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| .github | ||
| docs | ||
| .idea | ||
| ^_pkgdown\.yml$ | ||
| ^docs$ | ||
| ^pkgdown$ | ||
| ^\.github$ | ||
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| *.html |
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
| on: | ||
| push: | ||
| branches: [main, master] | ||
| pull_request: | ||
| branches: [main, master] | ||
| release: | ||
| types: [published] | ||
| workflow_dispatch: | ||
|
|
||
| name: pkgdown.yaml | ||
|
|
||
| permissions: read-all | ||
|
|
||
| jobs: | ||
| pkgdown: | ||
| runs-on: ubuntu-latest | ||
| # Only restrict concurrency for non-PR jobs | ||
| concurrency: | ||
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| permissions: | ||
| contents: write | ||
| services: | ||
| postgres: | ||
| image: postgres:latest | ||
| env: | ||
| POSTGRES_DB: strategus | ||
| POSTGRES_USER: user | ||
| POSTGRES_PASSWORD: password | ||
| POSTGRES_HOST: postgres | ||
| POSTGRES_PORT: 5432 | ||
| ports: | ||
| - 5432:5432 | ||
| options: --name postgres --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | ||
|
|
||
| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Setup Pandoc | ||
| uses: r-lib/actions/setup-pandoc@v2 | ||
|
|
||
| - name: Setup R | ||
| uses: r-lib/actions/setup-r@v2 | ||
| with: | ||
| use-public-rspm: true | ||
|
|
||
| - name: Setup R Dependencies | ||
| uses: r-lib/actions/setup-r-dependencies@v2 | ||
| with: | ||
| extra-packages: any::pkgdown, local::. | ||
| needs: website | ||
|
|
||
| - name: Build site | ||
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | ||
| shell: Rscript {0} | ||
|
|
||
| - name: Wait for PostgreSQL to be ready | ||
| run: | | ||
| until pg_isready -h 127.0.0.1 -p 5432 -U myuser; do | ||
| echo "Waiting for postgres..."; | ||
| sleep 3; | ||
| done | ||
| - name: Run SQL Script | ||
| run: | | ||
| PGPASSWORD=password psql -h 127.0.0.1 -U user -d strategus -f extras/rdms/full_data_model_pg.sql | ||
| - name: Configure SchemaSpy environment | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install default-jdk -y | ||
| sudo apt-get install postgresql-client -y | ||
| - name: Download PostgreSQL JDBC Driver | ||
| run: | | ||
| wget https://jdbc.postgresql.org/download/postgresql-42.2.24.jar -O $HOME/postgresql-jdbc.jar | ||
| - name: Execute SchemaSpy | ||
| run: | | ||
| java -jar extras/rdms/schemaspy-6.2.4.jar -vizjs -dp $HOME -configFile extras/rdms/schemaspy-config.properties -meta extras/rdms/schema_meta.xml -debug -desc "Results data model" -noTablePaging -noimplied | ||
| - name: Upload artifact | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: documentation-artifact | ||
| path: public | ||
|
|
||
| - name: download documentation | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| name: documentation-artifact | ||
| path: docs/results-schema | ||
|
|
||
| - name: Deploy to GitHub pages 🚀 | ||
| if: github.event_name != 'pull_request' | ||
| uses: JamesIves/[email protected] | ||
| with: | ||
| clean: false | ||
| branch: gh-pages | ||
| folder: docs |
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@@ -19,3 +19,7 @@ src/*.dll | |
| /Debug | ||
| standalone/build/* | ||
| _targets | ||
| docs | ||
|
|
||
| extras/rdms/public | ||
| extras/rdms/*.class | ||
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| Package: Strategus | ||
| Type: Package | ||
| Title: Coordinating and Executing Analytics Using HADES Modules | ||
| Version: 0.3.0 | ||
| Date: 2023-06-04 | ||
| Title: Coordinate and Execute OHDSI HADES Modules | ||
| Version: 1.0.0 | ||
| Date: 2024-10-08 | ||
| Authors@R: c( | ||
| person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")), | ||
| person("Anthony", "Sena", email = "[email protected]", role = c("aut", "cre")), | ||
| person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")), | ||
| person("Jamie", "Gilbert", role = c("aut")), | ||
| person("Observational Health Data Science and Informatics", role = c("cph")) | ||
| ) | ||
| Maintainer: Anthony Sena <[email protected]> | ||
| Description: An R package for coordinating and executing analytics using HADES modules. | ||
