NEWS.md

In mrc-ide/hintr: R API for calling naomi district level HIV model

hintr 1.1.25

• Use new rrq functions

hintr 1.1.24

• Return calibrate result path from /calibrate/result/path/<id> relative to the results directory

hintr 1.1.23

• Update to use new rrq free functions added in v0.7.10

hintr 1.1.22

• Remove hardcoded year2 value for ANC prevalance and ANC ART coverage

hintr 1.1.21

• Update tableMetadata to return id and label for row and column values.

hintr 1.1.20

• Add tableMetadata into the calibrate/result/<id> and calibrate/result/metadata/<id> endpoints for controlling how the new output table feature will look

hintr 1.1.19

• Ensure that plot data in submit_prerun is uploaded as a duckdb file.

hintr 1.1.18

• Add a function to migrate from naomi v 2.9.10 to 2.9.11. i.e. to migrate from plot data being stored as .qs files to being stored as duckdb database.

hintr 1.1.17

• Add a dummy download endpoint of type "agyw" for generating AGYW (adolescent girls and young women) tool

hintr 1.1.16

• Add a new endpoint /calibrate/result/path/<id> which will return the path to the calibration plot data output which can be read by web backend

hintr 1.1.15

• Add two new endpoints in preparation for web backend accessing the result data on disk directly
• /calibrate/result/metadata/<id> to return the metadata and warnings from the /calibrate/result/<id> endpoint
• /calibrate/result/data/<id> for returning only the data from the /calibrate/result/<id> endpoint

hintr 1.1.13

• Error early if reading data generates a warning, we cannot proceed with only a partial read of the data

hintr 1.1.10

• Update fallback anc year to 2022
• Remove stack trace from user display
• Return job_id in error response if error originated from async job

hintr 1.1.9

• Ensure Naomi options are translated based on accept-language header

hintr 1.1.8

• Add hintr_prerun function which takes model inputs and outputs, saves them onto the server and then returns output zip with state JSON which can be used to rehydrate model outputs

hintr 1.1.7

• Remove prerun_import and prerun_push functions, these are going to be replaced with a more transparent prerun method

hintr 1.1.6

• Add endpoint /internal/prerun to run a prerun which builds state JSON from input and output files

hintr 1.1.2

• Add default selections for each indicator in comparison plot

hintr 1.1.1

• Add fallback model and calibration options for unknown countries

hintr 1.0.1

• Remove PJNZ file from survey and programme data validation

hintr 1.0.44

• Fail early if comparison report output cannot be generated

hintr 1.0.41

• Add country specific default values to all model and calibration options

hintr 1.0.39

• Add dummy /comparison/plot/<id> endpoint to return data for comparison barchart

hintr 1.0.38

• Save project_state.json into info dir in the output zip to make it less visible to users

hintr 1.0.37

• Add endpoints /rehydrate/submit /rehydrate/status/<id> and /rehydrate/result/<id> for getting state JSON required by the front end for rehydrating a project

hintr 1.0.36

• Delete exited workers when API starts (so metrics on worker counts are up to date see mrc-2893)

hintr 1.0.35

• Download submit for spectrum can take optional state JSON which is saved out as is into the output zip which can be used to by the web end to recover the project

hintr 1.0.34

• Include input files when download_debug called with id from a calibrate run or output generation

hintr 1.0.33

• /download/submit/<type>/<id> can now take a body with notes which will be added to spectrum download zip, it is ignored for other download types.

hintr 1.0.32

• Temporarily stop warning generation from ANC & ART uploads as it is taking a long time (> 18s for Nigeria) which is causing time out issues in hint.

hintr 1.0.31

• Add new download type "comparison" to return input to output comparison report

hintr 1.0.29

• Return warnings from input time series aggregation

hintr 1.0.24

• Validate that spectrum file and geojson contains same spectrum region codes

hintr 1.0.23

• Ignore non-pjnz files from uploaded zip file instead of erroring (so that mac users whose system creates __MACOSX file in zip files do not get errors)

hintr 1.0.22

• Validate columns present before other validation checks

hintr 1.0.18

• Return ratios as indicator types in calibrate plot

hintr 1.0.17

• Add query param strict to endpoint /validate/survey-and-programme to allow running with relaxed validation, by default this will run in strict mode.
• Add /meta/plotting endpoint to return default plotting metadata.

