Gracefully handle pre-1.3.0 AQ XMLs when NULISAseqAQ unavailable

.github/workflows/build-and-deploy.yml

@@ -35,7 +35,7 @@ jobs:
           build-args: |
             GH_PAT=${{ secrets.UTILITY_ACCESS_TOKEN }}
             SOURCE_BRANCH=${{ github.event.pull_request.base.ref || github.ref_name }}
-            NULISASEQAQ_BRANCH=${{ github.event.pull_request.base.ref || github.ref_name }}
+            NULISASEQAQ_BRANCH=${{ contains(github.repository, '_internal') && (github.event.pull_request.base.ref || github.ref_name) || '' }}
           cache-from: type=gha
           cache-to: type=gha,mode=max
 

Dockerfile

@@ -27,9 +27,15 @@
     Rscript -e "library(methods); if (!requireNamespace('PCAtools', quietly = TRUE)) stop('Package PCAtools not installed')" && \
     Rscript -e "library(methods); if (!requireNamespace('kableExtra', quietly = TRUE)) stop('Package kableExtra not installed')" && \
     Rscript -e "remotes::install_github('Alamar-Biosciences/ComplexHeatmap', ref='master', auth_token = '${GH_PAT}')" && \
-    Rscript -e "library(methods); if (!requireNamespace('ComplexHeatmap', quietly = TRUE)) stop('Package ComplexHeatmap not installed')" && \
-    Rscript -e "devtools::install_github('Alamar-Biosciences/NULISAseqAQ', ref='${NULISASEQAQ_BRANCH}', auth_token = '${GH_PAT}')" && \
-    Rscript -e "library(methods); if (!requireNamespace('NULISAseqAQ', quietly = TRUE)) stop('Package NULISAseqAQ not installed')"
+    Rscript -e "library(methods); if (!requireNamespace('ComplexHeatmap', quietly = TRUE)) stop('Package ComplexHeatmap not installed')"
+
+# Only install NULISAseqAQ if NULISASEQAQ_BRANCH is provided (internal repo only)
+RUN if [ -n "${NULISASEQAQ_BRANCH}" ]; then \
+      Rscript -e "devtools::install_github('Alamar-Biosciences/NULISAseqAQ', ref='${NULISASEQAQ_BRANCH}', auth_token = '${GH_PAT}')" && \
+      Rscript -e "library(methods); if (!requireNamespace('NULISAseqAQ', quietly = TRUE)) stop('Package NULISAseqAQ not installed')"; \
+    else \
+      echo "Skipping NULISAseqAQ installation (NULISASEQAQ_BRANCH not set)"; \
+    fi
 
 RUN mkdir -p ${HOME}/NULISAseqR
 COPY . ${HOME}/NULISAseqR/.
@@ -38,6 +44,6 @@
     Rscript -e "library(methods); if (!requireNamespace('NULISAseqR', quietly = TRUE)) stop('Package NULISAseqR not installed')"
 
 EXPOSE 8000
 ENV PATH "${HOME}:$PATH"
 
 CMD ["bash"]

R/readNULISAseq.R

@@ -1328,10 +1328,11 @@ loadNULISAseq <- function(file,
           }
         }
       } else {
-        # Fallback not supported (XML version < 1.3) - NULISAseqAQ is required
-        stop("This XML file contains absolute quantification (AQ) data but has version < 1.3.0. ",
-             "The NULISAseqAQ package is required to process pre-1.3.0 AQ XML files, but it is not installed. ",
-             "writeUpdatedXML does not support pre-1.3.0 AQ XML files. Use NAS or contact Alamar support for help.")
+        # Fallback not supported (XML version < 1.3) - warn and treat as RQ
+        warning("This XML file contains AQ metadata but XML version < 1.3.0 and NULISAseqAQ is not installed. ",
+                "AQ data will not be available. Processing as RQ (relative quantification) instead.")
+        # Set AbsAssay to FALSE so downstream code treats this as RQ-only
+        AbsAssay <- FALSE
       }
     }
   }

inst/rmarkdown/templates/nulisaseq/skeleton/skeleton.Rmd

@@ -640,7 +640,7 @@ if(is.null(params$dataRuns)){
     )
   })
   for(i in 1:numFiles){
-    AbsData <- "Abs" %in% names(runs[[i]]$ExecutionDetails)
+    AbsData <- runs[[i]]$AbsAssay
     Tcriteria <- QCTargetCriteria(AQ=AbsData, advancedQC=params$advancedQC)
     AQSC_SC <- ifelse(AbsData, "AQSC", "SC") 
     AQSC_SC_full <- ifelse(AbsData, "AQ sample controls (AQSC)", "Sample controls (SC)")

tests/testthat/test-writeUpdatedXML.R

@@ -28,7 +28,7 @@ test_that("Test that we can turn a pre-1.3.0 AQ XML into a 1.3.0 AQ XML that inc
   })
 })
 
-test_that("Pre-1.3.0 AQ XML throws error when NULISAseqAQ is not available", {
+test_that("Pre-1.3.0 AQ XML warns and loads as RQ when NULISAseqAQ is not available", {
   # Mock NULISAseqAQ as unavailable
   local_mocked_bindings(
     requireNamespace = function(pkg, ...) {
@@ -41,6 +41,10 @@ test_that("Pre-1.3.0 AQ XML throws error when NULISAseqAQ is not available", {
   test_path <- paste0(testthat::test_path(), "./../inst/rmarkdown/templates/nulisaseq/skeleton/")
   input1 <- paste0(test_path, "Analysis_INF250_Lot4_AQ_LC_R3_20241229.xml")
 
-  # Should throw an error - conversion should not occur without NULISAseqAQ for pre-1.3 AQ XML
-  expect_error(loadNULISAseq(input1))
+  # Should warn but load successfully as RQ
+  expect_warning(data <- loadNULISAseq(input1), "AQ metadata")
+
+  # Verify it loaded successfully as RQ
+  expect_false(is.null(data$Data))
+  expect_true(is.null(data$AQ) || is.null(data$AQ$Data_AQ_aM))
 })