| License: Apache License 2.0 | ||
| URL: https://ohdsi.github.io/Strategus, https://github.com/OHDSI/Strategus | ||
| BugReports: https://github.com/OHDSI/Strategus/issues | ||
| Description: Coordinate and execute large scale analytics using OHDSI Health | ||
| Analytics Data-to-Evidence Suite (HADES) (<https://ohdsi.github.io/Hades/>) | ||
| modules. | ||
| Depends: | ||
| R (>= 4.2.0), | ||
| CohortGenerator (>= 0.8.0), | ||
| DatabaseConnector (>= 6.2.3) | ||
| CohortGenerator (>= 0.11.0), | ||
| DatabaseConnector (>= 6.2.3), | ||
| R6 | ||
| Imports: | ||
| targets, | ||
| renv (>= 1.0.0), | ||
| ParallelLogger (>= 3.1.0), | ||
| dplyr, | ||
| checkmate, | ||
| keyring, | ||
| rlang, | ||
| utils, | ||
| R.utils, | ||
| cli, | ||
| digest, | ||
| dplyr, | ||
| methods, | ||
| tibble, | ||
| ResultModelManager (>= 0.3.0), | ||
| SqlRender (>= 1.11.0), | ||
| semver, | ||
| httr2, | ||
| jsonlite | ||
| ParallelLogger (>= 3.1.0), | ||
| purrr, | ||
| readr, | ||
| ResultModelManager (>= 0.5.8), | ||
| rlang, | ||
| SqlRender (>= 1.18.0) | ||
| Suggests: | ||
| testthat (>= 3.0.0), | ||
| Characterization, | ||
| CirceR, | ||
| CohortDiagnostics, | ||
| CohortIncidence, | ||
| CohortMethod, | ||
| Cyclops, | ||
| Eunomia, | ||
| EvidenceSynthesis, | ||
| FeatureExtraction, | ||
| fs, | ||
| knitr, | ||
| PatientLevelPrediction, | ||
| rmarkdown, | ||
| Eunomia, | ||
| RSQLite, | ||
| SelfControlledCaseSeries, | ||
| testthat (>= 3.0.0), | ||
| withr | ||
| Remotes: | ||
| ohdsi/Characterization, | ||
| ohdsi/CohortDiagnostics, | ||
| ohdsi/CohortGenerator, | ||
| ohdsi/CohortIncidence, | ||
| ohdsi/CohortMethod, | ||
| ohdsi/PatientLevelPrediction, | ||
| ohdsi/ResultModelManager, | ||
| ohdsi/Eunomia | ||
| ohdsi/SelfControlledCaseSeries | ||
| License: Apache License 2.0 | ||
| VignetteBuilder: knitr | ||
| URL: https://ohdsi.github.io/Strategus, https://github.com/OHDSI/Strategus | ||
| BugReports: https://github.com/OHDSI/Strategus/issues | ||
| NeedsCompilation: no | ||
| RoxygenNote: 7.3.1 | ||
| RoxygenNote: 7.3.2 | ||
| Roxygen: list(markdown = TRUE) | ||
| Encoding: UTF-8 | ||
| Language: en-US | ||
| Config/testthat/edition: 3 |
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| # Generated by roxygen2: do not edit by hand | ||
|
|
||
| export(CharacterizationModule) | ||
| export(CohortDiagnosticsModule) | ||
| export(CohortGeneratorModule) | ||
| export(CohortIncidenceModule) | ||
| export(CohortMethodModule) | ||
| export(EvidenceSynthesisModule) | ||
| export(PatientLevelPredictionModule) | ||
| export(SelfControlledCaseSeriesModule) | ||
| export(StrategusModule) | ||
| export(addCharacterizationModuleSpecifications) | ||
| export(addCohortDiagnosticsModuleSpecifications) | ||
| export(addCohortGeneratorModuleSpecifications) | ||
| export(addCohortIncidenceModuleSpecifications) | ||
| export(addCohortMethodeModuleSpecifications) | ||
| export(addEvidenceSynthesisModuleSpecifications) | ||
| export(addModuleSpecifications) | ||
| export(addPatientLevelPredictionModuleSpecifications) | ||
| export(addSelfControlledCaseSeriesModuleSpecifications) | ||
| export(addSharedResources) | ||
| export(compareLockFiles) | ||
| export(createCdmExecutionSettings) | ||
| export(createEmptyAnalysisSpecificiations) | ||
| export(createResultDataModels) | ||
| export(createResultDataModel) | ||
| export(createResultsDataModelSettings) | ||
| export(createResultsExecutionSettings) | ||
| export(ensureAllModulesInstantiated) | ||
| export(execute) | ||
| export(getModuleList) | ||
| export(installLatestModule) | ||
| export(retrieveConnectionDetails) | ||
| export(storeConnectionDetails) | ||
| export(syncLockFile) | ||
| export(unlockKeyring) | ||
| export(validateLockFile) | ||
| export(verifyModuleInstallation) | ||
| export(getCdmDatabaseMetaData) | ||
| export(uploadResults) | ||
| export(zipResults) | ||
| import(CohortGenerator) | ||
| import(DatabaseConnector) | ||
| import(R6) | ||
| import(dplyr) | ||
| importFrom(methods,is) | ||
| importFrom(rlang,.data) |
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