Merge pull request #138 from NIDAP-Community/update_cd

feat: CI/CD and Conda Recipe

.github/workflows/Manual_Deployment_to_NIDAP.yml

@@ -0,0 +1,105 @@
+name: Manual Deployment to NIDAP
+run-name: Manual Deployment to NIDAP by ${{ github.actor }} 
+
+on:
+  workflow_dispatch:
+    inputs:
+
+      image_to_use:
+        required: true
+        default: "<Replace with your image>"
+        type: string
+
+      package_to_deploy:
+        required: true
+        type: string
+
+      artifact_rid:
+        required: true
+        default: "<Replace with your artifact RID>"
+        type: string
+
+      token_to_use:
+        required: true
+        type: string
+
+
+jobs:
+  Adding_documentation_files_and_publish_page:
+    runs-on: ubuntu-latest
+    container:
+      image: ${{ inputs.image_to_use }}
+      credentials:
+         username: ${{ github.actor }}
+         password: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - run: echo "Checking in ${{ inputs.image_to_use }}"
+      - uses: actions/checkout@v3
+        with:
+          token: ${{secrets.GITHUB_TOKEN}}
+
+      - name: Continuous Deployment to NIDAP
+        id: nidap-cd
+        run: |
+          export current_wd="/__w/${GITHUB_REPOSITORY#*/}/${GITHUB_REPOSITORY#*/}"
+          cd $current_wd
+
+          export MY_GIT_TOKEN=${{ secrets.GITHUB_TOKEN }}
+          export MY_GIT_USERNAME=${{ github.actor }}
+          export MY_GIT_EMAIL=${{ github.event.pusher.email }}
+          
+          git config --global user.name "$MY_GIT_USERNAME"
+          git config --global user.email "$MY_GIT_EMAIL"
+          git config --global url."https://api:[email protected]/".insteadOf "https://github.com/"
+          git config --global url."https://ssh:[email protected]/".insteadOf "ssh://[email protected]/"
+          git config --global url."https://git:[email protected]/".insteadOf "[email protected]:"
+          
+          git config --global --add safe.directory "$current_wd"
+          
+          git clone https://github.com/${GITHUB_REPOSITORY}.git
+          
+          cd ${GITHUB_REPOSITORY#*/}
+
+          BRANCH_NAME="Conda_Package"
+
+          git checkout $BRANCH_NAME
+
+          echo "########## Git setup complete, moving to deployment... ##########"
+
+          conda install curl
+
+          current_pkg="${{ inputs.package_to_deploy }}"
+          
+          echo "Package to Upload: $current_pkg"
+
+          TOKEN="${{ inputs.token_to_use }}"
+          PACKAGE="$current_pkg"
+          PLATFORM="linux-64" # replace with the package platform (e.g. noarch, linux-64, osx-64)
+          response=$(curl \
+                    -H "Authorization: Bearer $TOKEN" \
+                    -H "Content-Type: application/octet-stream" \
+                    --data-binary "@$PACKAGE" \
+                    -XPUT "https://nidap.nih.gov/artifacts/api/repositories/${{ inputs.artifact_rid }}/contents/release/conda/$PLATFORM/$PACKAGE" \
+                    2>&1)
+
+
+          echo "#########################################################"
+
+          current_datetime="$(date +"%Y-%m-%d %H:%M:%S")"
+
+          # Check if the response contains an error message
+          if echo "$response" | grep -q "errorCode"; then
+            status=$(echo "$response" | grep -o '"errorName":"[^"]*' | awk -F'"' '{print $4}')
+            echo "Error message: $status"
+            echo "<br>Deployment Time: $current_datetime; Deployment Status: $status" >> README.md
+          else
+            status="Success"
+            echo "Update Success!"
+            echo "Package ${{ env.current_pkg }} is now on NIDAP."
+            echo "<br>Deployment Time: $current_datetime; Deployment Status: Success" >> README.md
+          fi
+
+          git commit -a -m "Deployment Performed on $current_datetime with Status: $status."
+
+          git push -f origin $BRANCH_NAME    

