Use GitHub Actions

.Rbuildignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^check\.R$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check-plus.yaml

@@ -0,0 +1,95 @@
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check-plus
+
+jobs:
+  R-CMD-check-plus:
+    runs-on: macOS-latest
+
+    name: ${{ matrix.config.check }} ${{ matrix.config.file }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {check: "checkRawFiles", file: "gene_expression_files"}
+          - {check: "checkRawFiles", file: "gene_expression_matrices"}
+          - {check: "checkRawFiles", file: "fcs_control_files"}
+          - {check: "checkRawFiles", file: "fcs_sample_files"}
+          - {check: "checkRawFiles", file: "protocols"}
+          - {check: "checkStudyCompliance"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      ISR_login: ${{ secrets.ISR_login }}
+      ISR_pwd: ${{ secrets.ISR_pwd }}
+
+    steps:
+      - name: Set environment for branch
+        run: |
+          if [[ $GITHUB_REF == "refs/heads/master" ]]; then
+              echo "ISR_machine=www.immunespace.org" >> "$GITHUB_ENV"
+          else
+              echo "ISR_machine=test.immunespace.org" >> "$GITHUB_ENV"
+          fi
+        shell: bash
+
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: R CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Check
+        run: |
+          labkey.netrc.file <- ImmuneSpaceR:::.get_env_netrc()
+          labkey.url.base <- ImmuneSpaceR:::.get_env_url()
+          ImmuneSpaceMaintenance::check("{{ matrix.config.check }}", "{{ matrix.config.file }}")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ matrix.config.check }}-r${{ matrix.config.file }}-results
+          path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ImmuneSpaceMaintenance
 Title: Utility Package for ImmuneSpace Maintenance
-Version: 0.0.0.9000
+Version: 0.0.1
 Authors@R:
     person("ImmuneSpace Maintainer",
            email = "[email protected]",
@@ -15,11 +15,14 @@ Imports:
   Rlabkey,
   rjson,
   parallel,
-  httr
+  httr,
+  testthat
+Remotes:
+  RGLab/ImmuneSpaceR
 License: GPL-2
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
 Collate: 
     'ISM.R'
     'ISM-checkExpressionSet.R'
@@ -29,3 +32,4 @@ Collate:
     'ISM-checkStudyCompliance.R'
     'ISM-removeOrphanGEMs.R'
     'ISM-utils.R'
+    'check.R'

NAMESPACE

@@ -1,6 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ISM)
+export(check)
+import(ImmuneSpaceR)
 import(data.table)
 importFrom(R6,R6Class)
 importFrom(Rlabkey,labkey.executeSql)
@@ -14,3 +16,4 @@ importFrom(httr,http_type)
 importFrom(parallel,detectCores)
 importFrom(parallel,mclapply)
 importFrom(rjson,fromJSON)
+importFrom(testthat,capture_messages)

R/check.R

@@ -0,0 +1,64 @@
+#' @import ImmuneSpaceR data.table
+#' @importFrom testthat capture_messages
+#' @export
+check <- function(check_type, file_type, batch = "") {
+  con <- ISM$new("")
+
+  if (check_type == "checkStudyCompliance") {
+    msg <- testthat::capture_messages(
+      res <- con$checkStudyCompliance()
+    )
+
+    # Remove studies with known GEM issues that are not fixable at the moment
+    badGE <- c(
+      "SDY74",
+      "SDY314",
+      "SDY789",
+      "SDY820",
+      "SDY903",
+      "SDY1092",
+      "SDY1361"
+    )
+    res <- res[ !names(res) %in% badGE ]
+
+    if (length(res) > 0) {
+      dt <- as.data.table(do.call(rbind, res))
+      dt[, study := names(res)]
+      setcolorder(dt, c("study", "modules"))
+      print(dt[])
+
+      stop(
+        "\n",
+        length(res), " studies are not compliant: ",
+        paste(names(res), collapse = ", "),
+        "\n",
+        msg
+      )
+    }
+
+  } else if (check_type == "checkRawFiles" & file_type != "") {
+    msg <- testthat::capture_messages(
+      res <- con$checkRawFiles(file_type = file_type,
+                               mc.cores = 1, # > 1 cores generates errors
+                               batch = batch)
+    )
+
+    if (sum(!res$file_exists) > 0) {
+      res <- res[!res$file_exists, c("study_accession", "file_info_name")]
+      res <- res[ , list(files_missing = .N), by = study_accession]
+      print(res)
+      stop("Please download studies above!")
+    }
+    print(msg[1])
+
+  } else if (check_type == "checkPublicVsStudySchema"){
+    msg <- testthat::capture_messages(
+      res <- con$checkPublicVsStudySchema()
+    )
+    if (any(lengths(res)) > 0){
+      res <- res[ lengths(res) > 0 ]
+      print(res)
+      stop(msg)
+    }
+  }
+}

README.md

@@ -1,6 +1,19 @@
-# Initialize an ISM connection
+# ImmuneSpace Maintenance Tasks
 
-```R
+<!-- badges: start -->
+  [![R-CMD-check-plus](https://github.com/RGLab/ImmuneSpaceMaintenance/workflows/R-CMD-check-plus/badge.svg)](https://github.com/RGLab/ImmuneSpaceMaintenance/actions)
+  <!-- badges: end -->
+
+## Installation
+
+``` r
+# install.packages("remotes")
+remotes::install_github("ImmuneSpaceMaintenance")
+```
+
+## Initialize an `ISM` connection
+
+``` r
 library(ImmuneSpaceMaintenance)
 con <- ISM$new(study = "", onTest = TRUE)
 ```