Release version 2.2

Note checks failed because R 4.1.0 on mac os

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 extras
 man-roxygen
 license_header_stub.txt
@@ -21,4 +23,7 @@ docs
 compare_versions
 _pkgdown.yml
 examplePhenotypeLibraryPackage
-examplePackage
+examplePackage
+.github
+deploy.sh
+compare_versions

.github/workflows/R_CMD_check_Hades.yml

@@ -0,0 +1,193 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches:
+      - '**'
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: windows-latest, r: 'release'}  # Does not appear to have Java 32-bit, hence the --no-multiarch
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
+      CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
+      CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
+      CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
+      CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
+      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
+      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
+      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
+      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
+      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
+      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
+      CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
+      CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
+      CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
+      CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
+      CDM5_POSTGRESQL_COHORT_DIAGNOSTICS_SCHEMA: 'cohort_diagnostics'
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v1
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+      - name: Install libssh
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get install libssh-dev
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE, INSTALL_opts=c("--no-multiarch"))
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install covr
+        if: runner.os == 'macOS'
+        run: |
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Remove check folder if exists
+        if: runner.os == 'macOS'
+        run: unlink("check", recursive = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--no-multiarch"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@v2
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Upload source package
+        if: success() && runner.os == 'macOS' && github.event_name != 'pull_request' && github.ref == 'refs/heads/master'
+        uses: actions/upload-artifact@v2
+        with:
+          name: package_tarball
+          path: check/*.tar.gz
+
+      - name: Test coverage
+        if: runner.os == 'macOS'
+        run: covr::codecov()
+        shell: Rscript {0}
+
+  Release:
+    needs: R-CMD-Check
+
+    runs-on: macOS-latest
+
+    env:
+      GH_TOKEN: ${{ secrets.GH_TOKEN }}
+
+    if: ${{ github.event_name != 'pull_request' && github.ref == 'refs/heads/master' }}
+
+    steps:
+
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Check if version has increased
+        run: |
+          echo "new_version="$(perl compare_versions --tag) >> $GITHUB_ENV
+
+      - name: Display new version number
+        if: ${{ env.new_version != '' }}
+        run: |
+          echo "${{ env.new_version }}"
+
+      - name: Create release
+        if: ${{ env.new_version != '' }}
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GH_TOKEN }}
+        with:
+          tag_name: ${{ env.new_version }}
+          release_name: Release ${{ env.new_version }}
+          body: |
+            See NEWS.md for release notes.
+          draft: false
+          prerelease: false
+
+      - uses: r-lib/actions/setup-r@v1
+        if: ${{ env.new_version != '' }}
+
+      - name: Install drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          install.packages('drat')
+        shell: Rscript {0}
+
+      - name: Remove any tarballs that already exists
+        if: ${{ env.new_version != '' }}
+        run: |
+          rm -f *.tar.gz
+
+      - name: Download package tarball
+        if: ${{ env.new_version != '' }}
+        uses: actions/download-artifact@v2
+        with:
+          name: package_tarball
+
+      - name: Push to drat
+        if: ${{ env.new_version != '' }}
+        run: |
+          bash deploy.sh
+      - name: Push to BroadSea
+        if: ${{ env.new_version != '' }}
+        run: |
+          curl --data "build=true" -X POST https://registry.hub.docker.com/u/ohdsi/broadsea-methodslibrary/trigger/f0b51cec-4027-4781-9383-4b38b42dd4f5/

.github/workflows/nightly_cleanup_Hades.yml

@@ -0,0 +1,18 @@
+name: 'nightly artifacts cleanup'
+on:
+  schedule:
+    - cron: '0 1 * * *' # every night at 1 am UTC
+
+jobs:
+  remove-old-artifacts:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+
+    steps:
+    - name: Remove old artifacts
+      uses: c-hive/gha-remove-artifacts@v1
+      with:
+        age: '7 days'
+        # Optional inputs
+        # skip-tags: true
+        skip-recent: 1