.github/workflows/gitflow-R-action.yml

@@ -1,17 +1,23 @@
 name: Gitflow Action for R Package Development
-run-name: ${{ github.actor }} now ${{ github.event_name }} to ${{ github.ref_name }}
+run-name: ${{ github.actor }} ${{ github.event_name }} to ${{ github.ref_name }}
 
 on:
   push:
-    branches: ['*', '!dev', '!main']
+    branches: ['*', '!dev', '!main', '!release_dev', '!Conda_Package', '!github_page']
 
   pull_request:
     types: ['opened', 'closed']
     branches: ['main', 'release*']
 
 jobs:
   Activating_Parser:
-    uses: fnlcr-bids-sdsi/gitflow-R/.github/workflows/parser.yml@DSPWorkflow
+    uses: fnlcr-bids-sdsi/gitflow-R/.github/workflows/parser.yml@master
     with:
       image_to_use: ghcr.io/nidap-community/dsp_ci_cd:latest
-
+      package_name: "r-dspworkflow"
+      r_version: "4.1.3"
+      artifact_rid_production: "ri.artifacts.main.repository.20ce29a2-3803-4eae-b325-8fe367d47d1e"
+      artifact_rid_development: "ri.stemma.main.repository.2172e505-c98f-43d4-881a-47e170aadbe1"
+    secrets:
+      NIDAP_TOKEN_PRODUCTION: ${{ secrets.NIDAP_TOKEN_PRODUCTION }}
+      NIDAP_TOKEN_DEVELOPMENT: ${{ secrets.NIDAP_TOKEN_DEVELOPMENT }}

