Merge pull request #1281 from virtualcell/1280-publication-edit-form

publication edit form properly handle biomodel and mathmodel ref ids

.github/workflows/CI-full.yml

@@ -6,11 +6,11 @@ on:
     types: [published]
 
 env:
-  python-version: "3.9"
+  python-version: "3.10"
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
     - name: Get the VCell version from tags

docker/build/Dockerfile-batch-dev

@@ -1,4 +1,4 @@
-FROM ghcr.io/virtualcell/vcell-solvers:v0.8.1.2
+FROM ghcr.io/virtualcell/vcell-solvers:v0.8.1.3
 
 RUN apt-get -y update && \
     apt-get install -y  curl && \

docker/build/batch/JavaPostprocessor64

@@ -41,13 +41,13 @@ jvmprop="${jvmprop} -Dvcell.mongodb.database=${mongodb_database}"
 jvmprop="${jvmprop} -Dvcell.mongodb.host.internal=${mongodbhost_internal}"
 jvmprop="${jvmprop} -Dvcell.mongodb.port.internal=${mongodbport_internal}"
 
-jvmoptions="-XX:MaxRAMPercentage=100 -Xms64M -Xmx${java_mem_Xmx} -XX:+PrintFlagsFinal -XshowSettings:vm"
+#jvmoptions="-XX:MaxRAMPercentage=100 -Xms64M -Xmx${java_mem_Xmx} -XX:+PrintFlagsFinal -XshowSettings:vm"
+jvmoptions="-XX:MaxRAMPercentage=100 -Xms64M -Xmx${java_mem_Xmx}"
 
 arguments=$*
 
 echo "starting postprocessor"
 
-echo "expecting jre 1.8_144 or later for memory options"
 java -version
 
 java ${jvmoptions} ${jvmprop} ${postprocessor_mainclass} ${arguments}

docker/build/batch/JavaPreprocessor64

@@ -41,13 +41,13 @@ jvmprop="${jvmprop} -Dvcell.mongodb.database=${mongodb_database}"
 jvmprop="${jvmprop} -Dvcell.mongodb.host.internal=${mongodbhost_internal}"
 jvmprop="${jvmprop} -Dvcell.mongodb.port.internal=${mongodbport_internal}"
 
-jvmoptions="-XX:MaxRAMPercentage=80 -Xms64M -Xmx${java_mem_Xmx}  -XX:+PrintFlagsFinal -XshowSettings:vm"
+#jvmoptions="-XX:MaxRAMPercentage=80 -Xms64M -Xmx${java_mem_Xmx}  -XX:+PrintFlagsFinal -XshowSettings:vm"
+jvmoptions="-XX:MaxRAMPercentage=80 -Xms64M -Xmx${java_mem_Xmx}"
 
 arguments=$*
 
 echo "starting preprocessor"
 
-echo "expecting jre 1.8_144 or later for memory options"
 java -version
 
 java ${jvmoptions} ${jvmprop} ${preprocessor_mainclass} ${arguments}

docker/build/batch/JavaSimExe64

@@ -37,11 +37,11 @@ jvmprop="${jvmprop} -Dvcell.mongodb.database=${mongodb_database}"
 jvmprop="${jvmprop} -Dvcell.mongodb.host.internal=${mongodbhost_internal}"
 jvmprop="${jvmprop} -Dvcell.mongodb.port.internal=${mongodbport_internal}"
 
-jvmoptions="-XX:MaxRAMPercentage=80 -Xms64M -Xmx${java_mem_Xmx} -XX:+PrintFlagsFinal -XshowSettings:vm"
+#jvmoptions="-XX:MaxRAMPercentage=80 -Xms64M -Xmx${java_mem_Xmx} -XX:+PrintFlagsFinal -XshowSettings:vm"
+jvmoptions="-XX:MaxRAMPercentage=80 -Xms64M -Xmx${java_mem_Xmx}"
 
 echo "starting java solver"
 
-echo "expecting jre 1.8_144 or later for memory options"
 java -version
 
 arguments=$*

docker/build/build.sh

@@ -230,20 +230,19 @@ build_mongo() {
 }
 
 build_batch_singularity() {
+  # turn on logging of commands
+  set -x
 	if [ "$skip_singularity" == "false" ]; then
 		if [ -x "$(command -v singularity)" ]; then
 			build_batch_singularity_direct
 			if [[ $? -ne 0 ]]; then echo "failed to build singularity image using singularity commands"; exit 1; fi
 		else 
-			if [ -x "$(command -v vagrant)" ]; then
-				build_batch_singularity_vagrant
-				if [[ $? -ne 0 ]]; then echo "failed to build singularity image using singularity vagrant box"; exit 1; fi
-			else
-				echo "found neither singularity nor vagrant, cannot build singularity image"
-				exit 1
-			fi
-		fi
+      echo "singularity not found, cannot build singularity image"
+      exit 1
+    fi
 	fi
+	# turn off logging of commands
+	set +x
 }
 
