R API for Naomi app
App to show district level estimates of HIV indicators
Docker images are built on travis, if on master branch run via:
docker run --rm -d --network=host --name hintr_redis redis
docker run --rm -d --network=host --mount type=volume,src=upload_volume,dst=/uploads \
-e USE_MOCK_MODEL=true --name hintr mrcide/hintr:master
For a more complete example of running on a network see docker test script.
Test that container is working by using
$ curl -s http://localhost:8888
{
"status": "success",
"errors": null,
"data": "Welcome to hintr"
}Validate PJNZ
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_pjnz_payload.json \
http://localhost:8888/validate/baseline-individual
{
"status": "success",
"errors": null,
"data": {
"hash": "12345",
"type": "pjnz",
"data": {
"country": "Malawi",
"iso3": "MWI"
},
"filename": "Malawi2019.PJNZ",
"fromADR": false,
"resource_url": "https://adr.unaids.org/file/123.csv",
"filters": null
}
}Validate shape file and return serialised data
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_shape_payload.json \
http://localhost:8888/validate/baseline-individual
{
"status": "success",
"errors": null,
"data": {
"hash": "12345",
"type": "shape",
"data": {
"type": "FeatureCollection",
"name": "demo_areas",
"crs": {
"type": "name",
"properties": {
"name": "urn:ogc:def:crs:OGC:1.3:CRS84"
}
},
"features": [
{
"type": "Feature",
"properties": {
"area_id": "MWI",
... truncated 144125 lines of outputValidate population data
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_population_payload.json \
http://localhost:8888/validate/baseline-individual
{
"status": "success",
"errors": null,
"data": {
"hash": "12345",
"type": "population",
"data": null,
"filename": "original.csv",
"fromADR": false,
"resource_url": null,
"filters": null
}
}Validate baseline data
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_baseline_payload.json \
http://localhost:8888/validate/baseline-combined
{
"status": "success",
"errors": null,
"data": {
"consistent": true
}
}Validate programme ART data
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_programme_payload.json \
http://localhost:8888/validate/survey-and-programme
{
"status": "success",
"errors": null,
"data": {
"hash": "12345",
"type": "programme",
"data": [
{
"area_id": "MWI_4_1_demo",
"area_name": "Chitipa",
"sex": "both",
"age_group": "Y000_014",
"year": 2011,
"calendar_quarter": "CY2011Q4",
"art_current": 127,
"art_new": 9,
"vl_tested_12mos": null,
"vl_suppressed_12mos": null
},
{
... truncated 6180 lines of outputValidate ANC data
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_anc_payload.json \
http://localhost:8888/validate/survey-and-programme
{
"status": "success",
"errors": null,
"data": {
"hash": "12345",
"type": "anc",
"data": [
{
"area_id": "MWI_4_1_demo",
"age_group": "Y015_049",
"year": 2011,
"anc_clients": 4330,
"anc_known_pos": 24,
"anc_already_art": 0,
"anc_tested": 2105,
"anc_tested_pos": 50,
"anc_known_neg": 217,
"births_facility": 3279,
"anc_prevalence": 0.0315,
"anc_art_coverage": 0
... truncated 3626 lines of outputValidate survey data
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/validate_survey_payload.json \
http://localhost:8888/validate/survey-and-programme
{
"status": "success",
"errors": null,
"data": {
"hash": "12345",
"type": "survey",
"data": [
{
"indicator": "prevalence",
"survey_id": "DEMO2004DHS",
"survey_mid_calendar_quarter": "CY2004Q4",
"area_id": "MWI",
"area_name": "Malawi - Demo",
"res_type": "all",
"sex": "both",
"age_group": "Y015_049",
"n_clusters": 512,
"n_observations": 5136,
"n_eff_kish": 3125.6878,
"estimate": 0.1183,
... truncated 367974 lines of outputGet model run options
$ curl -s -X POST -H 'Content-Type: application/json' \
--data @inst/payload/model_run_options_payload.json \
http://localhost:8888/model/options
{
"status": "success",
"errors": null,