Conda_Recipe/meta.yaml

@@ -0,0 +1,109 @@
+{% set version = '<CURRENT_VERSION>' %}
+
+{% set posix = 'm2-' if win else '' %}
+{% set native = 'm2w64-' if win else '' %}
+
+package:
+  name: r-dspworkflow-test
+  version: {{ version|replace("-", "_") }}
+
+channels:
+  - conda-forge
+  - bioconda
+  - file:///local_channel
+
+source:
+
+  git_url: https://github.com/NIDAP-Community/DSPWorkflow/
+  git_tag: continuous_deployment
+
+build:
+  merge_build_host: True  # [win]
+  # If this is a new build for the same version, increment the build number.
+  number: 0
+  # no skip
+
+  # This is required to make R link correctly on Linux.
+  rpaths:
+    - lib/R/lib/
+    - lib/
+
+# Suggests: testthat (== 3.1.4)
+requirements:
+  build:
+    - {{ posix }}filesystem        # [win]
+    - {{ posix }}git
+    - {{ posix }}zip               # [win]
+
+  host:
+    - r-base =4.1.3=h2f963a2_5
+    - bioconductor-biobase =2.54.0=r41hc0cfd56_2
+    - bioconductor-biocgenerics =0.40.0=r41hdfd78af_0
+    - bioconductor-geomxtools =3.1.1=r41hdfd78af_0
+    - bioconductor-nanostringnctools =1.2.0
+    - bioconductor-spatialdecon =1.4.3
+    - bioconductor-complexheatmap =2.10.0=r41hdfd78af_0
+    - bioconductor-genomeinfodbdata =1.2.6
+    - r-cowplot =1.1.1=r41hc72bb7e_1
+    - r-dplyr =1.0.9=r41h7525677_0
+    - r-ggforce =0.3.4=r41h7525677_0
+    - r-ggplot2 =3.3.6=r41hc72bb7e_1
+    - r-gridextra =2.3=r41hc72bb7e_1004
+    - r-gtable =0.3.0=r41hc72bb7e_3
+    - r-knitr =1.40=r41hc72bb7e_1
+    - r-patchwork =1.1.2=r41hc72bb7e_1
+    - r-reshape2 =1.4.4=r41h7525677_2
+    - r-scales =1.2.1=r41hc72bb7e_1
+    - r-tibble =3.1.8=r41h06615bd_1
+    - r-tidyr =1.2.1=r41h7525677_1
+    - r-umap =0.2.9.0=r41h7525677_1
+    - r-rtsne =0.16=r41h37cf8d7_1
+    - r-magrittr =2.0.3=r41h06615bd_1
+    - r-rlang =1.1.0=r41h38f115c_0
+    - r-ggiraph=0.7.10=r41h03ef668_0
+
+  run:
+    - r-base =4.1.3=h2f963a2_5
+    - bioconductor-biobase =2.54.0=r41hc0cfd56_2
+    - bioconductor-biocgenerics =0.40.0=r41hdfd78af_0
+    - bioconductor-geomxtools =3.1.1=r41hdfd78af_0
+    - bioconductor-nanostringnctools =1.2.0
+    - bioconductor-spatialdecon =1.4.3
+    - bioconductor-complexheatmap =2.10.0=r41hdfd78af_0
+    - bioconductor-genomeinfodbdata =1.2.6  
+    - r-cowplot =1.1.1=r41hc72bb7e_1
+    - r-dplyr =1.0.9=r41h7525677_0
+    - r-ggforce =0.3.4=r41h7525677_0
+    - r-ggplot2 =3.3.6=r41hc72bb7e_1
+    - r-gridextra =2.3=r41hc72bb7e_1004
+    - r-gtable =0.3.0=r41hc72bb7e_3
+    - r-knitr =1.40=r41hc72bb7e_1
+    - r-patchwork =1.1.2=r41hc72bb7e_1
+    - r-reshape2 =1.4.4=r41h7525677_2
+    - r-scales =1.2.1=r41hc72bb7e_1
+    - r-tibble =3.1.8=r41h06615bd_1
+    - r-tidyr =1.2.1=r41h7525677_1
+    - r-umap =0.2.9.0=r41h7525677_1
+    - r-rtsne =0.16=r41h37cf8d7_1
+    - r-magrittr =2.0.3=r41h06615bd_1
+    - r-rlang =1.1.0=r41h38f115c_0
+    - r-ggiraph=0.7.10=r41h03ef668_0
+
+test:
+  commands:
+    # You can put additional test commands to be run here.
+    - $R -e "library('DSPWorkflow')"           # [not win]
+    - "\"%R%\" -e \"library('DSPWorkflow')\""  # [win]
+
+about:
+  home: https://github.com/NIDAP-Community/DSPWorkflow
+  license: MIT
+  summary: A set of functions for analyzing RNA data from the spatial transcriptomics approach
+    Digital Spatial Profiling (Nanostring). The user provides read count data and annotations,
+    and the package outputs normalized differential expression of genes and further
+    visualizations and analysis based on user input. It can be run in a docker container
+    and in user-friendly web-based interactive notebooks (NIDAP, Palantir Foundry).
+  license_family: MIT
+  license_file:
+    - '{{ environ["PREFIX"] }}/lib/R/share/licenses/MIT'
+    - LICENSE

