From ed2cdea7fb00cd181d22e05eafec7772a68d8bb1 Mon Sep 17 00:00:00 2001 From: Luke Duncan Date: Fri, 6 Dec 2024 11:04:04 +0300 Subject: [PATCH] Reset to be based on the SOPs and cleanout legacy files. Will copy them back in on a case by case basis to ensure alignment with the SOPs. --- .github/workflows/fhirbuild.yml | 23 + .github/workflows/ghbuild.yml | 23 + .github/workflows/release.yml | 35 + .github/workflows/repo_actions.yml | 20 + LICENSE.md | 57 +- README.md | 81 +- _autoPublish.bat | 32 - _gencontinuous.bat | 2 - _gencontinuous.sh | 2 - _genonce.sh | 0 _processDataDictionary.bat | 22 - _processDataDictionary.sh | 22 - _refresh.bat | 31 - _refresh.sh | 32 - _testMagick.sh | 74 - _updateCQFTooling.bat | 91 - _updateCQFTooling.sh | 61 - _updatePublisher.sh | 0 .../patient-core-profile-spreadsheet.xml | 6849 ---- badges.md | 6 + ig.ini | 8 +- .../.gitignore} | 0 .../operations.md => cql/.gitignore} | 0 input/cql/FHIRCommon.cql | 281 - input/cql/FHIRHelpers.cql | 407 - input/cql/IMMZCommon.cql | 338 - input/cql/IMMZCommonIzDataElements.cql | 31 - input/cql/IMMZConcepts.cql | 79 - input/cql/IMMZConfig.cql | 66 - input/cql/IMMZD18SMeaslesDose0HighTx.cql | 62 - input/cql/IMMZD18SMeaslesDose0LowTx.cql | 62 - input/cql/IMMZD18SMeaslesHighTx.cql | 95 - input/cql/IMMZD18SMeaslesLowTx.cql | 95 - input/cql/IMMZD18SMeaslesSupp.cql | 58 - input/cql/IMMZD18SYellowFever.cql | 56 - input/cql/IMMZD2DTDTPDelayed.cql | 309 - input/cql/IMMZD2DTDTPInput.cql | 318 - input/cql/IMMZD2DTDTPOnTime.cql | 378 - input/cql/IMMZD2DTDTPPregnancy.cql | 137 - input/cql/IMMZD2DTDTPPregnancy3.cql | 156 - input/cql/IMMZD2DTDTPPregnancy4.cql | 118 - input/cql/IMMZD2DTHepatitisB3Delayed.cql | 164 - input/cql/IMMZD2DTHepatitisB3OnTime.cql | 206 - input/cql/IMMZD2DTHepatitisB4OnTime.cql | 157 - input/cql/IMMZD2DTHepatitisBBirth.cql | 87 - input/cql/IMMZD2DTHepatitisBInput.cql | 219 - input/cql/IMMZD2DTMeaslesDose0.cql | 96 - input/cql/IMMZD2DTMeaslesHighTx.cql | 163 - input/cql/IMMZD2DTMeaslesInput.cql | 209 - input/cql/IMMZD2DTMeaslesLowTx.cql | 162 - input/cql/IMMZD2DTMeaslesSupp.cql | 75 - input/cql/IMMZD2DTMumps.cql | 161 - input/cql/IMMZD2DTMumpsInput.cql | 122 - input/cql/IMMZD2DTPolioBirth.cql | 79 - input/cql/IMMZD2DTPolioIPVOnly.cql | 230 - input/cql/IMMZD2DTPolioInput.cql | 386 - input/cql/IMMZD2DTPolioSequential.cql | 198 - input/cql/IMMZD2DTPoliobOPVIPV.cql | 569 - input/cql/IMMZD2DTRubellaHigh.cql | 113 - input/cql/IMMZD2DTRubellaInput.cql | 134 - input/cql/IMMZD2DTRubellaLow.cql | 110 - input/cql/IMMZD2DTYellowFever.cql | 98 - input/cql/IMMZD2DTYellowFeverInput.cql | 122 - input/cql/IMMZD5DTDTP.cql | 102 - input/cql/IMMZD5DTHepatitisB.cql | 45 - input/cql/IMMZD5DTMeasles.cql | 115 - input/cql/IMMZD5DTMumps.cql | 115 - input/cql/IMMZD5DTPolio.cql | 119 - input/cql/IMMZD5DTRubella.cql | 163 - input/cql/IMMZD5DTYellowFever.cql | 142 - input/cql/IMMZIND07MeaslesHighTx.cql | 65 - input/cql/IMMZIND07MeaslesLowTx.cql | 65 - input/cql/IMMZIND08Measles.cql | 65 - input/cql/IMMZIND26YellowFever.cql | 65 - input/cql/IMMZIND40Measles.cql | 79 - input/cql/IMMZINDMeasles.cql | 27 - input/cql/IMMZINDYellowFever.cql | 27 - input/cql/IMMZIndicatorCommon.cql | 222 - input/cql/IMMZStratifiers.cql | 82 - input/cql/IMMZVaccineLibrary.cql | 26 - input/cql/WHOCommon.cql | 167 - input/cql/WHOConcepts.cql | 16 - input/cql/cql-options.json | 18 - input/data/features.yaml | 4 + .../IMZDAKDataDictionaryDRAFT.xlsx | Bin 231559 -> 0 bytes input/datadictionary/WHO-DD.xlsx | Bin 1997445 -> 0 bytes input/datadictionary/readme.md | 20 - input/decision-logic/.gitignore | 0 input/dictionary/.gitignore | 0 input/examples/.gitignore | 0 input/extensions/.gitignore | 0 input/fsh/.gitignore | 1 + input/fsh/Aliases.fsh | 4 +- input/fsh/activitydefinitions/.gitignore | 1 + .../activitydefinitions/IMMZADrulesets.fsh | 18 - input/fsh/activitydefinitions/IMMZD2DTCR.fsh | 22 - .../fsh/activitydefinitions/IMMZD2DTDTPMR.fsh | 7 - .../IMMZD2DTHepatitisBMR.fsh | 7 - .../activitydefinitions/IMMZD2DTMeaslesMR.fsh | 7 - .../activitydefinitions/IMMZD2DTMumpsMR.fsh | 7 - .../IMMZD2DTPertussisMR.fsh | 7 - .../IMMZD2DTPolioIPVMR.fsh | 7 - .../IMMZD2DTPoliobOPVMR.fsh | 7 - .../activitydefinitions/IMMZD2DTRubellaMR.fsh | 7 - .../IMMZD2DTTetanusDiphtheraMR.fsh | 7 - .../IMMZD2DTYellowFeverMR.fsh | 7 - .../fsh/activitydefinitions/IMMZD5DTDTPMR.fsh | 7 - .../activitydefinitions/IMMZD5DTMeaslesMR.fsh | 7 - .../activitydefinitions/IMMZD5DTMumpsMR.fsh | 7 - .../IMMZD5DTPoliobOPVMR.fsh | 7 - .../activitydefinitions/IMMZD5DTRubellaMR.fsh | 7 - .../IMMZD5DTYellowFeverMR.fsh | 7 - input/fsh/actors/.gitignore | 1 + input/fsh/codesystems/.gitignore | 1 + input/fsh/codesystems/IMMZ.C.fsh | 27 - input/fsh/codesystems/IMMZ.D.fsh | 140 - input/fsh/codesystems/IMMZ.D1.fsh | 74 - input/fsh/codesystems/IMMZ.I.fsh | 36 - input/fsh/conceptmaps/.gitignore | 1 + input/fsh/conceptmaps/IMMZ.C.ConceptMap.fsh | 90 - .../IMMZ.C.SexToAdministrativeGender.fsh | 27 - input/fsh/conceptmaps/IMMZ.D.ConceptMap.fsh | 388 - input/fsh/conceptmaps/IMMZ.D1.ConceptMap.fsh | 147 - input/fsh/examples/.gitignore | 1 + .../IMMZ.C.QuestionnaireResponse.1.fsh | 75 - 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...c-query-client-record-business-process.png | Bin 118337 -> 0 bytes ...mmz-d-register-client-business-process.png | Bin 118315 -> 0 bytes ...-e-administer-vaccine-business-process.png | Bin 239623 -> 0 bytes ...mmz-f-client-reminder-business-process.png | Bin 113803 -> 0 bytes ...z-g-defaulter-tracing-business-process.png | Bin 152604 -> 0 bytes ...licate-client-records-business-process.png | Bin 106414 -> 0 bytes ...licate-vaccine-events-business-process.png | Bin 114375 -> 0 bytes ...z-j-report-generation-business-process.png | Bin 64403 -> 0 bytes input/immz.xml | 163 - input/immz.xml.backup | 147 - input/includes/menu.xml | 57 - input/indicators/.gitignore | 0 input/maps/.gitignore | 0 input/maps/IMMZCLMToPatient.fml | 42 - input/maps/IMMZCQRToLM.fml | 66 - input/maps/IMMZCQRToPatient.fml | 85 - input/maps/IMMZD1DTPQRToResources.fml | 20 - input/maps/IMMZD1HepatitisBLMToResources.fml | 51 - input/maps/IMMZD1HepatitisBQRToLM.fml | 27 - input/maps/IMMZD1HepatitisBQRToResources.fml | 20 - input/maps/IMMZD1LMToResources.fml | 117 - input/maps/IMMZD1MeaslesLMToResources.fml | 37 - input/maps/IMMZD1MeaslesQRToLM.fml | 23 - input/maps/IMMZD1MeaslesQRToResources.fml | 20 - input/maps/IMMZD1MumpsQRToResources.fml | 20 - input/maps/IMMZD1PolioLMToResources.fml | 40 - input/maps/IMMZD1PolioQRToLM.fml | 23 - input/maps/IMMZD1PolioQRToResources.fml | 20 - input/maps/IMMZD1QRToLM.fml | 61 - input/maps/IMMZD1RubellaQRToResources.fml | 20 - input/maps/IMMZD1YellowFeverQRToResources.fml | 20 - input/maps/IMMZD5LMToResources.fml | 20 - input/maps/IMMZD5QRToLM.fml | 21 - input/maps/IMMZD5QRToResources.fml | 20 - input/models/.gitignore | 0 input/pagecontent/adapting.md | 39 +- input/pagecontent/business-process.md | 1 + input/pagecontent/business-processes.md | 183 +- input/pagecontent/business-requirements.md | 18 +- input/pagecontent/changes.md | 4 +- input/pagecontent/codings.md | 9 + input/pagecontent/codings.xml | 11 - input/pagecontent/concepts.md | 28 +- input/pagecontent/concepts.md.old | 23 - input/pagecontent/data-models-and-exchange.md | 70 +- .../data-models-and-exchange.md.old | 9 - input/pagecontent/decision-logic.md | 876 +- input/pagecontent/dependencies.md | 45 +- input/pagecontent/dictionary.md | 34004 +--------------- input/pagecontent/documentation.md | 34 - input/pagecontent/downloads.md | 6 +- input/pagecontent/examples.xml | 11 - input/pagecontent/extensions.xml | 4 - input/pagecontent/feedback.md | 10 + input/pagecontent/functional-requirements.md | 309 +- input/pagecontent/index copy.md | 45 - input/pagecontent/index-dak.md | 59 + input/pagecontent/index-ig.md | 47 + input/pagecontent/index.md | 55 +- input/pagecontent/indicators-measures.md | 18 +- input/pagecontent/indicators.md | 662 +- input/pagecontent/indices.md | 0 input/pagecontent/license.md | 57 +- input/pagecontent/maps.md | 1 + .../non-functional-requirements.md | 86 +- input/pagecontent/personas.md | 86 +- input/pagecontent/profiles.xml | 3 - 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Silver, available from: https://www.argentixinfo.com/archives/156 +# Change log: +# v0.1.0 +# 2021-06-18: publish default branches to / , other branches branches/ +# 2021-11-26: reusable workflow + +name: FHIR CI Build + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events for any main branch + push: + branches-ignore: + - 'gh-pages' + pull_request: + + workflow_dispatch: + +jobs: + # This workflow contains a single job called "build" + call_build: + uses: WorldHealthOrganization/smart-base/.github/workflows/fhirbuild.yml@main diff --git a/.github/workflows/ghbuild.yml b/.github/workflows/ghbuild.yml new file mode 100644 index 0000000000..575defd4e1 --- /dev/null +++ b/.github/workflows/ghbuild.yml @@ -0,0 +1,23 @@ +# This workflow reuses the openHIE GitHub action for building IGs +# Initial idea by Carl Leitner, developed by Elliot Silver, available from: https://www.argentixinfo.com/archives/156 +# Change log: +# v0.1.0 +# 2021-06-18: publish default branches to / , other branches branches/ +# 2021-11-26: reusable workflow + +name: GitHub Pages build + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events for any main branch + push: + branches-ignore: + - 'gh-pages' + pull_request: + + workflow_dispatch: + +jobs: + # This workflow contains a single job called "build" + call_build: + uses: WorldHealthOrganization/smart-base/.github/workflows/ghbuild.yml@main diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000000..b2a8a6ef53 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,35 @@ +# This workflow calls a remote workflow for setting up a release publication, +# This workflow is triggered by the creation of a GitHub release and requires a file called publication-request.json in the branch. + +name: Release build + +on: + release: + types: [created] + workflow_dispatch: + +jobs: + check: + runs-on: ubuntu-latest + outputs: + file_exists: ${{ steps.checkfile.outputs.exists }} + steps: + - name: Checkout code + uses: actions/checkout@v3 + with: + ref: ${{ github.event.release.tag_name }} + + - name: Check for publication-request.json + id: checkfile + run: | + if [[ -f "publication-request.json" ]]; then + echo "::set-output name=exists::true" + else + echo "::set-output name=exists::false" + fi + + trigger: + needs: check + if: needs.check.outputs.file_exists == 'true' + uses: WorldHealthOrganization/smart-html/.github/workflows/release.yml@main + diff --git a/.github/workflows/repo_actions.yml b/.github/workflows/repo_actions.yml new file mode 100644 index 0000000000..fcb5388d39 --- /dev/null +++ b/.github/workflows/repo_actions.yml @@ -0,0 +1,20 @@ +# This workflow uses a remote action to do some repository actions like updating the readme files + +name: Call remote repo actions + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events for any main branch + push: + branches-ignore: + - 'gh-pages' + pull_request: + + workflow_dispatch: + +jobs: + call-update-readme: + uses: WorldHealthOrganization/smart-base/.github/workflows/update_readme.yml@main + with: + repositoryOwner: ${{ github.repository_owner }} + repositoryName: ${{ github.event.repository.name }} diff --git a/LICENSE.md b/LICENSE.md index 2956044bb4..e0bc849899 100644 --- a/LICENSE.md +++ b/LICENSE.md @@ -1,33 +1,44 @@ -> CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. 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+