.gitignore

@@ -2,11 +2,12 @@
 .Rhistory
 .RData
 .Ruserdata
-*.RData
-inst/shiny/DiagnosticsExplorer/data/phenotypeDescription.csv
-inst/shiny/DiagnosticsExplorer/data/cohortDescription.csv
 *.zip
 errorReportSql.txt
 errorReportR.txt
 *.tex
 .DS_Store
+*.history
+.RDataTmp
+*.log
+*log.txt

CohortDiagnostics.Rproj

@@ -13,6 +13,5 @@ RnwWeave: Sweave
 LaTeX: pdfLaTeX
 
 BuildType: Package
-PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
 PackageRoxygenize: rd,collate,namespace

DESCRIPTION

@@ -1,57 +1,64 @@
 Package: CohortDiagnostics
 Type: Package
 Title: Diagnostics for OHDSI Cohorts
-Version: 2.0.0
-Date: 2020-10-07
+Version: 2.1.0
+Date: 2021-05-24
 Authors@R: c(
-    person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
+    person("Gowtham", "Rao", email = "[email protected]", role = c("aut", "cre")),
     person("Martijn", "Schuemie", email = "[email protected]", role = c("aut")),
     person("Patrick", "Ryan", role = c("aut")),
     person("James", "Weaver", role = c("aut")),
+    person("Jamie", "Gilbert", role = c("aut")),
     person("Observational Health Data Science and Informatics", role = c("cph"))
   )
-Maintainer: Gowtham Rao <[email protected]>
+Maintainer: Gowtham Rao <[email protected]>
 Description: Diagnostics for cohorts that use the OMOP Common Data Model and the OHDSI tools.
 Depends:
-	DatabaseConnector (>= 3.0.0),
-	FeatureExtraction (>= 3.1.0),
-	R (>= 3.5.0)
+	DatabaseConnector (>= 4.0.0),
+	FeatureExtraction (>= 3.1.1),
+	R (>= 4.0.0)
 Imports:
   Andromeda,
   checkmate,
+  CirceR,
+  clock,
   digest,
   dplyr (>= 1.0.0),
-  ggplot2,
-  ggiraph,
+  methods,
   ParallelLogger (>= 2.0.0),
+  pool,
   readr (>= 1.4.0),
-  rlang,
   RJSONIO,
-  ROhdsiWebApi (>= 1.1.2),
-  SqlRender (>= 1.6.7),
+  rlang,
+  ROhdsiWebApi (>= 1.2.0),
+  SqlRender (>= 1.7.0),
   stringr,
-  tidyr (>= 1.0.0),
-  methods
+  tidyr (>= 1.0.0)
 Suggests:
-  shiny,
-  shinydashboard,
-  shinyWidgets,
   DT,
-  plotly,
+  Eunomia,
+  ggiraph,
+  ggplot2,
   htmltools,
-  RColorBrewer,
-  scales,
   knitr,
+  lubridate,
+  plotly,
+  purrr,
+  RColorBrewer,
   rmarkdown,
-  Eunomia,
-  testthat,
   RSQLite (>= 2.2.1),
+  scales,
+  shiny,
+  shinydashboard,
+  shinyWidgets,
+  testthat,
+  withr,
   zip
 Remotes:
   ohdsi/Eunomia,
   ohdsi/FeatureExtraction,
   ohdsi/ROhdsiWebApi,
-  ohdsi/DatabaseConnector,
+  ohdsi/CirceR
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/CohortDiagnostics, https://github.com/OHDSI/CohortDiagnostics

NAMESPACE

@@ -1,11 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-export(checkInputFileEncoding)
-export(createCohortTable)
 export(createResultsDataModel)
 export(getCohortCounts)
 export(getResultsDataModelSpecifications)
-export(instantiateCohort)
 export(instantiateCohortSet)
 export(launchCohortExplorer)
 export(launchDiagnosticsExplorer)
@@ -22,5 +19,7 @@ importFrom(rlang,.data)
 importFrom(stats,aggregate)
 importFrom(utils,install.packages)
 importFrom(utils,menu)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,txtProgressBar)
 importFrom(utils,unzip)
 importFrom(utils,write.csv)