"data": {
"controlSections": [
{
"label": "General",
"description": "Select general model options:",
"controlGroups": [
{
"label": "Trigger mock model error",
"controls": [
{
"name": "mock_model_trigger_error",
"type": "select",
"required": true,
"helpText": "Set TRUE to force the model fit to error",
"options": [
{
"id": "true",
... truncated 1826 lines of outputRun a model
$ curl -s --data '{
"data": {
"pjnz": {
"path": "testdata/Malawi2019.PJNZ",
"filename": "Malawi2019.PJNZ",
"hash": "12345",
"fromADR": false
},
"shape": {
"path": "testdata/malawi.geojson",
"filename": "malawi.geojson",
"hash": "12345",
"fromADR": false
},
"population": {
"path": "testdata/population.csv",
"filename": "population.csv",
"hash": "12345",
"fromADR": false
},
"survey": {
"path": "testdata/survey.csv",
"filename": "survey.csv",
"hash": "12345",
"fromADR": false
},
"programme": {
"path": "testdata/programme.csv",
"filename": "programme.csv",
"hash": "12345",
"fromADR": false
},
"anc": {
"path": "testdata/anc.csv",
"filename": "anc.csv",
"hash": "12345",
"fromADR": false
}
},
"options": {
"area_scope": "MWI",
"area_level": 4,
"calendar_quarter_t1": "CY2016Q1",
"calendar_quarter_t2": "CY2018Q3",
"calendar_quarter_t3": "CY2019Q2",
"survey_prevalence": [
"DEMO2016PHIA",
"DEMO2015DHS"
],
"survey_art_coverage": "DEMO2016PHIA",
"survey_recently_infected": "DEMO2016PHIA",
"include_art_t1": "true",
"include_art_t2": "true",
"anc_clients_year2": 2018,
"anc_clients_year2_num_months": "9",
"anc_prevalence_year1": 2016,
"anc_prevalence_year2": 2018,
"anc_art_coverage_year1": 2016,
"anc_art_coverage_year2": 2018,
"spectrum_population_calibration": "none",
"spectrum_plhiv_calibration_level": "none",
"spectrum_plhiv_calibration_strat": "sex_age_coarse",
"spectrum_artnum_calibration_level": "none",
"spectrum_artnum_calibration_strat": "sex_age_coarse",
"spectrum_infections_calibration_level": "none",
"spectrum_infections_calibration_strat": "sex_age_coarse",
"spectrum_aware_calibration_level": "none",
"spectrum_aware_calibration_strat": "sex_age_coarse",
"calibrate_method": "logistic",
"artattend_log_gamma_offset": -4,
"artattend": false,
"output_aware_plhiv": "true",
"rng_seed": 17,
"no_of_samples": 500,
"max_iter": 250
},
"version": {
"hintr": "1.1.9",
"naomi": "2.8.12",
"rrq": "0.5.7",
"traduire": "0.0.6"
}
}' \
-X POST -H 'Content-Type: application/json' \
http://localhost:8888/model/submit
{
"status": "success",
"errors": null,
"data": {
"id": "957800d3055d679195ffe18aaf3391ab"
}
}Query status of model run
$ curl -s http://localhost:8888/model/status/957800d3055d679195ffe18aaf3391ab
{
"status": "success",
"errors": null,
"data": {
"done": false,
"status": "RUNNING",
"success": null,
"queue": 0,
"progress": [
],
"id": "957800d3055d679195ffe18aaf3391ab"
}
}Get the result of a model run
$ curl -s http://localhost:8888/model/result/957800d3055d679195ffe18aaf3391ab
{
"status": "success",
"errors": null,
"data": {
"id": "957800d3055d679195ffe18aaf3391ab",
"complete": true,
"warnings": [
{
"text": "Zero population input for 8 population groups. Replaced with population 0.1.",
"locations": [
"model_fit"
]
}
]
}
}Calibrate a model
$ curl -s --data '{
"options": {
"spectrum_plhiv_calibration_level": "national",
"spectrum_plhiv_calibration_strat": "sex_age_group",
"spectrum_artnum_calibration_level": "national",
"spectrum_artnum_calibration_strat": "sex_age_coarse",
"spectrum_infections_calibration_level": "national",
"spectrum_infections_calibration_strat": "sex_age_coarse",
"spectrum_aware_calibration_level": "national",
"spectrum_aware_calibration_strat": "sex_age_coarse",
"calibrate_method": "logistic"
},
"version": {
"hintr": "1.1.9",
"naomi": "2.8.12",
"rrq": "0.5.7",
"traduire": "0.0.6"
}
}' \
-X POST -H 'Content-Type: application/json' \
http://localhost:8888/calibrate/submit/957800d3055d679195ffe18aaf3391ab
{
"status": "success",
"errors": null,
