI with MS SQL backend

DevOps: AllScripts connectivity

DevOps: Proxmox setup

Create data model and CRUD operations for patient data query tracing in MVP

MM Beta - Incremental bundle pull for Hypo

MM Beta: Verify IP count of automated monthly bundle report

DevOps: Test CDC build scripts

DevOps: Test CDC deploy scripts

Setup UNC Tenant in DEV/TEST Environments

Alpha UNC (CDI/HOB): Establish NHSNLink Connectivity to Facility's Sandbox Environment

Create data model and CRUD operations for shared data query tracing in MVP

Research feasibility in loading large CodeSystems into NHSNLink

Export and remove unused/old/archived devops pipelines

Validation pre-loads CodeSystem resources from a deployed folder

Create enumerated CodeSystem for SNOMED

Create enumerated CodeSystem for RXNORM

Create enumerated CodeSystem for LOINC

Ensure not using same database as other tenants

CDC Environment Training for QA

Add Profile Assertions to CQL

QA - Load Testing - MVP - 100

QA - Load Testing - MVP - 500

QA - Load Testing - MVP - 1000

QA - Load Testing - MVP - 1500

QA - Load Testing - MVP - 2000

QA - Load Testing - MVP - 3000

QA - Load Testing - MVP - 4000

QA - Load Testing - MVP - 5000

QA STU3 patient list vs Lanham list

Review Value Sets used in CQL and in data dictionary

MVP Security Scan - Path Manipulation (3)

Performance testing of CQF Ruler

Alpha MGB (Sepsis): Create Location ConceptMap

MGB (Alpha): Create concept map for Encounter.ty...