hintr 1.0.15

• Update programme & ANC validation to ensure only 1 area level per year is uploaded

hintr 1.0.13

• Add validation error to programme/ART data to ensure only 1 area level is uploaded

hintr 1.0.12

• Return warnings from model option validation, model fit and model calibrate endpoints

hintr 1.0.11

• Return format and accuracy metadata for data_type columns in input time series to specify how data of that type should be shown in the front end.

hintr 1.0.10

• Recode vls_tested and vls_suppressed to vl_tested_12mos and vl_suppressed_12mos. Affects tests only.

hintr 1.0.9

• Back /calibrate/plot/<id> endpoint with real data

hintr 1.0.8

• Remove time_step from input time series endpoints and add quarter

hintr 1.0.6

• Return area and time_period column info in input time series metadata

hintr 1.0.1

• Wire up /chart-data/input-time-series/<type> to return real data for time series plots

hintr 1.0.0

• Update downloads to be generated on demand instead of as part of model calibration

hintr 0.1.39

• Add dummy endpoint /chart-data/input-time-series/<type> to return dummy data for upcoming input time-series plots

hintr 0.1.38

• Add Portuguese translations

hintr 0.1.37

• Add dummy endpoint /calibrate/plot/<id> to return dummy data for upcoming calibrate plot

hintr 0.1.36

• Update to latest version of rrq

hintr 0.1.35

• Shorted output file names

hintr 0.1.34

• Remove deprecated /model/calibrate/<id> endpoint

hintr 0.1.33

• Return upload metadata from calibrate result response

hintr 0.1.32

• Update summary report

hintr 0.1.31

• Run model and calibration in a separate process to avoid memory leak

hintr 0.1.30

• Update tests for naomi 2.3.0: add new model option calibrate_method.

hintr 0.1.29

• Update to naomi 2.2.4, save calibrate outputs to new file

hintr 0.1.28

• Turn off validation for survey data n_cluster column, this is no longer required

hintr 0.1.27

• Add arg to worker entrypoint to enable starting calibration only worker

hintr 0.1.26

• Update test data options to new demo survey ids "DEMO2015DHS" and "DEMO2016PHIA".

hintr 0.1.25

• Queue calibration with higher priority than model run

hintr 0.1.24

• Add endpoints to enable async calibration
• /calibrate/submit - queue a model calibration
• /calibrate/status - get status of a calibration run
• /calibrate/result - get result of a calibration
• Add calibration options back in and remove from run options

hintr 0.1.23

• Update to naomi v2.1.11 (branch pin naomi@naomisup-ticket-11).

hintr 0.1.22

• Update to naomi v2.1.10 (branch pin naomi@infections-metadata).

hintr 0.1.20

• Pin to naomi@eppasm-0.5.9

hintr 0.1.18

• Update summary report

hintr 0.1.17

• Pin to naomi@aware-of-status

hintr 0.1.15

• Pin to naomi@option-output-aware

hintr 0.1.14

• Generalize functions assert_calendar_quarter_column() and assert_year_column() to accept argument col_name= to check columns of required specification with different name.

hintr 0.1.13

• Pin to naomi@issue-142

hintr 0.1.12

• Pin to naomi@anc-testing-cascade

hintr 0.1.11

• Add endpoint <+calendar_quarter_t1_default+> to select most recent survey calendar quarter as default 'time 1' option.

hintr 0.1.9

• Return helpText from model run

hintr 0.1.8

• Revise ART programme data schema to use column calendar_quarter instead of year.

hintr 0.1.7

• Depend on naomi 2.0.0 version for 2021 UNAIDS estimates.

