Merge pull request #1 from Sage-Bionetworks/ecs_setting

add docker image and specify environment variables

.github/workflows/Release_Docker_build.yml

@@ -0,0 +1,65 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+
+name: Create and publish a Docker image
+
+on:
+  push:
+    branches:
+      - 'master'
+    tags:
+      - 'v*'
+env:
+  REGISTRY: ghcr.io
+  IMAGE_PATH: ghcr.io/${{ github.repository }}
+
+jobs:
+  tagging:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: '0'
+      - name: Bump version and push tag
+        id: tag_version
+        uses: mathieudutour/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Create a GitHub release
+        uses: ncipollo/release-action@v1
+        with:
+          tag: ${{ steps.tag_version.outputs.new_tag }}
+          name: Release ${{ steps.tag_version.outputs.new_tag }}
+          body: ${{ steps.tag_version.outputs.changelog }}  
+
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/[email protected]
+        if: github.event_name == 'push'
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/[email protected]
+        with:
+          images: ${{ env.IMAGE_PATH }}
+
+      - name: Build and push Docker image
+        uses: docker/[email protected]
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags}}
+          labels: ${{ steps.meta.outputs.labels }}

.releaserc.json

@@ -0,0 +1,7 @@
+{
+  "plugins": [
+    "@semantic-release/commit-analyzer",
+    "@semantic-release/release-notes-generator",
+    "@semantic-release/github"
+  ]
+}

Dockerfile

@@ -0,0 +1,22 @@
+FROM sagebionetworks/shiny-base:release-1.0
+# This is the expected application installation folder
+WORKDIR /srv/shiny-server/app
+COPY --chown=shiny ./ ./
+
+# Set up Python and install the Synapse Python client
+RUN Rscript -e "install.packages('reticulate', repos='http://cran.rstudio.com/', verbose=FALSE)"
+RUN Rscript -e "library(reticulate); install_miniconda(); py_discover_config(); py_install(c('synapseclient', 'pandas'), pip = TRUE, pip_ignore_installed=TRUE)"
+
+# alternative to using renv
+#RUN Rscript -e "install.packages(c('shinydashboard','tidyverse','readxl','gt','gtsummary','survival','survminer','rsconnect','janitor','rjson'), repos='http://cran.rstudio.com/', verbose=FALSE)"
+
+# By default the log level is TRACE.  We bump up one level to DEBUG to make the logs a bit less verbose
+ENV SHINY_LOG_LEVEL=DEBUG
+
+# set up r packages via renv. Use binary lib matching the shiny-base ubuntu version
+# to speed up installatioon.
+RUN Rscript -e 'renv::restore(repos="https://packagemanager.rstudio.com/all/__linux__/jammy/latest"); renv::install("./")'
+
+# running that script, to pass a configuration env var to Shiny
+RUN chmod +x dccmonitor_startup.sh
+CMD ["./dccmonitor_startup.sh"]

R/zzz.R

@@ -7,11 +7,19 @@ app_url <- NULL
 claims_param <- NULL
 authorization_url <- NULL
 
+if (interactive()) {
+  # testing url
+  options(shiny.port = 8100)
+  app_url <- "http://127.0.0.1:8100"
+} else {
+  app_url <- Sys.getenv("APP_REDIRECT_URL")
+}
+
 .onLoad <- function(libname, pkgname) { # nolint
   synapse <<- reticulate::import("synapseclient", delay_load = TRUE)
   if (!interactive()) {
     setup_global_oauth_vars(
-      app_url = get_golem_config("app_url"),
+      app_url = Sys.getenv("app_url"),
       client_name = Sys.getenv("client_name"),
       client_id = Sys.getenv("client_id"),
       client_secret = Sys.getenv("client_secret")

app.R

@@ -2,7 +2,7 @@
 # To deploy, run: rsconnect::deployApp()
 # Or use the blue button on top of this file
 
-Sys.setenv(R_CONFIG_ACTIVE = "default", # Replace "default" with your config
+Sys.setenv(R_CONFIG_ACTIVE = Sys.getenv("R_CONFIG_ACTIVE"), # Replace "default" with your config
            R_CONFIG_FILE = "inst/config.yml")
 pkgload::load_all()
 options("golem.app.prod" = TRUE)

dccmonitor_startup.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/bash
+
+# Pass environment variable to Shiny
+echo "" >> .Renviron
+echo APP_REDIRECT_URL=$APP_REDIRECT_URL >> .Renviron
+
+# Now run the base start-up script
+./startup.sh

inst/config.yml

@@ -110,7 +110,7 @@ amp-ad:
       - "specimenID"
 
 pec:
-  app_url: "https://shinypro.synapse.org/users/kmontgomery/dccmonitor/"
+  #app_url: "https://shinypro.synapse.org/users/danlu/dccmonitor-pec/"
   samples_table: "syn22175287"
   annotations_table: "syn20981788"
   annotations_storage: "syn21763155"
@@ -174,3 +174,55 @@ pec:
       - "libraryPrep"
       - "libraryPreparationMethod"
       - "runType"
+
+1kD:
+  #app_url: "https://shinypro.synapse.org/users/danlu/dccmonitor_1kD/"
+  samples_table: "syn27817789"
+  annotations_table: "syn27806892"
+  annotations_storage: "syn27605404"
+  annotations_link: "https://www.synapse.org/#!Synapse:syn27817580"
+  annotation_keys:
+    - "age"
+    - "primaryDiagnosis"
+  consortium_fileview: "syn27646655"
+  teams:
+    - "3433360"
+  templates:
+    manifest_template: "syn27832372"
+    individual_templates:
+      human: "syn29358381"
+    biospecimen_templates:
+      human: "syn29358373"
+    assay_templates:
+  species_list:
+    - "human"
+  complete_columns:
+    manifest:
+      - "path"
+      - "parent"
+      - "fileFormat"
+      - "program"
+      - "project"
+      - "study"
+      - "resourceType"
+    individual:
+      - "program"
+      - "project"
+      - "study"
+      - "individualID"
+      - "householdID"
+      - "person"
+      - "sex"
+      - "noOfChildren"
+      - "noOfAdults"
+      - "spokenLanguage"
+    biospecimen:
+      - "program"
+      - "project"
+      - "study"
+      - "person"
+      - "individualID"
+      - "specimenID"
+      - "specimenType"
+      - "samplingAge"
+      - "samplingAgeUnits"