Release v1.0

.Rbuildignore

@@ -11,3 +11,7 @@ compare_versions
 .github
 docs
 .idea
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R_CMD_check_Hades.yaml

@@ -20,9 +20,6 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          #- {os: macOS-latest, r: '4.2.3', rtools: '42', rspm: "https://cloud.r-project.org"}
-          - {os: ubuntu-20.04, r: '4.2.3', rtools: '42', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: windows-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           - {os: macOS-latest, r: 'release', rtools: '', rspm: "https://cloud.r-project.org"}
           - {os: ubuntu-20.04, r: 'release', rtools: '', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
@@ -61,7 +58,6 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          rtools-version: ${{ matrix.config.rtools }}
 
       - uses: r-lib/actions/setup-tinytex@v2
 
@@ -70,11 +66,7 @@ jobs:
       - name: Install system requirements
         if: runner.os == 'Linux'
         run: |
-          sudo apt-get install -y make
-          sudo apt-get install -y default-jdk
-          sudo apt-get install -y libcurl4-openssl-dev
-          sudo apt-get install -y libssl-dev
-          sudo apt-get install -y libglpk-dev
+          sudo apt-get install -y libssh-dev
           while read -r cmd
           do
             eval sudo $cmd
@@ -93,7 +85,7 @@ jobs:
 
       - name: Upload source package
         if: success() && runner.os == 'Windows' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: package_tarball
           path: check/*.tar.gz
@@ -164,7 +156,7 @@ jobs:
       #
       # - name: Download package tarball
       #   if: ${{ env.new_version != '' }}
-      #   uses: actions/download-artifact@v2
+      #   uses: actions/download-artifact@v4
       #   with:
       #     name: package_tarball
       #

.github/workflows/pkgdown.yaml

@@ -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

.gitignore

@@ -19,3 +19,7 @@ src/*.dll
 /Debug
 standalone/build/*
 _targets
+docs
+
+extras/rdms/public
+extras/rdms/*.class

DESCRIPTION

@@ -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

NAMESPACE

@@ -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)

NEWS.md

@@ -1,3 +1,22 @@
+Strategus 1.0.0
+===============
+
+- Eliminated the dependencies for `keyring`, `renv` and `targets` (#135)
+- Centralized all modules into the Strategus package (#29, #45, #51, #140)
+- Strategus execution provides a summary of the execution time (#4) and continues after an error (#64, #141)
+- Modules provide functions for creating their results data model (#43) and to upload results.
+- Allow modules to obtain the full set of OMOP CDM metadata collected (#20, #154)
+- Adds the `cdm_holder` attribute to the database_id hash calculation (#48)
+- Moves the `incremental` setting to the execution settings vs. the module settings (#155)
+- Adds threading options via execution settings (#151)
+- Select subset of modules to execute from analysis specification (#169)
+- Ensure release of Strategus has Python dependencies (#22) and OHDSI Shiny App dependencies (#78). See [StrategusStudyRepoTemplate](https://github.com/ohdsi-studies/StrategusStudyRepoTemplate) for more details.
+- Document the results data model for HADES modules (#143)
+
+## Bug Fixes
+- Make negative control outcome shared resource optional (#153)
+- Export results data model specification file for PatientLevelPrediction (#165)
+
 Strategus 0.3.0
 ===============
 - Provide option to skip modules (#87)
@@ -27,7 +46,7 @@ Strategus 0.1.0
 - Robust handling of connection details via keyring (#74)
 - Ensures uniqueness of all CDM tables when gathering database metadata (#82)
 - `tempEmulationSchema` added to execution settings and passed properly to modules (#82)
-- Adding logging to module initalization to detect `renv` restore errors (#82)
+- Adding logging to module initialization to detect `renv` restore errors (#82)
 - Adopt HADES-wide lock file in latest versions of all modules (#83)
 - Use renv >= v1.0.0 for all modules and Strategus (#83)
 - Add GitHub unit tests for HADES adopted version (currently v4.2.3) and the latest R versions for all modules and Strategus. (#83)
@@ -60,7 +79,7 @@ Strategus 0.0.3
 - Breaking change: removed function `createExecutionSettings()` and replaced with 2 new functions: `createCdmExecutionSettings()` and `createResultsExecutionSettings()`. (#19)
 - Added Vignettes (#23)
 - Provide better support for `keyring` to handle named/locked keyrings (#24)
-- Add function to list Strategus modules (#30)
+- Add function to list HADES modules (#30)
 - Fixes from testing (#36)
 - Enforce module structure for proper use with renv (#37)
 - Support CDM 5.4 source table format (#41)