diff --git a/README.md b/README.md index 619047e0ad..06699989fa 100644 --- a/README.md +++ b/README.md @@ -1,75 +1,18 @@ -# WHO Immunization Implementation Guide (FHIR R4 (4.0.1)) + +[![License: CC BY-IGO 3.0](https://licensebuttons.net/l/by-nc/3.0/igo/80x15.png)](https://creativecommons.org/licenses/by/3.0/igo) +![CI Build](https://img.shields.io/github/actions/workflow/status/WorldHealthOrganization/smart-ig-empty/ghbuild.yml) + +![QA errors](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2FWorldHealthOrganization.github.io%2Fsmart-ig-empty%2Fqa.json&query=%24.errs&logoColor=red&label=QA%20errors&color=yellow) +![QA warnings](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2FWorldHealthOrganization.github.io%2Fsmart-ig-empty%2Fqa.json&query=%24.warnings&logoColor=orange&label=QA%20warnings&color=yellow) +![QA hints](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2FWorldHealthOrganization.github.io%2Fsmart-ig-empty%2Fqa.json&query=%24.hints&logoColor=yellow&label=QA%20hints&color=yellow) + -This implementation guide defines core data element profiles for use for the World Health Organization (WHO) Immunization computable guideline content. +# WHO SMART GUIDELINES - EMPTY IG -The current draft of the implementation guide is available [here](https://build.fhir.org/ig/WorldHealthOrganization/smart-immunizations/branches/main). +This is an empty framework, to be used to create SMART Implementation Guides. -The guide is published under a Creative Commons [license](LICENSE.md). -## Change Management +## Changes and feedback -Feedback and issues can be submitted via the [issues](issues) page, and will be incorporated into subsequent releases as time and resources allow. - -## Roadmap -### Completed - -* PlanDefinitions -* ActivityDefinitions -* Measures -* CQL libraries for Indicators -* CQL libraries for Decision Support - -### ToDo - -* Examples - -## Repository and Build Information - -This repository contains the source for the WHO Core Implementation Guide, and uses the [FHIR Implementation Guide publisher](http://wiki.hl7.org/index.php?title=IG_Publisher_Documentation) to produce a FHIR Implementation Guide. - -Commits to this repository will automatically trigger a new build of the implementation guide, which will then be published to the following location: - -[https://build.fhir.org/ig/WorldHealthOrganization/smart-immunizations/branches/main](https://build.fhir.org/ig/WorldHealthOrganization/smart-immunizations/branches/main) - -Build log is available here: - -[http://build.fhir.org.s3-website-us-east-1.amazonaws.com/logs/WorldHealthOrganization/smart-immunization](http://build.fhir.org.s3-website-us-east-1.amazonaws.com/logs/WorldHealthOrganization/smart-immunization) - -Debugging information is available here: - -[http://build.fhir.org/ig/WorldHealthOrganization/smart-immunization/debug.tgz](https://build.fhir.org/ig/WorldHealthOrganization/smart-immunizations/debug.tgz) - -### Local Build - -The HL7 IG Publisher can be downloaded locally to make building as easy as possible. To build locally, download the publisher tooling locally using the _updatePublisher script: - - _updatePublisher - -Once the publication tooling is cached locally, use the _genOnce script to build locally: - - _genOnce - -The output will be available in the `output` folder. - -### Refreshing CQL - -The CQF tooling can be installed or updated using the _updateCQFTooling script: - - _updateCQFTooling - -Once that has been updated