Merge pull request #1164 from mcneilco/ACAS-774

ACAS-774: Update Dockerfile to CentOS Stream 9 and Python 3.11

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/centos/centos:stream8
+FROM quay.io/centos/centos:stream9
 
 ARG BUILDTIME=1970-01-01T00:00:00Z
 ENV ACAS_CLIENT_ABOUT_ACAS_BUILDTIME=${BUILDTIME}
@@ -9,11 +9,6 @@ ENV ACAS_CLIENT_ABOUT_ACAS_VERSION=${VERSION}
 ARG REVISION=UNKNOWN
 ENV ACAS_CLIENT_ABOUT_ACAS_REVISION=${REVISION}
 
-# EOL for Centos8-Stream workaround 
-RUN sed -i 's/^mirrorlist=/#&/' /etc/yum.repos.d/*.repo && \
-    sed -i 's/^#baseurl=/baseurl=/' /etc/yum.repos.d/*.repo && \ 
-    sed -i 's/mirror.centos.org/vault.centos.org/' /etc/yum.repos.d/*.repo 
-
 # Update
 RUN \
   dnf update -y && \
@@ -26,11 +21,10 @@ RUN \
   dnf clean all
 
 #Install python dependencies
-RUN   dnf install -y python36 python3-pip
-RUN   alternatives --set python /usr/bin/python3
-RUN   alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
-RUN		pip install argparse requests
-RUN   dnf install -y initscripts python3-psycopg2
+RUN   dnf install -y python311 python3.11-pip initscripts
+RUN   alternatives --install /usr/bin/python python /usr/bin/python3.11 1
+RUN   alternatives --install /usr/bin/pip pip /usr/bin/pip3.11 1
+RUN		pip install argparse requests psycopg2-binary
 
 # node
 ENV NPM_CONFIG_LOGLEVEL warn

bin/setenv.sh

@@ -1,7 +1,14 @@
 # Example:
 #export LD_LIBRARY_PATH=/usr/lib/oracle/11.2/client64/lib:$LD_LIBRARY_PATH
-LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server/
-PATH=/usr/pgsql-9.4/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ARCH=$(uname -m)
+
+if [ "$ARCH" = "x86_64" ]; then
+    LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/amd64:/usr/lib/jvm/java-1.8.0/jre/lib/amd64/server/:/R-4.4.0/lib
+elif [ "$ARCH" = "aarch64" ]; then
+    LD_LIBRARY_PATH=/usr/lib/jvm/java-1.8.0/jre/lib/aarch64:/usr/lib/jvm/java-1.8.0/jre/lib/aarch64/server/:/R-4.4.0/lib
+fi
+
+export LD_LIBRARY_PATH
+PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
 R_LIBS=/home/runner/build/r_libs
 JAVA_HOME=/usr/lib/jvm/java-1.8.0
-if [ -e  "/opt/rh/rh-python36/enable" ]; then source /opt/rh/rh-python36/enable; fi;

modules/GenericDataParser/src/server/generic_data_parser.R

@@ -2018,7 +2018,7 @@ getExperimentByNameCheck <- function(experimentName, protocol, configList, dupli
     protocolOfExperiment <- getProtocolByCodeName(experimentList[[1]]$protocol$codeName)
 
 
-    if (is.na(protocol) || protocolOfExperiment$id != protocol$id) {
+    if (identical(protocol, NA) || protocolOfExperiment$id != protocol$id) {
       if (duplicateNamesAllowed) {
         experiment <- NA
       } else {
@@ -3580,7 +3580,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL,
   protocol <- NULL
   if (!useExisting) {
     protocol <- getProtocolByNameAndFormat(protocolName = validatedMetaData[,paste0(racas::applicationSettings$client.protocol.label," Name")][1], configList, inputFormat)
-    newProtocol <- is.na(protocol[[1]])
+    newProtocol <- identical(protocol[[1]], NA)
     if (!newProtocol) {
       validatedMetaData[,paste0(racas::applicationSettings$client.protocol.label," Name")][1] <- getPreferredProtocolName(protocol, validatedMetaData[,paste0(racas::applicationSettings$client.protocol.label," Name")][1])
     }
@@ -3741,7 +3741,7 @@ runMain <- function(pathToGenericDataFormatExcelFile, reportFilePath=NULL,
   }
 
   # Checks if we have a new experiment
-  newExperiment <- class(experiment[[1]])!="list" && is.na(experiment[[1]])
+  newExperiment <- class(experiment[[1]])!="list" && identical(experiment[[1]], NA)
 
   # If there are errors, do not allow an upload (yes, this is needed a second time)
   errorFree <- length(messenger()$errors)==0
@@ -4641,6 +4641,9 @@ getSubjectAndTreatmentData <- function (precise, genericDataFileDataFrame, calcu
 validateSubjectData <- function(subjectData, dryRun) {
   # Validates Subject Data
   # For now, just passes information to validateValue Kinds
+  if (is.null(subjectData)) {
+    return(NULL)
+  }
   uniqueDF <- unique(subjectData[, c("Class", "valueKind")])
   uniqueDF <- uniqueDF[!(uniqueDF$valueKind %in% c('flag cause', 'flag observation', 'flag status')), ]
   validateValueKinds(uniqueDF$valueKind, uniqueDF$Class, dryRun, reserved = NULL)