Catalog attempt with docker compose networking example

DESCRIPTION

@@ -5,8 +5,10 @@ Authors@R:
     c(person("Kyle", "Zollo-Venecek", , "kzollovenecek@tuftsmedicalcenter.org", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1615-590X")),
     person("Robert", "Miller", , "rmiller@minderoo.org", role = c("aut"),
-           comment = c(ORCID = "0000-0002-1787-2855")))
-Description: What the package does (one paragraph).
+           comment = c(ORCID = "0000-0002-1787-2855")),
+    person("Timothy", "Norris", , "tibben@ocf.berkeley.edu", role = c("aut"),
+           comment = c(ORCID = "0000-0002-0898-3027")))
+Description: GIS integration into the OHDSI assemblage of tools for EHR analysis.
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -23,6 +25,7 @@ Imports:
     DatabaseConnector,
     dplyr,
     magrittr,
+    plumber,
     plyr,
     rjson,
     rpostgis,

inst/.gitignore

@@ -0,0 +1,2 @@
+.DS_Store
+data/

inst/repository/R/Dockerfile

@@ -0,0 +1,83 @@
+FROM ubuntu:latest
+
+# get necessary system utilties
+RUN apt-get update && \
+    apt-get install -y \
+    software-properties-common \
+    default-jre \
+    default-jdk
+
+# add needed repository for GIS tools
+RUN add-apt-repository ppa:ubuntugis/ppa
+RUN apt update && apt upgrade -y
+
+# get libraries for GIS tools
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt-get install -y \
+    libgdal-dev gdal-bin \
+    libproj22 \
+    libproj-dev \
+    libfontconfig1-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libudunits2-dev \
+    libsodium-dev \
+    r-base
+
+# install all known dependencies for gaiaCore
+RUN R -e "install.packages(c( \
+    'devtools', \
+    'bit', \
+    'bit64', \
+    'blob', \
+    'checkmate', \
+    'class', \
+    'classInt', \
+    'DatabaseConnector', \
+    'DBI', \
+    'dbplyr', \
+    'dplyr', \
+    'e1071', \
+    'generics', \
+    'hms', \
+    'KernSmooth', \
+    'lattice', \
+    'MASS', \
+    'plyr', \
+    'plumber', \
+    'progress', \
+    'proxy', \
+    'raster', \
+    'readr', \
+    'rgeos', \
+    'rJava', \
+    'rjson', \
+    'rpostgis', \
+    'RPostgreSQL', \
+    'sf', \
+    'sp', \
+    'SqlRender', \
+    'terra', \
+    'tidyr', \
+    'tidyselect', \
+    'triebeard', \
+    'tzdb', \
+    'units', \
+    'urltools', \
+    'usethis', \
+    'vroom' \
+    ))"
+
+# install gaiaCore
+RUN R -e "library('devtools'); devtools::install_github('OHDSI/GIS')"
+
+# copy DatabaseConnector jar file for postgres
+RUN mkdir /ohdsi-gis && mkdir /ohdsi-gis/dbJars
+COPY ./dbJars /ohdsi-gis/dbJars
+ENV DATABASECONNECTOR_JAR_FOLDER /ohdsi-gis/dbJars
+
+# copy api app for gaiaCore
+COPY ./R /ohdsi-gis
+WORKDIR /ohdsi-gis
+
+CMD ["sh", "-c", "Rscript gaia.R"]

inst/repository/R/R/gaia.R

@@ -0,0 +1,21 @@
+# plumber.R
+
+library(gaiaCore)
+library(DatabaseConnector)
+library(plumber)
+
+# set database connection 
+# from R docker container to gaiaDB docker container - network gaiadb_default
+connectionDetails <- DatabaseConnector::createConnectionDetails(
+  dbms = "postgresql",
+  server = "gis_postgis/gaiaDB",
+  port = 5432,
+  user="postgres",
+  password = "mysecretpassword") 
+
+# initialize DB connection
+gaiaCore::initializeDatabase(connectionDetails)
+
+# configure and run endpoint
+root <- pr("plumber.R")
+root %>% pr_run(port=8000,host='0.0.0.0')

inst/repository/R/R/plumber.R

@@ -0,0 +1,14 @@
+#* Load the variable from the variable_source
+#* @param variable_id The variable to load
+#* @get /load
+function(variable_id=-1){
+  if (variable_id > 0) {
+    res <- capture.output(
+      gaiaCore::loadVariable(connectionDetails,variable_id),
+      type='message'
+    )
+  } else {
+    res <- 'You must pass a variable_id'
+  }
+  list(res)
+}

inst/repository/R/example.R

@@ -0,0 +1,45 @@
+# install.packages("devtools")
+# install.packages("roxygen2")
+library(devtools)
+library(roxygen2)
+library(DatabaseConnector)
+setwd("d:/Sync/gitRepos/projects/ohdsi-gis/")
+load_all(".")
+# devtools::install_github("OHDSI/GIS")
+library(gaiaCore)
+
+# must download driver first, see: https://ohdsi.github.io/DatabaseConnectorJars/
+Sys.setenv("DATABASECONNECTOR_JAR_FOLDER" = "d:/Sync/gitRepos/GIS/dbJars")
+
+# set database connection
+connectionDetails <- DatabaseConnector::createConnectionDetails(
+  dbms = "postgresql",
+  server = "localhost/gaiaDB",
+  port = 5433,
+  user="postgres",
+  password = "mysecretpassword") 
+
+# initialize DB connection
+gaiaCore::initializeDatabase(connectionDetails) 
+
+# create index tables
+gaiaCore::createIndices(connectionDetails) 
+
+conn <- DatabaseConnector::connect(connectionDetails)
+on.exit(DatabaseConnector::disconnect(conn))
+backboneExists <- DatabaseConnector::querySql(conn, sql = "SELECT schema_name FROM information_schema.schemata WHERE schema_name = 'backbone';")
+backboneExists
+
+gaiaCore::loadVariable(connectionDetails,33)
+
+dataSourceTable <- gaiaCore::getDataSourceTable(connectionDetails = connectionDetails)
+print(names(dataSourceTable))
+uuids <- dataSourceTable$DATA_SOURCE_UUID
+print(uuids)
+
+conn <-  DatabaseConnector::connect(connectionDetails)
+on.exit(DatabaseConnector::disconnect(conn))
+attrIndex <- DatabaseConnector::dbReadTable(conn, "backbone.attr_index", check.names = FALSE)
+print(names(attrIndex))
+names(attrIndex) <- tolower(names(attrIndex))
+print(names(attrIndex))

inst/repository/docker-compose.yml

@@ -1,21 +1,39 @@
 version: "3.9"
 
 services:
-  ohdsi:
-    container_name: gis_repo
+  gaia_r:
+    container_name: gaia-r
+    build: ./R/
+    image: gaia_r
+    ports:
+      - "8000:8000"
+    networks:
+      - gaiadb
+  gis_repo:
+    container_name: gis-repo
     build: ./searchApp/
-    image: ohdsi_repo
+    image: gis_repo
     ports:
       - "5000:5000"
+    networks:
+      - gaiadb
     links:
       - "solr:index"
+      - "gaia_r:gaiaCore"
   solr:
     container_name: solr
     image: solr
+    networks:
+      - gaiadb
     volumes:
       - ./collections:/collections
       - solr-data:/var/solr
 
 volumes:
   solr-data:
-    name: ohdsi-solr-index
+    name: ohdsi-solr-index
+
+networks:
+  gaiadb:
+    name: gaiadb_default
+    external: true