the _refresh script can be used to generate the CQL Libraries and create test bundles for the applicable PlanDefinitions. - - _refresh - -### Organizing Tests - -The tests were generated using [BulkFSH repo](https://github.com/PuraJuniper/bulk-fsh)). - -Use the _testMagick.sh scrip to sort the tests into the appropriate folders to execute the CQL tests. - -### Executing CQL Tests - -Using a CQL plugin in Atom or [VSCode](https://github.com/PuraJuniper/bulk-fsh), right click on your CQL file and click "Execute Tests" - -After running the _testMagick.sh script this should produce an output file with the results of how each CQL file executed against your test patients. +Feedback and issues about this empty framework can be submitted via the [issues](issues) page, and will be incorporated into subsequent releases. diff --git a/_autoPublish.bat b/_autoPublish.bat deleted file mode 100644 index 4b2483853f..0000000000 --- a/_autoPublish.bat +++ /dev/null @@ -1,32 +0,0 @@ -@ECHO off -SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar -SET input_cache_path=%~dp0input-cache -SET resources_path=%~dp0input/resources -SET ig_resource_path=input/core.xml -SET fsoption=http://localhost:8080/cqf-ruler-r4/fhir/ -SET publisher_jar=publisher.jar -SET test_path=D:\Projects\connectathon\fhir401\input\tests -SET fhir_version=4.0.1 -SET ini_file=ig.ini - - cmd /c _updatePublisher.bat /f - ECHO Done with updatePublisher - - cmd /c _updateCQFTooling.bat /f - ECHO Done with updateCQFTooling - - cmd /c _processDataDictionary.bat - ECHO Done with ProcessAcceleratorKit - - JAVA -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp=%resources_path% -ip=%ig_resource_path% -t -d -p -fs=%fsoption% - ECHO Done with -RefreshIG - - JAVA -jar "%input_cache_path%\%tooling_jar%" -TestIG -ini=%ini_file% -root-dir=%~dp0 -fv=%fhir_version% -tcp=%test_path% -fs=%fsoption% - ECHO Done with -TestIGOperation - - REM from _genonce.bat - JAVA -jar "%input_cache_path%\%publisher_jar%" -ig . %txoption% - -REM TODO - PUBLISH to "web site" copy output dir to another location - ECHO  Done with publish to web site - ECHO  diff --git a/_gencontinuous.bat b/_gencontinuous.bat deleted file mode 100644 index ca2867a5f0..0000000000 --- a/_gencontinuous.bat +++ /dev/null @@ -1,2 +0,0 @@ -@ECHO OFF -CALL ./_genonce.bat -watch \ No newline at end of file diff --git a/_gencontinuous.sh b/_gencontinuous.sh deleted file mode 100755 index b9ac5933d9..0000000000 --- a/_gencontinuous.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/bash -./_genonce.sh -watch diff --git a/_genonce.sh b/_genonce.sh old mode 100755 new mode 100644 diff --git a/_processDataDictionary.bat b/_processDataDictionary.bat deleted file mode 100644 index a91bebff94..0000000000 --- a/_processDataDictionary.bat +++ /dev/null @@ -1,22 +0,0 @@ -@ECHO off -SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar -SET input_cache_path=%~dp0input-cache -SET datadictionary_directory=input/datadictionary/ -SET datadictionary_filename=%datadictionary_directory%\IMZDAKDataDictionaryDRAFT.xlsx -SET datadictionary_sheetname=Master-1.0 -SET scope=Core -SET tooling=%input_cache_path%\%tooling_jar% -SET upper_path=%%~dpx - -if EXIST "%tooling%" ( - JAVA -jar "%tooling%" -ProcessAcceleratorKit -s="%scope%" -pts="%datadictionary_filename%" -dep="%datadictionary_sheetname%" -op=. -) ELSE ( - ECHO "%tooling%" - if EXIST "%tooling%" ( - JAVA -jar $tooling -ProcessAcceleratorKit -s=$scope -pts=./input/datadictionary/$datadictionary_filename -dep=$datadictionary_sheetname -op=. - ) ELSE ( - ECHO  ProcessAcceloratorKit NOT FOUND in input-cache or parent folder. Please run _updateCQFTooling. Aborting... - ECHO  - ) -) - diff --git a/_processDataDictionary.sh b/_processDataDictionary.sh deleted file mode 100755 index dc717a5646..0000000000 --- a/_processDataDictionary.sh +++ /dev/null @@ -1,22 +0,0 @@ -#!