Have URLs periodically checked (#673)

* Testing git on terminal

* Revert changes

* Initial pass at URL checker

* Test URL checker by running every 2 mint

* Fix syntax

* Syntax

* chatgpt?

* Fix spacing

* Remove "shell:bash"

* Please work

* Add spacing and indents

* Fix indentation

* Tryna find this indentation

* Add config option

* Add workflow dispatch button too

* temporarily have a pull_request trigger

* Add URL config

* Add a delete step

* Fix spec

* Update for branch problem

* Add issue creating infrastructure

* Add issue template

* Add steps:

* Declare docker

* get rid of dash

* Move if

* Add a needs argument

* Add an option for it branch exists

* missing paranthesis

* Make sure its checked out

* Try mapfile?

* Add a file

* Didn't fix template issue

* Put file link

* Fix link

* Fix less than or greater than

* Add in a spelling error to check if this works

* Add spelling errors to test part 2

* Try to fix

* Reverse order or < and =

* Change branch name

* Make sure branch is checked out

* Look for an issue

* Trying a different issue finder

* Gonna make my own issue finder

* Add find issue bits

* Add CRAN mirror

* Fix syntax

* Delete spelling errors

* Add a missing githubr::

* Install from github

* Fix GH_PAT

* Install from CRAN again

* Install from github but use devtools

* dependencies = TRUE

* Install from CRAN instead

* Test variables

* Retrigger a run for GHA

* Print out session info

* Actually what I did won't work!

* use cat() instead

* unlist

* I need cat() too

* Why is GHA not printing this out? Try message()

* Save session info to a file and archive upload it

* Shut off the other things so this step completes

* Comment out one more step

* Order dictionary.txt

* Add broken URL

* Make it so blank is the logic

* Just retrigger the check

* Try again

* fix true

* drop quotes

* Let's try this

* repo_name -> repo

* change per_page

* mysterious error

* Print out clues

* Update script

* Fix logic

* fix so runs once a month

---------

Co-authored-by: howardbaek <howardbaek.fh@gmail.com>
Co-authored-by: Howard Baek <50791792+howardbaek@users.noreply.github.com>

.github/ISSUE_TEMPLATE/url-error.md

@@ -0,0 +1,8 @@
+---
+title: Broken URLs found in the course!
+labels: url-error
+---
+URL's in this course were just checked and some broken URLs were found.
+
+**Number of errors:** {{ env.ERROR_NUM }}  
+**File where errors are:** [url checks file here]({{ env.FILE_URL }})

.github/workflows/check-url.yml

@@ -0,0 +1,107 @@
+name: Periodic URL Check
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  set-up:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+    outputs:
+      toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
+
+  url-check:
+    name: Check URLs
+    needs: set-up
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/base_ottr:main
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    # Delete the branch if this has been run before
+    - name: Delete branch locally and remotely
+      run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+    # Make the branch fresh
+    - name: Make the branch fresh
+      run: |
+        git config --global --add safe.directory $GITHUB_WORKSPACE
+        git config --global user.email "itcrtrainingnetwork@gmail.com"
+        git config --global user.name "jhudsl-robot"
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(cat check_reports/url_checks.tsv | wc -l)
+        error_num="$((error_num-1))"
+        echo "error_num=$error_num" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: Print out error variables
+      run: |
+        echo ${{ steps.check-report.outputs.error_url }}
+        echo ${{ steps.check-report.outputs.error_num }}
+
+    - name: Find issues
+      id: find-issue
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        echo "$GH_PAT"
+        echo "$GITHUB_REPOSITORY"
+        issue_exists=$(Rscript --vanilla scripts/find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
+        echo URL issue exists: $issue_exists
+        echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
+
+    - name: If too many URL errors, then make an issue
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
+      uses: JasonEtco/create-an-issue@v2
+      with:
+        filename: .github/ISSUE_TEMPLATE/url-error.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        FILE_URL: ${{ steps.check-report.outputs.error_url }}
+        ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+    - name: If no URL errors than delete the branch we made
+      if: ${{ steps.check-report.outputs.error_num < 1 }}
+      run: |
+        git config --system --add safe.directory "$GITHUB_WORKSPACE"
+        git push origin --delete preview-spell-error || echo "No branch to delete"

