Merge pull request #423 from OHDSI/develop

v2.1.1 release
OHDSI · Feb 28, 2023 · c468ebc · c468ebc
2 parents b0957c8 + 7d8da8a
commit c468ebc
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Showing 43 changed files with 212 additions and 103 deletions.
diff --git a/.github/workflows/R_CMD_check_Hades.yaml → .github/workflows/R_CMD_check_Hades.yml b/.github/workflows/R_CMD_check_Hades.yaml → .github/workflows/R_CMD_check_Hades.yml
@@ -51,9 +51,13 @@ jobs:
       CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
       CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
+      WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
+      WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
+      WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -81,6 +85,7 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           args: 'c("--no-manual", "--as-cran")'
+          build_args: 'c("--compact-vignettes=both")'
           error-on: '"warning"'
           check-dir: '"check"'
 
@@ -114,7 +119,7 @@ jobs:
 
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
@@ -140,33 +145,33 @@ jobs:
           draft: false
           prerelease: false
 
-      # - uses: r-lib/actions/setup-r@v2
-      #   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/
+      - uses: r-lib/actions/setup-r@v2
+        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/
 
diff --git a/.github/workflows/R_CMD_check_main_weekly.yaml b/.github/workflows/R_CMD_check_main_weekly.yaml
@@ -0,0 +1,71 @@
+on:
+  schedule:
+    - cron: '0 17 * * 0' # every Sunday at 5pm UTC
+
+name: 'R check'
+
+jobs:
+  R-CMD-check-main:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
+      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_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
+      CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
+      CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
+      CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
+      CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
+      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
+      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
+      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
+      WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
+      WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
+      WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
+      WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-tinytex@v2
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          args: 'c("--no-manual", "--as-cran")'
+          error-on: '"warning"'
+          check-dir: '"check"'
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,10 +1,11 @@
 Package: DataQualityDashboard
 Type: Package
 Title: Execute and View Data Quality Checks on OMOP CDM Database
-Version: 2.1.0
-Date: 2023-02-13
+Version: 2.1.1
+Date: 2023-02-27
 Authors@R: c(
-  person("Clair", "Blacketer", , "mblacke@its.jnj.com", role = c("aut", "cre")),
+  person("Katy", "Sadowski", email = "sadowski@ohdsi.org", role = c("aut", "cre")),
+  person("Clair", "Blacketer", role = c("aut")),
   person("Ajit", "Londhe", role = c("aut")),
   person("Anthony", "Sena", role = c("aut")),
   person("Anthony", "Molinaro", role = c("aut")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
+DataQualityDashboard 2.1.1
+==========================
+
+1. Updating author list in DESCRIPTION.
+
 DataQualityDashboard 2.1.0
-===========================
+==========================
 This release includes:
 
 ### Bugfixes

diff --git a/README.md b/README.md
@@ -6,6 +6,8 @@ DataQualityDashboard
 [![Build Status](https://github.com/OHDSI/DataQualityDashboard/workflows/R-CMD-check/badge.svg)](https://github.com/OHDSI/DataQualityDashboard/actions?query=workflow%3AR-CMD-check)
 <!-- badges: end -->
 
+DataQualityDashboard is part of [HADES](https://ohdsi.github.io/Hades).
+
 The goal of the Data Quality Dashboard (DQD) project is to design and develop an open-source tool to expose and evaluate observational data quality. 
 
 Introduction

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/AddNewCheck.html b/docs/articles/AddNewCheck.html
diff --git a/docs/articles/CheckStatusDefinitions.html b/docs/articles/CheckStatusDefinitions.html
diff --git a/docs/articles/CheckTypeDescriptions.html b/docs/articles/CheckTypeDescriptions.html
diff --git a/docs/articles/DataQualityDashboard.html b/docs/articles/DataQualityDashboard.html
diff --git a/docs/articles/DqdForCohorts.html b/docs/articles/DqdForCohorts.html