"data": {
"id": "d5d08f4783975d8092e049adec43726b"
}
}Query status of calibrate run
$ curl -s http://localhost:8888/calibrate/status/d5d08f4783975d8092e049adec43726b
{
"status": "success",
"errors": null,
"data": {
"done": false,
"status": "RUNNING",
"success": null,
"queue": 0,
"progress": [
],
"id": "d5d08f4783975d8092e049adec43726b"
}
}Get the result of a calibrate run
$ curl -s http://localhost:8888/calibrate/result/d5d08f4783975d8092e049adec43726b
{
"status": "success",
"errors": null,
"data": {
"data": [
{
"area_id": "MWI",
"sex": "both",
"age_group": "Y015_049",
"calendar_quarter": "CY2016Q1",
"indicator": "population",
"mode": 7631061.6527,
"mean": 7631061.6527,
"lower": 7631061.6527,
"upper": 7631061.6527
},
{
"area_id": "MWI",
"sex": "both",
"age_group": "Y015_064",
... truncated 3403007 lines of outputInitialise download generation, type spectrum, coarse_output, summary or comparison
$ curl -s --data '{
"notes": {
"project_notes": {
"name": "My project 123",
"updated": "2022/05/17 12:34:21",
"note": "These are my project notes"
},
"version_notes": [
{
"name": "Version 2",
"updated": "2022/05/17 12:34:21",
"note": "Notes specific to this version"
},
{
"name": "Version 1",
"updated": "2022/05/14 09:12:54",
"note": "Notes from the first version"
}
]
},
"state": {
"datasets": {
"pjnz": {
"path": "72A9B1F58AAA743ADA64C6AE985CF228.pjnz",
"filename": "demo_mwi2019.pjnz"
},
"population": {
"path": "651105353D7153381ED29363DF0D772F.csv",
"filename": "demo_population_agesex.csv"
},
"shape": {
"path": "EBE533976BFAF0CABCA2C2E1B611B9C7.geojson",
"filename": "demo_areas.geojson"
},
"survey": {
"path": "F669CA9AA38A3993B5A9E9D3EB717C7D.csv",
"filename": "demo_survey_hiv_indicators.csv"
},
"programme": {
"path": "8301300AB39BE177FA593571B9DD94C4.csv",
"filename": "demo_art_number.csv"
},
"anc": {
"path": "E6323AAEB045D31E4A267398F669CF20.csv",
"filename": "demo_anc_testing.csv"
}
},
"model_fit": {
"options": {
"area_scope": "MWI",
"area_level": 4,
"calendar_quarter_t1": "CY2016Q1",
"calendar_quarter_t2": "CY2018Q3",
"calendar_quarter_t3": "CY2019Q2",
"survey_prevalence": [
"DEMO2016PHIA",
"DEMO2015DHS"
],
"survey_art_coverage": "DEMO2016PHIA",
"survey_recently_infected": "DEMO2016PHIA",
"include_art_t1": "true",
"include_art_t2": "true",
"anc_clients_year2": 2018,
"anc_clients_year2_num_months": "9",
"anc_prevalence_year1": 2016,
"anc_prevalence_year2": 2018,
"anc_art_coverage_year1": 2016,
"anc_art_coverage_year2": 2018,
"spectrum_population_calibration": "none",
"spectrum_plhiv_calibration_level": "none",
"spectrum_plhiv_calibration_strat": "sex_age_coarse",
"spectrum_artnum_calibration_level": "none",
"spectrum_artnum_calibration_strat": "sex_age_coarse",
"spectrum_infections_calibration_level": "none",
"spectrum_infections_calibration_strat": "sex_age_coarse",
"spectrum_aware_calibration_level": "none",
"spectrum_aware_calibration_strat": "sex_age_coarse",
"calibrate_method": "logistic",
"artattend_log_gamma_offset": -4,
"artattend": false,
"output_aware_plhiv": "true",
"rng_seed": 17,
"no_of_samples": 500,
"max_iter": 250
},
"id": "17d40b32f8e649349e047561a6831144"
},
"calibrate": {
"options": {
"spectrum_plhiv_calibration_level": "national",
"spectrum_plhiv_calibration_strat": "sex_age_group",
"spectrum_artnum_calibration_level": "national",
"spectrum_artnum_calibration_strat": "sex_age_coarse",
"spectrum_infections_calibration_level": "national",
"spectrum_infections_calibration_strat": "sex_age_coarse",
"spectrum_aware_calibration_level": "national",
"spectrum_aware_calibration_strat": "sex_age_coarse",
"calibrate_method": "logistic"
},
"id": "6e457f5a9f0413708624b7b0384e5fd0"
},
"version": {
"hintr": "1.1.9",
"naomi": "2.8.12",
"rrq": "0.5.7",
"traduire": "0.0.6"
}
}
}' \
-X POST -H 'Content-Type: application/json' \
http://localhost:8888/download/submit/spectrum/d5d08f4783975d8092e049adec43726b