.github/workflows/pull_request.yml

@@ -39,7 +39,7 @@ jobs:
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name
+          git push --set-upstream origin $branch_name || echo echo branch exists remotely
         shell: bash
 
 

01-intro.Rmd

@@ -4,6 +4,7 @@ ottrpal::set_knitr_image_path()
 ```
 
 # Introduction
+https://ahuidshiushiufhs.com
 
 
 ## Motivation

OTTR_template.Rproj

@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: knitr
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+
+BuildType: Website

README.md

@@ -30,4 +30,3 @@ _This template and guide helps you_:
 - Check out our [course on using Leanpub](https://hutchdatascience.org/Using_Leanpub/index.html) for help publishing on this platform.
 - Please take a look at the [code of conduct](./code_of_conduct.md).
 - If you encounter any problems or have ideas for improvements to this template repository or this getting started guide, please [file an issue here](https://github.com/jhudsl/OTTR_Template/issues/new/choose)! Your feedback is very much appreciated.
-

config_automation.yml

@@ -12,6 +12,8 @@ spell-check: yes
 style-code: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
+# Should URLs be tested periodically?
+url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content

resources/dictionary.txt

@@ -1,33 +1,67 @@
 AnVIL
+Audiographer
+Audiography
+automagic
 BIPOC
 Bloomberg
 Bookdown
+chapt
 Coursera
+creativecommons
 css
 Datatrail
 DataTrail
+DISCOVERABLE
 Dockerfile
 Dockerhub
 dropdown
+enforceability
+faq
 favicon
+FirstName
+Funder
+fyi
 GDSCN
-GitHub
-Github
+Generis
 GH
+Github
+GitHub
+https
+ies
+iframe
+immunities
 impactful
 ITCR
 itcrtraining
 ITN
-fyi
+LastName
 Leanpub
+Licensor
+LICENSOR
 Markua
 mentorship
+MERCHANTABILITY
+Muschelli
 NCI
 NHGRI
+OTTR
 ottrpal
+ottrproject
 Pandoc
+png
+pre
+reproducibility
+rmarkdown
+RMarkdown
+Savonen
+sexualized
+socio
+synched
+tada
 UE
 UE5
-reproducibility
 underserved
+Videographer
+Videography
+WIPO	
 www

scripts/find_issue.R

@@ -0,0 +1,55 @@
+#!/usr/bin/env Rscript
+
+# Written by Candace Savonen Sept 2021
+
+if (!("optparse" %in% installed.packages())){
+  install.packages("optparse")
+}
+
+library(optparse)
+
+option_list <- list(
+  optparse::make_option(
+    c("--repo"),
+    type = "character",
+    default = NULL,
+    help = "GitHub repository name, e.g. jhudsl/OTTR_Template",
+  ),
+  optparse::make_option(
+    c("--git_pat"),
+    type = "character",
+    default = NULL,
+    help = "GitHub personal access token",
+  )
+)
+
+# Read the arguments passed
+opt_parser <- optparse::OptionParser(option_list = option_list)
+opt <- optparse::parse_args(opt_parser)
+
+repo <- opt$repo
+git_pat <- opt$git_pat
+
+if (!is.character(repo)) {
+  repo <- as.character(repo)
+}
+
+# Github api get
+result <- httr::GET(
+  paste0("https://api.github.com/repos/", repo, "/issues"),
+  httr::add_headers(Authorization = paste0("Bearer ", git_pat)),
+  httr::accept_json()
+)
+
+if (httr::status_code(result) != 200) {
+  httr::stop_for_status(result)
+}
+
+# Process and return results
+result_content <- httr::content(result, "text")
+result_list <- jsonlite::fromJSON(result_content)
+
+issue_exists <- length(grep('Broken URLs found in the course!', result_list$title))
+
+# Print out the result
+write(issue_exists, stdout())