hintr 0.1.6

• Reflect pkgapi rename

hintr 0.1.5

• Add endpoint for downloading dummy summary report

hintr 0.1.4

• Return number formatting metadata from /meta/plotting/ and /model/result endpoints

hintr 0.1.3

• Add model calibration endpoint

hintr 0.1.2

• Rename /download/summary endpoint to /download/coarse-output to be more representative of actual content and in preparation for adding an endpoint for downloading summary report

hintr 0.1.1

• Fix file naming to work with old model runs where country name is not available

hintr 0.1.0

• Switch API implementation to use pkgapi

hintr 0.0.36

• Return uncertainty range metadata from model result for choropleth

hintr 0.0.34

• Accept semicolon delimited data as csv inputs (common in countries with non-Anglo number formats)

hintr 0.0.33

• Language preference is passed through to naomi during model runs.

hintr 0.0.32

• New debug endpoint for locally getting a copy of failing data.

hintr 0.0.31

• Extend time options back to Q1 2010 to support household survey datasets back to 2010 (Burkina Faso).

hintr 0.0.30

• Remove "survey_year" from required columns in survey datasets.

hintr 0.0.28

• Add default values for area level and calendar quarter to generate estimates for

hintr 0.0.27

• Support for stopping jobs (mrc-732)

hintr 0.0.25

• Add receiving_art output indicator

hintr 0.0.24

• Return better error message from geojson reading

hintr 0.0.23

• No longer require ancrt_hiv_status
• Internationalisation support (mrc-788)

hintr 0.0.22

• Update for changes to model options in naomi v0.0.21
• Support prerun model results (mrc-1155)

hintr 0.0.21

• Errors in the hint model run are returned with stack traces (mrc-714)

hintr 0.0.20

• Accept and validate zip of PJNZ files

hintr 0.0.19

• Return version info from model run options response
• Require version info in model run submit endpoint
• Update filter ordering and naming

hintr 0.0.18

• Add model options validate endpoint
• Update input data structures including
• Move quarter_id to use calendar_quarter instead in format CY2016Q3 for population and output data
• Move quarter_id to use year for ANC, ART,
• Move age_group_id to age_group format e.g. 00-04, 15+, 05-09 etc. in ANC, ART, population, programme, survey and output data
• Update model run options
• Update region IDS to be formatted as e.g. MWI_2_1 for first region in level 2. Top level region remains as just ISO3 code e.g. MWI
• Update filters and metadata to reflect data changes
• Add advanced model run options

hintr 0.0.17

• Not found (404) responses now conform to the error schema (mrc-596)

hintr 0.0.16

• Download endpoints return Content-Disposition headers

hintr 0.0.15

• Add HEAD endpoints for summary and spectrum downloads

hintr 0.0.14

• Return plotting metadata for barchart with the model result response

hintr 0.0.13

• Caching enabled for geojson reading

hintr 0.0.12

• Update model download endpoint from indicators to summary
• Get downloads from model run
• Replace model run code with a mock that returns expected format
• Allow running up hintr docker container with env var USE_MOCK_MODEL to mock a model response

hintr 0.0.11

• Return iso3 code from PJNZ upload
• Use iso3 to locate plotting metadata instead of country name

hintr 0.0.10

• Iterate model run option endpoint to return complete options, to always return an ID and label for each option and to return regions as a hierarchy

hintr 0.0.9

• Add stub endpoints for downloading key indicators and spectrum digest

hintr 0.0.8

• Add endpoint for retrieving model run options

hintr 0.0.7

• New GET /hintr/version and GET /hintr/worker/status endpoints, the first in a series of hintr informational endpoints

hintr 0.0.6

• Fix plotting metadata for output dataset
• Return indicator filters for input data
• Make input and output data responses more consistent

hintr 0.0.5

• Add endpoint for retrieving plotting metadata

hintr 0.0.4

• Rename validate/input endpoint to validate/baseline-individual and rename validate/baseline to validate/baseline-combined for clarity

hintr 0.0.3

• Validate survey and programme data using a different endpoint from the validation of baseline data

hintr 0.0.2

• Add baseline validation endpoint and update validation endpoint names

hintr 0.0.1

• Initialise package

mrc-ide/hintr documentation built on May 1, 2024, 5:33 a.m.