Release v2.1.0 (#228)

* updating aggregate characterization

* Dockerfile and image that can be built on release (#222)

* Sccs 5.1.0 nesting (#223)

* Fixed and changed query to support nesting names

* Added functions for checking if migrations are present and requiring migrations

* Modified data pulls to get indications (with mapped exposure cohorts in field)

* Added a names callback to the input selection to support more complex inputs

* Ran migrations on sqlite sccs test file

* Require migrations for nesting cohorts

* Fixed evidence synthesis module ui and results handler for change

* fixed unit tests for es module

* improved test coverage

* Cd dm changes 5.2.0 (#226)

* removed fields from result

* Fields removed from col defs

* Ran migrations on sqlite file

* Cd orphan concept load issues (#227)

* Distinct results as temp_fix

* Re-wrote orphan concepts table

* Package maintenance

* Updated to version 2.1.0

---------

Co-authored-by: jreps <jreps@its.jnj.com>

.github/workflows/build-docker-image.yml

@@ -0,0 +1,73 @@
+name: build-and-push-ohdsi-docker-image-to-Docker-Hub
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+env:
+  DOCKER_IMAGE: ohdsi/ohdsi-shiny-modules
+  MAINTAINER: Jamie Gilbert <gilbert@ohdsi.org>
+  AUTHOR: Jamie Gilbert <gilbert@ohdsi.org>
+  APP_NAME: ohdsi-shiny-modules
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Docker meta
+        id: docker_meta
+        uses: crazy-max/ghaction-docker-meta@v1
+        with:
+          images: ${{ env.DOCKER_IMAGE }}
+          tag-match: v(.*)
+          tag-match-group: 1
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v1
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      - name: Build Docker image and push to Docker Hub
+        id: build_and_push
+        uses: docker/build-push-action@v2
+        with:
+          context: ./
+          file: ./Dockerfile
+          cache-from: type=local,src=/tmp/.buildx-cache
+          cache-to: type=local,dest=/tmp/.buildx-cache,mode=max
+          platforms: linux/amd64,linux/arm64
+          push: true
+          build-args: |
+            APP_NAME=${{ env.APP_NAME }}
+            GIT_BRANCH=${{ steps.docker_meta.outputs.version }}
+            GIT_COMMIT_ID_ABBREV=${{ steps.build_params.outputs.sha8 }}
+            GITHUB_PAT=${{ secrets.GH_TOKEN }}
+          tags: ${{ steps.docker_meta.outputs.tags }}
+          labels: |
+            ${{ steps.docker_meta.outputs.labels }}
+            maintainer=${{ env.MAINTAINER }}
+            org.opencontainers.image.authors=${{ env.AUTHOR }}
+            org.opencontainers.image.vendor=OHDSI
+            org.opencontainers.image.licenses=Apache-2.0
+
+      - name: Inspect Docker image
+        run: |
+          docker pull ${{ env.DOCKER_IMAGE }}:${{ steps.docker_meta.outputs.version }}
+          docker image inspect ${{ env.DOCKER_IMAGE }}:${{ steps.docker_meta.outputs.version }}

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: OhdsiShinyModules
 Type: Package
 Title: Repository of Shiny Modules for OHDSI Result Viewers
-Version: 2.0.2
+Version: 2.1.0
 Author: Jenna Reps
 Maintainer: Jenna Reps <reps@ohdsi.org>
 Description: Install this package to access useful shiny modules for building shiny apps to explore results using the OHDSI tools .

Dockerfile

@@ -0,0 +1,36 @@
+# Set base image
+FROM ohdsi/broadsea-shiny
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG CRAN=https://packagemanager.posit.co/cran/__linux__/focal/latest
+ARG JAVA_PARAMS=-Xss100m
+
+# Set an argument for the app name
+ARG APP_NAME
+# Set arguments for the GitHub branch and commit id abbreviation
+ARG GIT_BRANCH='main'
+ARG GIT_COMMIT_ID_ABBREV
+
+ENV DATABASECONNECTOR_JAR_FOLDER /root
+
+# install additional required OS dependencies
+RUN apt-get update && \
+    apt-get install -y openjdk-8-jre && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Sets CRAN to latest (or user specified) version
+RUN echo "options(repos=c(CRAN='$CRAN'))" >> /root/.Rprofile
+# Specify java params
+RUN echo "options(java.parameters = '$JAVA_PARAMS')" >> /root/.Rprofile
+RUN R -e 'install.packages(c("remotes", "rJava", "dplyr", "DatabaseConnector", "shiny", "RSQLite"))'
+# run java conf for r
+RUN R CMD javareconf
+RUN R -e "DatabaseConnector::downloadJdbcDrivers('postgresql', pathToDriver='/root')"
+RUN R -e "remotes::install_github('OHDSI/ResultModelManager', update='always')"
+# install git ref or branch
+RUN R -e "ref <- Sys.getenv('GIT_COMMIT_ID_ABBREV', unset=Sys.getenv('GIT_BRANCH')); remotes::install_github('OHDSI/OhdsiShinyModules', ref=ref, update='always')"
+
+# Expose default Shiny app port
+EXPOSE 3838
+

NEWS.md

@@ -1,3 +1,10 @@
+OhdsiShinyModules v2.1.0
+========================
+Support for data models from SCCS version 5.2.0
+Support for data models from Cohort Method version 5.2.0
+Fixes for CohortDiagnostics Orpahan concept table by re-writing with DB level pagination
+Automated release of Docker Images upon package release
+
 OhdsiShinyModules v2.0.2
 ========================
 edited characterization server to work with new aggregate features method in characterization package

R/OhdsiShinyModules.R

@@ -1,6 +1,6 @@
 # @file OhdsiShinyModules.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of OhdsiShinyModules
 # 

R/about-main.R

@@ -1,6 +1,6 @@
 # @file about-main.R
 #
-# Copyright 2023 Observational Health Data Sciences and Informatics
+# Copyright 2024 Observational Health Data Sciences and Informatics
 #
 # This file is part of PatientLevelPrediction
 #