{
"status": "success",
"errors": null,
"data": {
"id": "930202bce97ebe49df170f0e59512357"
}
}Query status of download generation
$ curl -s http://localhost:8888/download/status/930202bce97ebe49df170f0e59512357
{
"status": "success",
"errors": null,
"data": {
"done": false,
"status": "RUNNING",
"success": null,
"queue": 0,
"progress": [
],
"id": "930202bce97ebe49df170f0e59512357"
}
}Headers for summary download result
$ curl -s -I http://localhost:8888/download/result/930202bce97ebe49df170f0e59512357
HTTP/1.1 200 OK
Date: Mon, 23 Jan 2023 18:44:36 GMT
Content-Type: application/octet-stream
Content-Disposition: attachment; filename="MWI_naomi-output_20230123-1844.zip"
X-Porcelain-Validated: false
Content-Length: 18810039
Get the summary download result
$ curl -s http://localhost:8888/download/result/930202bce97ebe49df170f0e59512357
Hidden 74802 bytes of outputGet plotting metadata for Malawi
$ curl -s http://localhost:8888/meta/plotting/Malawi
{
"status": "success",
"errors": null,
"data": {
"anc": {
"choropleth": {
"indicators": [
{
"indicator": "anc_prevalence",
"value_column": "anc_prevalence",
"indicator_column": "",
"indicator_value": "",
"name": "ANC HIV prevalence",
"min": 0,
"max": 0.5,
"colour": "interpolateOranges",
"invert_scale": false,
"scale": 1,
"accuracy": null,
"format": "0.0%"
... truncated 798 lines of outputGet information about hintr versions
$ curl -s http://localhost:8888/hintr/version
{
"status": "success",
"errors": null,
"data": {
"hintr": "1.1.9",
"naomi": "2.8.12",
"rrq": "0.5.7",
"traduire": "0.0.6"
}
}Get information about hintr's workers
$ curl -s http://localhost:8888/hintr/worker/status
{
"status": "success",
"errors": null,
"data": {
"capsizable_pipit_1": "IDLE",
"capsizable_pipit_2": "IDLE"
}
}Docker container can be cleaned up using
docker rm -f hintr hintr_redis
Input data should be written to the shared upload_volume. When requesting validation pass the absolute path to the file in the request JSON e.g.
{
"type": "pjnz",
"path": "/uploads/Botswana.pjnz"
}
To turn on validation of requests and responses you need to set the environmental variable VALIDATE_JSON_SCHEMAS to true. You can do that by writing to a .Renviron file, on linux echo -e "VALIDATE_JSON_SCHEMAS=true" >> .Renviron.
To run tests locally:
- Install all dependencies with
devtools::install_deps("."). You may be prompted to install some operating system packages; these should be available via your package manager but forprotocyou may need the following instructions: https://askubuntu.com/questions/1072683/how-can-i-install-protoc-on-ubuntu-16-04 - Some packages need to be installed from GitHub:
devtools::install_github("ropensci/jsonvalidate")devtools::install_github("mrc-ide/eppasm")devtools::install_github("mrc-ide/naomi")devtools::install_github("mrc-ide/rrq")
- Install the hintr package:
R CMD INSTALL . - If running all tests, including those that require redis, start a redis docker container
docker run --rm -d --network=host --name hintr_redis redis
Finally tests can be run with devtools::test().
To run tests which use sensitive data you need to clone the private naomi-data repo into tests/testthat/testdata/sensitive.
git clone git@github.com:mrc-ide/naomi-data.git tests/testthat/testdata/sensitive
Details here will depend on the deploy (and that will be the place to look for the running version).
Use hintr::prerun_push, specifying the relative filenames of the output, spectrum and summary files.
First, run a model using naomi::hintr_run_model into some directory, say mydir
Then import the data into the production copy of naomi with
hintr::prerun_push("mydir",
output = "malawi_output.qs",
spectrum = "malawi_spectrum_download.zip",
summary = "malawi_summary_download.zip")
Make a note of the hash that is returned - you'll need that if you want to delete the data.
You must be on the VPN for this to work.