/bin/bash -#DO NOT EDIT WITH WINDOWS -tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar -input_cache_path=./input-cache -datadictionary_filename="IMZDAKDataDictionaryDRAFT.xlsx" -datadictionary_sheetname="Master-1.0" -scope="Core" - -set -e - -tooling=$input_cache_path/$tooling_jar -if test -f "$tooling"; then - JAVA -jar $tooling -ProcessAcceleratorKit -s=$scope -pts=./input/datadictionary/$datadictionary_filename -dep=$datadictionary_sheetname -op=. -else - tooling=../$tooling_jar - echo $tooling - if test -f "$tooling"; then - JAVA -jar $tooling -ProcessAcceleratorKit -s=$scope -pts=./input/datadictionary/$datadictionary_filename -dep=$datadictionary_sheetname -op=. - else - echo ProcessAcceloratorKit NOT FOUND in input-cache or parent folder. Please run _updateCQFTooling. Aborting... - fi -fi diff --git a/_refresh.bat b/_refresh.bat deleted file mode 100644 index 04b38ebdcf..0000000000 --- a/_refresh.bat +++ /dev/null @@ -1,31 +0,0 @@ -@ECHO OFF -SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar -SET input_cache_path=%~dp0input-cache -SET resources_path=%~dp0input/resources -SET ig_resource_path=input/immz.xml - -ECHO Checking internet connection... -PING tx.fhir.org -n 1 -w 1000 | FINDSTR TTL && GOTO isonline -ECHO We're offline... -SET fsoption= -GOTO igpublish - -:isonline -ECHO We're online, setting publish to the Connectathon sandbox FHIR server -rem SET fsoption=-fs http://localhost:8080/cqf-ruler-r4/fhir/ - -:igpublish - -SET JAVA_TOOL_OPTIONS=-Dfile.encoding=UTF-8 - -IF EXIST "%input_cache_path%\%tooling_jar%" ( - ECHO running: JAVA -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption% - JAVA -Xmx2048M -jar "%input_cache_path%\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption% -) ELSE If exist "..\%tooling_jar%" ( - ECHO running: JAVA -jar "..\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption% - JAVA -Xmx2048M -jar "..\%tooling_jar%" -RefreshIG -root-dir=%~dp0 -rp="%resources_path%" -ip="%ig_resource_path%" -t -d -p %fsoption% -) ELSE ( - ECHO IG Refresh NOT FOUND in input-cache or parent folder. Please run _updateCQFTooling. Aborting... -) - -PAUSE diff --git a/_refresh.sh b/_refresh.sh deleted file mode 100755 index 62249da864..0000000000 --- a/_refresh.sh +++ /dev/null @@ -1,32 +0,0 @@ -#!/bin/bash -#DO NOT EDIT WITH WINDOWS -tooling_jar=tooling-cli-2.4.0.jar -input_cache_path=./input-cache -ig_ini_path=$PWD/ig.ini - -set -e -echo Checking internet connection... -wget -q --spider tx.fhir.org - -if [ $? -eq 0 ]; then - echo "Online" - fsoption="" -else - echo "Offline" - fsoption="" -fi - -echo "$fsoption" - -tooling=$input_cache_path/$tooling_jar -if test -f "$tooling"; then - java -jar $tooling -RefreshIG -ini="$ig_ini_path" -d -p -t $fsoption -else - tooling=../$tooling_jar - echo $tooling - if test -f "$tooling"; then - java -jar $tooling -RefreshIG -ini="$ig_ini_path" -d -p -t $fsoption - else - echo IG Refresh NOT FOUND in input-cache or parent folder. Please run _updateCQFTooling. Aborting... - fi -fi \ No newline at end of file diff --git a/_testMagick.sh b/_testMagick.sh deleted file mode 100755 index 43a6c2de10..0000000000 --- a/_testMagick.sh +++ /dev/null @@ -1,74 +0,0 @@ -#!