Merge pull request #1 from jhudsl/cansavvy/testing

Testing if ottr-reports work

.github/workflows/main.yml

@@ -1,35 +1,44 @@
 # Candace Savonen Mar 2022
 
 name: Testing ottr-reports
-on: [pull_request]
+on:
+  pull_request:
+    branches: [ main ]
 
 jobs:
-  run:
+
+  spell-check:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout Actions Repository
       uses: actions/checkout@v2
 
-
-    - name: Checkout
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 0
-
     - name: Check spelling
       uses: ./
       with:
-        check_type: "spelling"
+        check_type: spelling
         error_min: 3
 
+  urls-check:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Actions Repository
+      uses: actions/checkout@v2
+
     - name: Check URLs
       uses: ./
       with:
-        check_type: "urls"
+        check_type: urls
         error_min: 0
 
+  quiz-format:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout Actions Repository
+      uses: actions/checkout@v2
+
     - name: Check quiz formatting
       uses: ./
       with:
-        check_type: "quiz_format"
+        check_type: quiz_format
         error_min: 0

Dockerfile

@@ -1,5 +1,31 @@
-# Container image that runs your code
-FROM jhudsl/course_template:main
-COPY entrypoint.sh /entrypoint.sh
+FROM rocker/r-base
+LABEL maintainer="cansav09@gmail.com"
+
+# Install apt-getable packages to start
+RUN apt-get update && apt-get install -y --no-install-recommends apt-utils dialog
+RUN apt-get install -y --no-install-recommends \
+    libxt6 \
+    libpoppler-cpp-dev \
+    vim \
+    libglpk40 \
+    curl \
+    libxml2-dev \
+    libcurl4-openssl-dev \
+    libssl-dev
+
+# Needed R packages
+RUN Rscript -e  "options(warn = 2);install.packages( \
+    c('tidyverse', \
+      'rprojroot', \
+      'spelling', \
+      'ottrpal', \
+      'optparse'), \
+      repos = 'https://cloud.r-project.org/')"
+
+COPY scripts/* ./scripts/
 WORKDIR /github/workspace
-ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]
+
+ARG CHECK_TYPE
+ENV CHECK_TYPE=${INPUT_CHECK_TYPE}
+
+ENTRYPOINT ["echo", "$CHECK_TYPE", ">>", "check_type.txt", ";", "Rscript", "scripts/check_type.R"]

action.yml

@@ -0,0 +1,20 @@
+name: 'ottr-reports'
+author: "Candace Savonen"
+description: "Run OTTR checks for spelling, urls, and quiz formats"
+
+inputs:
+  check_type:
+    description: "There are three types of reports that can be done and specified: 'spelling', 'urls', or 'quiz_format'."
+    required: true
+    type: string
+  error_min:
+    description: "What number of errors should make this check fail?"
+    default: 0
+    type: number
+
+runs:
+  using: 'docker'
+  image: 'jhudsl/ottr-reports'
+  args:
+    - ${{ inputs.check_type }}
+    - ${{ inputs.error_min }}

quizzes/quiz_ch1.md

@@ -0,0 +1,53 @@
+
+{quiz, id: quiz_name_here, attempts: 10}
+
+## Template quiz
+
+Put any other instructions your quiz takers need to know here like: Choose the best answer.
+
+{choose-answers: 4}
+? First question to ask goes here. (Note- you need a question mark at end like this. Just one is required if using a question mark in your question field)?
+
+C) One correct answer here marked with a "C"
+C) A second correct answer here
+m) Mandatory incorrect answers have an "m"
+m) A second mandatory incorrect answer
+o) An optional incorrect answer here marked with an "o"
+o) A second optional incorrect answer here
+
+{choose-answers: 4}
+? Question example with just a question mark?
+
+C) One correct answer here marked with a "C"
+C) A second correct answer here
+m) Mandatory incorrect answers have an "m"
+m) A second mandatory incorrect answer
+o) An optional incorrect answer here marked with an "o"
+o) A second optional incorrect answer here
+
+{choose-answers: 4}
+? Second question to ask goes here?
+
+C) A correct answer here!
+m) Mandatory incorrect answers have an "m"
+m) A second mandatory incorrect answer
+o) An optional incorrect answer here marked with an "o"
+o) A second optional incorrect answer here
+
+
+{choose-answers: 4}
+? A more complicated example. Note the question mark at the end of the options! Which of the following are correct
+1. An option described
+2. A second option
+3. A third option
+4. A fourth option
+5. A fifth option ?
+
+C) All of the examples listed except 5
+C) All of the listed examples except 5
+m) 1, 3, and 5
+m) 1, 2, and 3
+o) All of the examples except 1 and 5
+o) All of the examples listed
+
+{/quiz}

resources/dictionary.txt

@@ -0,0 +1,22 @@
+AnVIL
+BIPOC
+Bloomberg
+Datatrail
+DataTrail
+dropdown
+GDSCN
+impactful
+ITCR
+itcrtraining
+ITN
+fyi
+Leanpub
+Markua
+mentorship
+NCI
+NHGRI
+UE
+UE5
+reproducibility
+underserved
+www

scripts/check_type.R

@@ -0,0 +1,12 @@
+#!/usr/bin/env Rscript
+# Written by Candace Savonen March 2022
+
+library(optparse)
+
+check_type <- readLines('check_type.txt')
+
+print(paste("Check type specified:", opt$check_type))
+
+if (check_type == "spelling") source("scripts/spell-check.R")
+if (check_type == "urls") source("scripts/url-check.R")
+if (check_type == "quiz_format") source("scripts/quiz-check.R")

scripts/quiz-check.R

@@ -0,0 +1,32 @@
+#!/usr/bin/env Rscript
+
+# Adapted for this jhudsl repository by Candace Savonen Mar 2022
+
+# Run spell check and save results
+
+library(magrittr)
+
+# Find .git root directory
+root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
+
+ottrpal::check_quizzes(quiz_dir = file.path(root_dir, 'quizzes'), write_report = TRUE, verbose = TRUE)
+
+if (file.exists("question_error_report.tsv")) {
+  quiz_errors <- readr::read_tsv("question_error_report.tsv")
+
+  # Print out how many quiz check errors
+  write(nrow(quiz_errors), stdout())
+} else {
+  quiz_errors <- data.frame()
+
+  # Print out how many quiz check errors
+  write("1", stdout())
+}
+
+if (nrow(quiz_errors) > 0) {
+  if (!dir.exists("resources")) {
+    dir.create("resources")
+    }
+  # Save question errors to file
+  readr::write_tsv(quiz_errors, file.path("resources", "question_error_report.tsv"))
+}