Merge branch 'main' into dev

.github/workflows/comprehensive.yml

@@ -45,7 +45,7 @@ jobs:
           - {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: '3.6.3'}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: r-lib/actions/setup-r@v2-branch
         with:
           r-version: ${{ matrix.config.r }}
@@ -76,7 +76,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Deploy main dispatch
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v3
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           repository: abbvie-internal/OmicNavigatorCD

.github/workflows/pin-app.yml

@@ -14,7 +14,7 @@ jobs:
   dev:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
 

.github/workflows/quick.yml

@@ -22,7 +22,7 @@ jobs:
   quick:
     runs-on: ubuntu-22.04
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup r2u
       run: sudo bash scripts/setup-r2u.sh
     - name: Install R packages
@@ -57,7 +57,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Deploy dev dispatch
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v3
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           repository: abbvie-internal/OmicNavigatorCD

.github/workflows/release.yml

@@ -11,7 +11,7 @@ jobs:
     steps:
     - name: Extract package version from tag reference
       run: echo "version=${GITHUB_REF#refs/tags/v}" >> $GITHUB_ENV
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Setup r2u
       run: sudo bash scripts/setup-r2u.sh
     - name: Install R packages
@@ -104,7 +104,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Deploy release dispatch
-        uses: peter-evans/repository-dispatch@v1
+        uses: peter-evans/repository-dispatch@v3
         with:
           token: ${{ secrets.REPO_ACCESS_TOKEN }}
           repository: abbvie-internal/OmicNavigatorCD

DESCRIPTION

@@ -11,7 +11,7 @@ Description:
   deployed online to be explored by collaborators. The dashboard includes
   'sortable' tables, interactive plots including network visualization, and
   fine-grained filtering based on statistical significance.
-Version: 1.13.17
+Version: 1.13.20
 Authors@R: c(
   person("Terrence", "Ernst", role = c("aut"),
          comment = "Web application"),

NEWS.md

@@ -1,3 +1,17 @@
+# 1.13.20
+
+* The release tarball includes version 1.9.3 of the web app
+
+* Fix bug in `importStudy()` that resulted in mapping table not being imported.
+
+# 1.13.19
+
+* The release tarball includes version 1.9.2 of the web app
+
+# 1.13.18
+
+* The release tarball includes version 1.9.1 of the web app
+
 # 1.13.17
 
 * The release tarball includes version 1.9.0 of the web app

R/import.R

@@ -72,6 +72,7 @@ importStudy <- function(study, libraries = NULL) {
     plots = getPlots(study, quiet = TRUE, libraries = libraries),
     barcodes = getBarcodes(study, quiet = TRUE, libraries = libraries),
     reports = reports,
+    mapping = getMapping(study, quiet = TRUE, libraries = libraries),
     resultsLinkouts = getResultsLinkouts(study, quiet = TRUE, libraries = libraries),
     enrichmentsLinkouts = getEnrichmentsLinkouts(study, quiet = TRUE, libraries = libraries),
     metaFeaturesLinkouts = getMetaFeaturesLinkouts(study, quiet = TRUE, libraries = libraries),

R/zzz.R

@@ -10,7 +10,7 @@ OmicNavigatorPrefix <- "ONstudy"
 
 # The R package is meant to be used with a specific version of the app. If a
 # user has an older or newer version installed, send a warning.
-versionAppPinned <- "1.9.0"
+versionAppPinned <- "1.9.3"
 
 # The extra packages required to run the app
 appPackages <- c(