/bin/sh - -# This script will take the output of the BulkFSH tool (JSON files) -# and will place individual files into appropriate subdirectories -# so the tester can easily remove or change data per test case in their -# IG. The process is quite simple: -# -# 1. Get the contents of the input directory -# 2. For each CQL file in the input/cql directory create the appropriate test structure -# 3. ??? -# 4. Test! - - -# Read a yes or no answer from user -read_yesno() { - local inp='' - while [ "$inp" != "y" ] && [ "$inp" != "n" ]; - do - read -p "$1 [y/n]:" inp - done - - eval $2="$inp" -} - -# Where the Bulk FSH output in format Patient-XXXXXX is located -declare FSH_OUTPUT_ROOT='./input/tests' -# Where the output for test library should be output -declare TEST_OUTPUT='./input/tests/library' -# CQL Source code -declare CQL_SOURCE='./input/cql' -# Test Case Prefix -declare TEST_PREFIX='IMMZ-Patient' - -if [ ! -d $CQL_SOURCE ]; then - >&2 echo "Missing $CQL_SOURCE directory! Do you have CQL files located there?" - exit 999 -fi -if [ ! -d $FSH_OUTPUT_ROOT ]; then - >&2 echo "Missing the $FSH_OUTPUT_ROOT! Have you run the FSH generator?" - exit 911 -fi -if [ ! -d $TEST_OUTPUT ]; then - mkdir $TEST_OUTPUT -else - read_yesno "$TEST_OUTPUT exists - do you want to remove it and re-copy the test cases?" REMOVE_SOURCE - if [ "$REMOVE_SOURCE" = "y" ]; then - rm -rf $TEST_OUTPUT - mkdir $TEST_OUTPUT - fi -fi - -echo "Scanning for Libraries" -# Find the library IDs from the CQL files -cat $(ls $CQL_SOURCE/*.cql) | grep "^library\s.*$" | sed -E 's/library\s([A-Za-z0-9]*).*$/\1/ig' | while read LIB ; do - - # Create output directory - declare LIB_DIR=$TEST_OUTPUT/$LIB - echo "$LIB => $LIB_DIR" - if [ ! -d $LIB_DIR ]; then - mkdir $LIB_DIR - fi - - # For each FSH file copy them - ls $FSH_OUTPUT_ROOT/*.json | sed -E 's/^\.\/input\/tests\/(.*)$/\1/I' | while read RESOURCE ; do - declare TEST_CASE_ID=`echo $RESOURCE | sed -E 's/^.*-(.*?)-([m|f])\.json$/\1-\2/g'` - declare SOURCE_FILE=$FSH_OUTPUT_ROOT/$RESOURCE - declare DEST_DIR=$TEST_OUTPUT/$LIB/$TEST_PREFIX-$TEST_CASE_ID - declare DEST_FILE=`echo $RESOURCE | sed -E 's/^[^\-]*-(.*?)$/\1/g'` - if [ ! -d $DEST_DIR ]; then - mkdir $DEST_DIR - fi - cp $SOURCE_FILE $DEST_DIR/$DEST_FILE - done -done diff --git a/_updateCQFTooling.bat b/_updateCQFTooling.bat deleted file mode 100644 index fb1cd0cf2d..0000000000 --- a/_updateCQFTooling.bat +++ /dev/null @@ -1,91 +0,0 @@ -@ECHO OFF - -SETLOCAL - -SET dlurl=https://oss.sonatype.org/service/local/artifact/maven/redirect?r=snapshots^&g=org.opencds.cqf^&a=tooling^&v=1.4.1-SNAPSHOT^&c=jar-with-dependencies -SET tooling_jar=tooling-1.4.1-SNAPSHOT-jar-with-dependencies.jar -SET input_cache_path=%~dp0input-cache\ -SET skipPrompts=false -IF "%~1"=="/f" SET skipPrompts=true - -FOR %%x IN ("%CD%") DO SET upper_path=%%~dpx - -IF NOT EXIST "%input_cache_path%%tooling_jar%" ( - IF NOT EXIST "%upper_path%%tooling_jar%" ( - SET jarlocation=%input_cache_path%%tooling_jar% - SET jarlocationname=Input Cache - ECHO IG Refresh is not yet in input-cache or parent folder. - REM we don't use jarlocation below because it will be empty because we're in a bracketed if statement - GOTO create - ) ELSE ( - ECHO IG RefreshFOUND in parent folder - SET jarlocation=%upper_path%%tooling_jar% - SET jarlocationname=Parent folder - GOTO upgrade - ) -) ELSE ( - ECHO IG Refresh FOUND in input-cache - SET jarlocation=%input_cache_path%%tooling_jar% - SET jarlocationname=Input Cache - GOTO upgrade -) - -:create - -IF "%skipPrompts%"=="y" ( - SET create=Y -) ELSE ( - SET /p create="Ok? (Y/N) " -) -IF /I "%create%"=="Y" ( - ECHO Will place publisher jar here: %input_cache_path%%tooling_jar% - MKDIR "%input_cache_path%" 2> NUL - GOTO download -) -GOTO done - - -:upgrade -IF "%skipPrompts%"=="false" ( - SET /p overwrite="Overwrite %jarlocation%? (Y/N)" - IF /I "%overwrite%"=="Y" ( - GOTO download - ) -) ELSE ( - GOTO download -) -GOTO:done - -:download -ECHO Downloading most recent refresh to %jarlocationname% - it's ~70 MB, so this may take a bit - -FOR /f "tokens=4-5 delims=. " %%i IN ('ver') DO SET VERSION=%%i.