revise (#1)

Modify based on reviewers' suggestions, 1. Add tutorial 2. Optimize performance of the web interface by adding cache to database and figures 3. Optimize the database filter function 4. Add a docker image for offline use
rujinlong · Dec 18, 2022 · 6daa7af · 6daa7af
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diff --git a/.github/workflows/docker_build_push.yml b/.github/workflows/docker_build_push.yml
@@ -0,0 +1,45 @@
+name: DockerHub build and push
+
+on:
+  push:
+    tags:
+      - 'd*'
+      - 'v*'
+
+jobs:
+  push_to_registry:
+    name: Push Docker image to Docker Hub
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - dockerfile: ./Dockerfile
+            image: jinlongru/deepsmirud_web
+    permissions:
+      contents: read
+      packages: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v3
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          username: ${{ secrets.DOCKER_USER }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ matrix.image }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: "."
+          file: ${{ matrix.dockerfile }}
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
diff --git a/.github/workflows/shinyapps_io.yml b/.github/workflows/shinyapps_io.yml
@@ -0,0 +1,62 @@
+name: deploy shinyapps.io
+
+on:
+  push:
+    tags:
+      - 'shiny*'
+
+jobs:
+  shinyapps:
+
+    runs-on: ubuntu-latest
+    timeout-minutes: 90
+
+    env:
+      RENV_PATHS_ROOT: ~/.local/share/renv
+      SHINY_ACCOUNT: ${{ secrets.SHINY_ACCOUNT }}
+      SHINY_TOKEN: ${{ secrets.SHINY_TOKEN }}
+      SHINY_SECRET: ${{ secrets.SHINY_SECRET }}
+
+    steps:
+
+      # Check out code
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: R setup
+        uses: r-lib/actions/setup-r@v2
+        with:
+          # don't reinstall R
+          install-r: false
+          # use RStudio's CRAN mirror with precompiled binaries
+          use-public-rspm: true
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update -y
+          sudo apt-get install -y libcurl4-openssl-dev
+          sudo apt-get install -y libssl-dev
+          sudo apt-get install -y libgsl-dev
+          sudo apt-get install -y libclang-dev
+    
+      - name: Cache packages
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-renv-
+      
+      - name: Restore packages
+        shell: Rscript {0}
+        run: |
+          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
+          renv::restore()
+        
+      - name: Deploy to shinyapps.io
+        run: |
+          install.packages("rsconnect")
+          rsconnect::setAccountInfo(name="${{secrets.SHINY_ACC_NAME}}", token="${{secrets.TOKEN}}", secret="${{secrets.SECRET}}")
+          rsconnect::deployApp(appName = 'viroprofiler-viewer')
+        shell: Rscript {0}
+
diff --git a/Dockerfile b/Dockerfile
@@ -1,6 +1,27 @@
-FROM --platform=linux/amd64 rocker/tidyverse:4.2.0
+FROM rocker/shiny-verse:4.2
 
 LABEL author="Jinlong Ru"
 
-RUN R -e 'install.packages(c("remotes", "argparser"), repos="https://cloud.r-project.org/")'
-RUN R -e 'remotes::install_github("Jasonlinchina/RCSM")'
+# copy the app to the image
+ADD app /srv/shiny-server/
+COPY renv* /srv/shiny-server/
+
+WORKDIR /srv/shiny-server/
+
+RUN apt-get update && apt-get install -y \
+    libcurl4-gnutls-dev \
+    libssl-dev \
+    libgsl-dev \
+    libclang-dev
+
+# install R packages using renv
+RUN R -e "install.packages('renv')"
+RUN R -e "install.packages('Matrix', version='1.5-1')"
+RUN R -e "renv::install()"
+
+
+# select port
+EXPOSE 3838
+
+# run app
+CMD ["R", "-e", "shiny::runApp('/srv/shiny-server', host = '0.0.0.0', port = 3838)"]
diff --git a/R/data4heatmap.R b/R/data4heatmap.R
@@ -1,6 +1,9 @@
+library(here)
 
+prj_path <- here()
+dpath <- here(prj_path, "data")
 load(here(prj_path, "data/row_col_order.Rdata"))
-cmap_g1 <- readRDS(here(dpath, "GSEAweight1Score.rds"))
+cmap_g1 <- readRDS(here(dpath, "main/GSEAweight1Score.rds"))
 cmap_rst <- cmap_g1
 
 ftitle <- "GSEAweight1"

diff --git a/README.md b/README.md
@@ -4,23 +4,52 @@
 <!-- badges: start -->
 <!-- badges: end -->
 
-The goal of DeepsmirUD_web is to ...
+Source code of the web interface of [DeepsmirUD](https://github.com/2003100127/deepsmirud).
 
-## Installation
+## How to run
 
-You can install the development version of DeepsmirUD_web from [GitHub](https://github.com/rujinlong/DeepsmirUD_web) with:
+Due to the computation resource limitation of the cloud service, it is
+highly recommened to run DeepsmirUD_web on your local computer. You
+could use one of following approaches,
 
-``` r
-# install.packages("devtools")
-devtools::install_github("rujinlong/DeepsmirUD_web")
+### Using Docker image (recommended)
+
+``` sh
+docker run --rm jinlongru/deepsmirud_web
+
+# if the default port 3838 is occupied, you could set a new port by adding `-p` option
+docker run --rm -p 3838:3838 jinlongru/deepsmirud_web
+```
+
+Then open your browser and visit `http://localhost:3838/` to use the DeepsmirUD database.
+
+### Run from GitHub
+
+You need to manually install dependent packages in `renv.lock` file before running the following command.
+
+``` sh
+# You need to install dependent packages manually
+R -e "shiny::runGitHub('DeepsmirUD_web/app', 'rujinlong', subdir = 'app')"
 ```
 
-## Example
+### Run a cloned version
 
-This is a basic example which shows you how to solve a common problem:
+You need to manually install dependent packages in `renv.lock` file before running the following command.
 
-``` r
-library(DeepsmirUD_web)
-## basic example code
+``` sh
+git clone https://github.com/rujinlong/DeepsmirUD_web.git
+R -e "shiny::runApp('DeepsmirUD_web/app')"
 ```
 
+### Online version
+
+[https://rujinlong.shinyapps.io/DeepsmirUD/](https://rujinlong.shinyapps.io/DeepsmirUD/)
+
+Please note that the online version is not stable and may not work properly.
+
+## Citation
+
+If you use DeepsmirUD in your research, please cite the following paper:
+
+> Sun, Jianfeng, Jinlong Ru, Zihao Chen, Fei Qi, Lorenzo Ramos-Mucci, Suyuan Chen, Adam P. Cribbs, Li Deng, and Xia Wang. "DeepsmirUD: Precise prediction of regulatory effects on miRNA expression mediated by small molecular compounds using competing deep learning frameworks." bioRxiv (2022).
+