Dockerfile/Conda_container/Building_R_environment/DESCRIPTION

@@ -0,0 +1,41 @@
+Type: project
+Description: Digital-Spatial-Profiling v3.1.1 environment for DSP package.
+Repository:
+    CRAN,
+    biocsoftv314,
+    biocsoftv315,
+    biocanadatav313,
+    biocexpdatav314,
+    biocworkflowv314
+Depends:
+    backports (== 1.4.1),
+    Biobase (== 2.54.0),
+    BiocGenerics (== 0.40.0),
+    cowplot (== 1.1.1),
+    dplyr (== 1.0.9),
+    GeomxTools (== 3.1.1),
+    ggforce (== 0.3.4),
+    ggplot2 (== 3.3.6),
+    ggiraph (== 0.8.3),
+    dbplyr (== 2.2.1),
+    gridExtra (== 2.3),
+    gtable (== 0.3.0),
+    knitr (== 1.40),
+    NanoStringNCTools (== 1.4.0),
+    patchwork (== 1.1.2),
+    reshape2 (== 1.4.4),
+    Rmpfr (== 0.8-9),
+    Rtsne (== 0.16),
+    scales (== 1.2.1),
+    stats (== 4.1.3),
+    SpatialDecon (== 1.4.3),
+    tibble (== 3.1.8),
+    tidyr (== 1.2.1),
+    tidyverse (== 1.3.2),
+    umap (== 0.2.9.0),
+    pheatmap (== 1.0.12),
+    stringr
+Remotes:
+    url::https://bioconductor.org/packages/3.15/workflows/src/contrib/GeoMxWorkflows_1.2.0.tar.gz,
+    git::https://github.com/Nanostring-Biostats/SpatialOmicsOverlay.git,
+    git::https://github.com/Nanostring-Biostats/GeomxTools.git

Dockerfile/Conda_container/Building_R_environment/Generate_Renv.R

@@ -0,0 +1,44 @@
+# 9/13/2022 [email protected]
+# Creating renv environment now
+
+#############################################################
+
+print("Loading repos...")
+repos <- c(CRAN = "https://cloud.r-project.org", 
+           biocsoftv314 = "https://bioconductor.org/packages/3.14/bioc/",
+           biocsoftv315 = "https://bioconductor.org/packages/3.15/bioc/",
+           biocanadatav313 = "https://bioconductor.org/packages/3.14/data/annotation/",
+           biocexpdatav314 = "https://bioconductor.org/packages/3.14/data/experiment/",
+           biocworkflowv314 = "https://bioconductor.org/packages/3.14/workflows/")
+options(repos = repos)
+print("Repos loaded.")
+
+###############################################################
+
+print("Setting up plain R environment now...")
+
+if(!file.exists("DESCRIPTION")){
+
+  print("No existing DESCRIPTION file in current working directory:")
+  print(getwd())
+  print("Exiting Environment setup now.")
+
+  auto.snapshot <- getOption("renv.config.auto.snapshot")
+  options(renv.config.auto.snapshot = TRUE)
+  break
+
+}else{
+
+  print("Installing Packages from DESCRIPTION now...")
+
+  renv::install()
+
+  print("Packages installed.")
+
+
+  auto.snapshot <- getOption("renv.config.auto.snapshot")
+  options(renv.config.auto.snapshot = TRUE)
+
+}
+
+

Dockerfile/Conda_container/Building_R_environment/Initiate_Renv.R

@@ -0,0 +1,18 @@
+# 9/13/2022 [email protected]
+# Creating renv environment now
+
+# initiate <- FALSE
+if (initiate){
+
+  auto.snapshot <- getOption("renv.config.auto.snapshot")
+  options(renv.config.auto.snapshot = FALSE)
+
+  renv::settings$snapshot.type("implicit")
+  renv::init(bare = TRUE)
+  print("Environment Initiated")
+
+}else{
+
+  print("Environment Not Initiated")
+
+}

Dockerfile/Conda_container/Building_R_environment/Load_packages.R

@@ -0,0 +1,17 @@
+print("Loading and recording sessionInfo now...")
+
+# Load packages
+list_of_package <- scan("package_list.txt", what="", sep="\n")
+
+for (packages in list_of_package){
+  lapply(packages,
+         function(x) suppressMessages(library(x,
+                                              character.only = TRUE,
+                                              quietly=TRUE,
+                                              warn.conflicts = FALSE)))
+}
+
+
+sessionInfoName <- "sessionInfo.txt"
+writeLines(capture.output(sessionInfo()), sessionInfoName)
+print("SessionInfo printed.")

Dockerfile/Conda_container/Building_R_environment/package_list.txt

@@ -0,0 +1,6 @@
+GeomxTools
+NanoStringNCTools
+SpatialDecon
+tidyverse
+pheatmap
+stringr