%%j -IF "%version%" == "10.0" GOTO win10 -IF "%version%" == "6.3" GOTO win8.1 -IF "%version%" == "6.2" GOTO win8 -IF "%version%" == "6.1" GOTO win7 -IF "%version%" == "6.0" GOTO vista - -ECHO Unrecognized version: %version% -GOTO done - -:win10 -POWERSHELL -command "if ('System.Net.WebClient' -as [type]) {(new-object System.Net.WebClient).DownloadFile('%dlurl%','%jarlocation%') } else { Invoke-WebRequest -Uri '%dlurl%' -Outfile '%jarlocation%' }" -ECHO Download complete. -GOTO done - -:win7 -bitsadmin /transfer GetRefresh /download /priority normal "%dlurl%" "%jarlocation%" -ECHO Download complete. -GOTO done - -:win8.1 -:win8 -:vista -ECHO This script does not yet support Windows %winver%. Please ask for help on https://chat.fhir.org/#narrow/stream/179207-connectathon-mgmt/topic/Clinical.20Reasoning.20Track -GOTO done - -:done -IF "%skipPrompts%"=="false" ( - PAUSE -) diff --git a/_updateCQFTooling.sh b/_updateCQFTooling.sh deleted file mode 100755 index c0356b3db0..0000000000 --- a/_updateCQFTooling.sh +++ /dev/null @@ -1,61 +0,0 @@ -#!/bin/bash -#DO NOT EDIT WITH WINDOWS -#exit 1 - -r=releases -g=org.opencds.cqf -a=tooling-cli -v=2.4.0 - -dlurl='https://oss.sonatype.org/service/local/artifact/maven/redirect?r='${r}'&g='${g}'&a='${a}'&v='${v}'' - -echo ${dlurl} - -input_cache_path=./input-cache/ -tooling_jar=tooling-cli-2.4.0.jar - -set -e -if ! type "curl" > /dev/null; then - echo "ERROR: Script needs curl to download latest IG Tooling. Please install curl." - exit 1 -fi - -tooling="$input_cache_path$tooling_jar" -if test -f "$tooling"; then - echo "IG Tooling FOUND in input-cache" - jarlocation="$tooling" - jarlocationname="Input Cache" - upgrade=true -else - tooling="../$tooling_jar" - upgrade=true - if test -f "$tooling"; then - echo "IG Tooling FOUND in parent folder" - jarlocation="$tooling" - jarlocationname="Parent Folder" - upgrade=true - else - echo IG Tooling NOT FOUND in input-cache or parent folder... - jarlocation="$input_cache_path$tooling_jar" - jarlocationname="Input Cache" - upgrade=false - fi -fi - -if $upgrade ; then - message="Overwrite $jarlocation? [Y/N] " -else - #echo Will place tooling jar here: $input_cache_path$tooling_jar - echo Will place tooling jar here: $jarlocation - message="Ok? [Y/N]" -fi - -read -r -p "$message" response -if [[ "$response" =~ ^([yY])$ ]]; then - echo "Downloading most recent tooling to $jarlocationname - it's ~110 MB, so this may take a bit" -# wget "https://oss.sonatype.org/service/local/repositories/snapshots/content/org/opencds/cqf/tooling/1.0-SNAPSHOT/tooling-1.0-20200107.163002-6-jar-with-dependencies.jar" -O "$jarlocation" - curl $dlurl -L -o "$jarlocation" --create-dirs - echo "Download complete." -else - echo cancel... -fi \ No newline at end of file diff --git a/_updatePublisher.sh b/_updatePublisher.sh old mode 100755 new mode 100644 diff --git a/archive/resources/patient-core-profile-spreadsheet.xml b/archive/resources/patient-core-profile-spreadsheet.xml deleted file mode 100644 index 09b6ca4d69..0000000000 --- a/archive/resources/patient-core-profile-spreadsheet.xml +++ /dev/null @@ -1,6849 +0,0 @@ - - - - - Grahame - Bryn - 2012-03-19T11:12:07Z - 2019-07-01T04:53:06Z - 16.00 - - - e60e6d61-cdda-4dc6-8888-32ae3d5d57ba - - - - - - 8490 - 21570 - 32767 - 32767 - 2 - 1 - - False - False - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - FHIR Profile-authoring Spreadsheet - - - This spreadsheet is used to support the definition of profiles containing structures, extension definitions and or search criteria definitions. A complete set of instructions on the various tabs, columns and rules associated with populating this spreadsheet can be found here: - - - http://wiki.hl7.org?title=FHIR_Spreadsheet_Authoring - - - As well, additional guidance on profile-creation can be found here: - - - http://wiki.hl7.org?title=FHIR_Spreadsheet_Profile_Authoring - -
- - -
-