ci to update all literature monthly

dashnowlab · Dec 30, 2024 · b65663c · b65663c
1 parent 61a08d9
commit b65663c
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Showing 3 changed files with 50 additions and 9 deletions.
diff --git a/.github/workflows/update-loci.yaml b/.github/workflows/update-loci.yaml
@@ -2,6 +2,7 @@ name: Update data
 
 permissions:
   contents: write
+  pull-requests: write
 
 on:
   pull_request:
@@ -11,6 +12,8 @@ on:
       - "scripts/**"
       - "workflow/**"
       - ".github/workflows/**"
+  schedule:
+    - cron: "45 2 1 * *" # Run monthly at 2:45 am
   workflow_dispatch:
 
 jobs:
@@ -41,18 +44,38 @@ jobs:
           conda info
 
       - name: Check loci and update bed files (short)
-        #if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'}}
+        if: ${{ github.event_name == 'pull_request'}}
         run: snakemake --config stages="skip-refs"
 
+      # Enable this step to open an SSH session for debugging
+      # - name: SSH debug
+      #   uses: mxschmitt/action-tmate@v3
+
+      - name: Find new literature (intermediate)
+        if: ${{ github.event_name == 'workflow_dispatch' }}
+        run: |
+          conda init
+          source /home/runner/.bashrc
+          conda activate strchive
+          snakemake --config stages="new-refs"
+
+      - name: Update all literature (long)
+        if: ${{ github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'}}
+        run: |
+          conda init
+          source /home/runner/.bashrc
+          conda activate strchive
+          snakemake
+
       - name: Open pull request with updated files
-        if: ${{ !(github.event_name == 'pull_request') }}
+        if: ${{ !(github.event_name == 'pull_request') || github.event_name == 'schedule' }}
         uses: peter-evans/create-pull-request@v7
         with:
           branch: update-data
           title: Update data
 
       - name: Commit updated files to current pull request
-        if: ${{ github.event_name == 'pull_request' }}
+        if: ${{ github.event_name == 'pull_request' || github.event_name == 'schedule' }}
         uses: stefanzweifel/git-auto-commit-action@v5
         with:
-          commit_message: Update data
+          commit_message: Update data
diff --git a/scripts/environment.yml b/scripts/environment.yml
@@ -13,7 +13,9 @@ dependencies:
   - jsbeautifier
   - statsmodels
   - plotly
+  - zlib
   - r-essentials
+  - r-base
   - r-jsonlite
   - r-dplyr
   - r-rentrez

diff --git a/scripts/get-literature.R b/scripts/get-literature.R
@@ -4,14 +4,26 @@
 # More useful error messages
 options(error=traceback)
 
+## Set default CRAN mirror
+local({r <- getOption("repos")
+       r["CRAN"] <- "https://cran.r-project.org"
+       options(repos=r)
+})
+
 # Install biomaRt if not already installed
-if (!requireNamespace("biomaRt", quietly = TRUE)) {
-  if (!requireNamespace("BiocManager", quietly = TRUE)) {
-    install.packages("BiocManager")
+tryCatch({
+  if (!requireNamespace("biomaRt", quietly = TRUE)) {
+    if (!requireNamespace("BiocManager", quietly = TRUE)) {
+      install.packages("BiocManager", ask = FALSE, update = FALSE)
+    }
+    BiocManager::install("biomaRt", ask = FALSE)
   }
-  BiocManager::install("biomaRt")
-}
+}, error = function(e) {
+  cat("Error installing biomaRt package.\n", file=stderr())
+  quit(status = 1)
+})
 
+tryCatch({
 suppressPackageStartupMessages({
   library(jsonlite)
   library(dplyr)
@@ -21,6 +33,10 @@ suppressPackageStartupMessages({
   library(stringr)
   library(purrr)
 })
+}, error = function(e) {
+  cat("Error loading required packages.\n", file=stderr())
+  quit(status = 1)
+})
 
 ### Data Setup
 args <- commandArgs(trailingOnly = TRUE)