Merge pull request #7 from CRI-iAtlas/api_update

Api update
CRI-iAtlas · Aug 9, 2021 · 311cc00 · 311cc00
2 parents 40c0510 + 4af23fb
commit 311cc00
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,3 @@
-# NOTE: This workflow is overkill for most R packages
-# check-standard.yaml is likely a better choice
-# usethis::use_github_action("check-standard") will install it.
-#
-# 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:
@@ -26,74 +20,64 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: ubuntu-18.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/bionic/latest"}
+          - {os: windows-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
 
     env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@v1
-        id: install-r
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       - uses: r-lib/actions/setup-pandoc@v1
 
-      - name: Install pak and query dependencies
+      - name: Query dependencies
         run: |
-          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
-          saveRDS(pak::pkg_deps("local::.", dependencies = TRUE), ".github/r-depends.rds")
+          install.packages('remotes', repos = "http://cran.us.r-project.org")
+          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: Restore R package cache
         uses: actions/cache@v2
         with:
-          path: |
-            ${{ env.R_LIBS_USER }}
-            !${{ env.R_LIBS_USER }}/pak
-          key: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
-          restore-keys: ${{ matrix.config.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+          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 system dependencies
         if: runner.os == 'Linux'
         run: |
-          pak::local_system_requirements(execute = TRUE)
-          pak::pkg_system_requirements("rcmdcheck", execute = TRUE)
-        shell: Rscript {0}
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
 
       - name: Install dependencies
         run: |
-          pak::local_install_dev_deps(upgrade = TRUE)
-          pak::pkg_install("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Session info
-        run: |
-          options(width = 100)
-          pkgs <- installed.packages()[, "Package"]
-          sessioninfo::session_info(pkgs, include_base = TRUE)
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
       - name: Check
         env:
-          _R_CHECK_CRAN_INCOMING_: false
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
         run: |
           options(crayon.enabled = TRUE)
           rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: iatlas.modules2
 Title: iAatlas Modules2
 Type: Package
-Version: 0.2.2
+Version: 0.2.3
 Date: 2021-1-30
 Author: Andrew Lamb
 Maintainer: Andrew Lamb <[email protected]>

diff --git a/R/cohort_group_selection_server.R b/R/cohort_group_selection_server.R
@@ -144,7 +144,7 @@ cohort_group_selection_server <- function(
         } else {
           group_object$group_display <- group_choice() %>%
             iatlas.api.client::query_tags(tags = .) %>%
-            dplyr::pull("short_display")
+            dplyr::pull("tag_short_display")
           group_object$group_type <- "tag"
         }
 

diff --git a/R/driver_associations_univariate_server.R b/R/driver_associations_univariate_server.R
@@ -42,7 +42,7 @@ univariate_driver_server <- function(id, cohort_obj) {
           cohorts = cohort_obj()$dataset,
           parent_tags = cohort_obj()$group_name
         ) %>%
-          dplyr::pull("name")
+          dplyr::pull("tag_name")
       })
 
       volcano_plot_tbl <- shiny::reactive({

diff --git a/R/elements_functions.R b/R/elements_functions.R
@@ -4,5 +4,5 @@ build_tag_filter_list <- function(parent_tag_name, dataset){
     cohorts = dataset,
     parent_tags = parent_tag_name
   ) %>%
-    dplyr::pull("name")
+    dplyr::pull("tag_name")
 }