v0.2.3

[ginberg]

see milestone

[cebarboza]

Hi @ginberg I will review and send it by Monday.

[Copilot]

Pull request overview

This PR updates PatientGenerator for the 0.2.x release line by expanding supported CDM tables and enhancing the Shiny designer (including timeline rendering), while adding new tests and refreshing fixtures/lockfiles.

Changes:

• Expanded supported CDM tables (adds observation and death) and updated JSON loading/exporting behavior.
• Enhanced patientDesigner() UX (publishable app export, optional chat tab, xlsx upload/download hooks, improved timeline formatting/rendering).
• Added/updated test coverage and updated test fixtures + renv.lock for the new behaviors.

Reviewed changes

Copilot reviewed 31 out of 112 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
tests/testthat/testCases/test_diabetes_patients.json	Updates diabetes fixture data (people, observation periods, events, drug exposures, procedures, measurements).
tests/testthat/testCases/patient_chat_ovarian_stages.json	Normalizes fixture values (e.g., gender labels, dates, observation period type).
tests/testthat/test-xlsx-upload.R	Adds tests for xlsx import/export round-tripping.
tests/testthat/test-timelineHelpers.R	Adds unit tests for timeline date formatting and end-date normalization helpers.
tests/testthat/test-prompts.R	Updates diabetes workflow prompt expectation.
tests/testthat/test-patientDesigner.R	Adds tests for publishable designer directory creation.
tests/testthat/test-patientChat.R	Adjusts model initialization test to avoid unsupported model id.
tests/testthat/test-conceptSearchModule.R	Adds tests for concept-id-to-label helper behavior.
tests/testthat/test-cdmTableModules.R	Adds tests for label display logic and server behaviors (dates, concepts, death handling).
tests/testthat/test-cdmTableClass.R	Adds coverage for cdmTable$add() accepting explicit date values.
tests/testthat/test-cdmConstructor.R	Expands constructor tests to include observation/death and end-date backfilling.
tests/testthat/helper-internals.R	Exposes additional internal helpers for testing.
renv.lock	Updates R version and dependency lock entries for the new release state.
R/updateFunctions.R	Adds inputDisplayLabel() and improves module input rendering + selector/date update behavior.
R/timelineHelpers.R	Introduces normalizeBarEndUpdate() and date formatting helpers for timeline/table display.
R/patientsDesigner.R	Expands patientDesigner() options (publishable export, chat tab, xlsx hooks) and adds observation/death plumbing.
R/patientChat.R	Improves system prompt and adds CLI progress/success messaging.
R/conceptSearchModule.R	Adds hecateConceptLabel() helper to resolve concept ids to display labels.
R/cdmTableModules.R	Enhances CDM table module behavior (concept label UI, add/update handling, date sync).
R/cdmTableClass.R	Adjusts table id/concept/date column resolution for death/observation.
R/cdmConstructor.R	Adds observation/death, xlsx import/export, more robust JSON loading, and timeline shaping.
R/cdm54data.R	Introduces supportedCdmTables() and switches table-spec reading from parquet to rds.
NEWS.md	Adds release notes for 0.2.0–0.2.3.
NAMESPACE	Adds cli imports for new console messaging.
man/patientDesigner.Rd	Documents new patientDesigner() parameters.
man/patientChat.Rd	Reflows/updates generated Rd content for patientChat.
inst/shiny/app.R	Adds minimal packaged Shiny template entrypoint.
inst/d3/cdm_timeline.js	Improves timeline rendering (tooltips, labels, measurement markers, observation support).
gui-crash.md	Adds a proposal document describing the GUI crash/end-date behavior and suggested approach.
DESCRIPTION	Updates package version and dependencies for the new release line.

Comments suppressed due to low confidence (1)

R/cdmTableModules.R:241

• The field-update observer currently excludes all inputs whose name contains "date". That prevents non-start/end date fields (e.g., verbatim_end_date in drug_exposure) from ever being persisted via cdm[[id]]$update(), because only the start/end date inputs are handled by updateDates().

        no_date_inputs <- table_inputs[grep(
          "date",
          names(table_inputs),
          invert = TRUE
        )]

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