-
Notifications
You must be signed in to change notification settings - Fork 11
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
229 changed files
with
15,525 additions
and
19,330 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -11,3 +11,7 @@ compare_versions | |
| .github | ||
| docs | ||
| .idea | ||
| ^_pkgdown\.yml$ | ||
| ^docs$ | ||
| ^pkgdown$ | ||
| ^\.github$ | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| *.html |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| # 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -19,3 +19,7 @@ src/*.dll | |
| /Debug | ||
| standalone/build/* | ||
| _targets | ||
| docs | ||
|
|
||
| extras/rdms/public | ||
| extras/rdms/*.class | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,55 +1,69 @@ | ||
| 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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,25 +1,36 @@ | ||
| # 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) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.