Add Docker run instructions

.gitignore

@@ -51,3 +51,6 @@ inst_real
 
 # Error reports
 errorReportSql.txt
+
+# Docker environment files
+.env

docker/Dockerfile

@@ -0,0 +1,117 @@
+FROM rocker/r-ver:4.1.0
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+      git \
+      libbz2-dev \
+      liblzma-dev \
+      libcairo2-dev \
+      libcurl4-openssl-dev \
+      libfontconfig1-dev \
+      libpcre3-dev \
+      libssl-dev \
+      libxml2 \
+      libxml2-dev \
+      openjdk-11-jdk-headless \
+      pandoc \
+      zlib1g-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64 \
+  LD_LIBRARY_PATH=/usr/lib/jvm/java-11-openjdk-amd64/lib/server
+
+RUN R CMD javareconf \
+    && ln -s /usr/local/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
+    && install.r \
+      devtools \
+      Andromeda \
+      base64enc \
+      benchmarkme \
+      benchmarkmeData \
+      bit64 \
+      bitops \
+      broom \
+      car \
+      checkmate \
+      codemetar \
+      colorspace \
+      curl \
+      clock \
+      conquer \
+      data.table \
+      devtools \
+      doParallel \
+      DT \
+      dplyr \
+      digest \
+      farver \
+      fastmap \
+      ff \
+      flextable \
+      foreach \
+      gdtools \
+      generics \
+      ggplot2 \
+      ggiraph \
+      gtable \
+      gridtext \
+      haven \
+      hms \
+      httpuv \
+      isoband \
+      iterators \
+      jpeg \
+      KMsurv \
+      labeling \
+      lme4 \
+      lubridate \
+      maptools \
+      munsell \
+      officer \
+      openxlsx \
+      pool \
+      plyr \
+      plotly \
+      png \
+      RColorBrewer \
+      RCurl \
+      readr \
+      readxl \
+      renv \
+      rJava \
+      rjson \
+      RJSONIO \
+      RSQLite \
+      rlang \
+      rmarkdown \
+      scales \
+      shiny \
+      shinydashboard \
+      shinyWidgets \
+      snow \
+      sourcetools \
+      survminer \
+      systemfonts \
+      tidyr \
+      tinytex \
+      tsibble \
+      utf8 \
+      uuid \
+      viridisLite \
+      vroom \
+      withr \
+      XML \
+      xml2 \
+      xtable \
+      zip \
+   && installGithub.r \
+      OHDSI/CohortDiagnostics \
+      OHDSI/CirceR \
+      OHDSI/Eunomia \
+      OHDSI/FeatureExtraction \
+      OHDSI/ParallelLogger \
+      OHDSI/ROhdsiWebApi \
+      OHDSI/SqlRender \
+      OHDSI/DatabaseConnector \
+      OHDSI/DatabaseConnectorJars \ 
+      ohdsi-studies/[email protected]

docker/README-Docker.md

@@ -0,0 +1,49 @@
+Docker container instructions
+=============================
+
+This folder contains a number of files that can help you to run the study package within a Docker container.
+Ready-to-go containers are also published on [Docker Hub](https://hub.docker.com/repository/docker/keesvanbochove/pioneer-package).
+
+# Instructions
+These instructions assume you would like to use the published container, but of course
+you can also choose to build it from source yourself using the provided `Dockerfile`.
+
+## 1. Supply configuration variables and create the cointainer
+You can use the file `pioneer-package.env` in this folder to update environment variables
+needed to run the study. Please copy it to a file named `.env` and fill in your details.
+You can then create and start the container using the following command:
+```
+docker run -itd --env-file .env --name pioneer keesvanbochove:pioneer-package
+```
+Note that depending on your Docker configuration you may need to add other arguments, such as the target network.
+
+## 2. Copy your private SFTP upload key to the container
+```
+docker cp study-data-site-pioneer pioneer:/
+```
+
+## 3. Run the study
+You can use the following command to attach to the R session started within the container:
+```
+docker attach pioneer
+```
+You can now follow the instructions in `extras/CodeToRun.R` from section 2 on as if you were running locally.
+
+A few comments:
+* If you want to temporarily return to your command line but keep the container running, the default detach sequence is `CTRL-p CTRL-q`
+* Please don't forget to run the `uploadDiagnosticsResults` and `uploadStudyResults` commands to upload to the OHDSI SFTP server! This requires your container to have internet connection.
+* If you exit the R session (using `q()`), the container will be stopped, so don't do that until you are finished.
+
+## 4. Copy the results out of the container onto your filesystem
+By default, the results are in a folder named identical to your database ID.
+So if your database ID is `SP` and you would like to copy the result folder to your current path, you would run:
+```
+docker cp pioneer:/SP .
+```
+
+5. Destroy the container
+After you copied and inspected the results, you can safely destroy the container.
+However, this will not delete the results in the result tables in your database (see `COHORT_SCHEMA`).
+```
+docker rm pioneer
+```

docker/pioneer-package.env

@@ -0,0 +1,10 @@
+GITHUB_PAT=
+DBMS=postgresql
+DB_USER=postgres
+DB_PASSWORD=postgres
+DB_SERVER=host.docker.internal
+DB_PORT=5432
+CONNECTION_STRING=jdbc:postgresql://host.docker.internal:5432/ohdsi
+PATH_TO_DRIVER=/usr/local/lib/R/site-library/DatabaseConnectorJars/java
+CDM_SCHEMA=cdm_synpuf
+COHORT_SCHEMA=pioneer

extras/CodeToRun.R

@@ -147,7 +147,7 @@ cohortIdsToExcludeFromExecution <- c()
 cohortIdsToExcludeFromResultsExport <- NULL
 
 # For uploading the results. You should have received the key file from the study coordinator, input the correct path here:
-keyFileName <- "your-home-folder-here/.ssh/study-data-site-pioneer"
+keyFileName <- "study-data-site-pioneer"
 userName <- "study-data-site-pioneer"
 
 # Run cohort diagnostics -----------------------------------