 build_batch_singularity_direct() {
@@ -301,103 +300,16 @@ EOF
 	cd ..
 }
 
-build_batch_singularity_vagrant() {
-	echo ""
-	cmd="cd singularity-vm"
-	cd singularity-vm
-	echo ""
-	echo "CURRENT DIRECTORY IS $PWD"
-
-	#
-	# prepare Vagrant Singularity box for building the singularity image (bring up, install cert)
-	#
-	echo ""
-	echo "generating singularity image for vcell-batch and uploading to remote server for HTC cluster"
-	cmd="sudo scp $ssh_key [email protected]:/usr/local/deploy/registry_certs/domain.cert ."
-	echo $cmd
-	($cmd) || (echo "failed to download cert from vcell-docker private Docker registry")
-
-	echo ""
-	echo "vagrant up"
-	vagrant up
-	if [[ $? -ne 0 ]]; then echo "failed to bring vagrant up"; fi
-
-	echo ""
-	remote_cmd="sudo cp /vagrant/domain.cert /usr/local/share/ca-certificates/vcell-docker.cam.uchc.edu.crt"
-	echo "vagrant ssh -c \"$remote_cmd\""
-	vagrant ssh -c "$remote_cmd"
-	if [[ $? -ne 0 ]]; then echo "failed to upload domain.cert to trust the private Docker registry" && exit 1; fi
-
-	echo ""
-	remote_cmd="sudo update-ca-certificates"
-	echo "vagrant ssh -c \"$remote_cmd\""
-	vagrant ssh -c "$remote_cmd"
-	if [[ $? -ne 0 ]]; then
-	    echo "failed to update ca certificates in vagrant box" && exit 1
-	fi
-	#
-	# create temporary Singularity file which imports existing docker image from registry and adds a custom entrypoint
-	#
-	_vcell_batch_docker_name="${repo}/vcell-batch:${tag}"
-	_singularity_image_file="${_vcell_batch_docker_name//[\/:]/_}.img"
-	_singularity_file="Singularity_${_vcell_batch_docker_name//[\/:]/_}"
-
-cat <<EOF >$_singularity_file
-Bootstrap: docker
-From: $_vcell_batch_docker_name
-
-%runscript
-
-    exec /vcellscripts/entrypoint.sh "\$@"
-
-%labels
-
-AUTHOR jcschaff
-EOF
-
-	echo ""
-	echo "wrote Singularity file $_singularity_file"
-	cat $_singularity_file
-
-	#
-	# build the singularity image and place in singularity-vm directory
-	#
-	echo ""
-	remote_cmd="sudo singularity build /vagrant/$_singularity_image_file /vagrant/$_singularity_file"
-	echo "vagrant ssh -c \"$remote_cmd\""
-	vagrant ssh -c "$remote_cmd"
-	if [[ $? -ne 0 ]]; then echo "failed to build singularity image from vagrant" && exit 1; fi
-
-	#
-	# bring down Vagrant Singularity box
-	#
-	echo ""
-	echo "vagrant halt"
-	vagrant halt
-	if [[ $? -ne 0 ]]; then echo "failed to stop vagrant box"; fi
-
-	echo ""
-	echo "created Singularity image for vcell-bash ./$local_singularity_image_name locally (in ./singularity-vm folder), can be pushed to remote server during deploy"
-	echo ""
-	echo "cd .."
-	cd ..
-}
 
 build_opt_singularity() {
 	if [ "$skip_singularity" == "false" ]; then
 		if [ -x "$(command -v singularity)" ]; then
 			build_opt_singularity_direct
 			if [[ $? -ne 0 ]]; then echo "failed to build opt singularity image using singularity commands"; exit 1; fi
 		else
-#			if [ -x "$(command -v vagrant)" ]; then
-#				build_opt_singularity_vagrant
-#				if [[ $? -ne 0 ]]; then echo "failed to build opt singularity image using singularity vagrant box"; exit 1; fi
-#			else
-#				echo "found neither singularity nor vagrant, cannot build opt singularity image"
-				echo "singularity not found, cannot build opt singularity image (vagrant build not implemented)"
-				exit 1
-			fi
-#		fi
+      echo "singularity not found, cannot build opt singularity image"
+      exit 1
+    fi
 	fi
 }
 

pythonCopasiOpt/Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.9-slim-buster
+FROM python:3.10-slim-buster
 
 RUN apt -y update && apt -y upgrade &&  \
     apt-get install -y curl

pythonCopasiOpt/vcell-opt/pyproject.toml

@@ -6,7 +6,7 @@ authors = ["Jim Schaff <[email protected]>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "3.9.*"
+python = "^3.9"
 copasi-basico = "0.40"
 python-copasi = "4.37.264"
 jupyter = "^1.0.0"

pythonVtk/pyproject.toml

@@ -6,7 +6,7 @@ authors = ["Jim Schaff <[email protected]>"]
 readme = "README.md"
 
 [tool.poetry.dependencies]
-python = "3.9.*"
+python = "^3.9"
 vtk = "^9.2.6"
 thrift = "^0.16.0"
 

vcell-client/src/main/java/cbit/vcell/client/data/SimResultsViewer.java

@@ -387,7 +387,7 @@ private int getSelectedParamScanJobIndex(){
 	}
 	int selectedJobIndex = -1;
 	try {
-		selectedJobIndex = BeanUtils.coordinateToIndex(indices, bounds);
+		selectedJobIndex = BeanUtils.parameterScanCoordinateToJobIndex(indices, bounds);
 	} catch (RuntimeException exc) {
 		exc.printStackTrace();
 	}

vcell-client/src/main/java/cbit/vcell/client/desktop/biomodel/AnnotationsPanel.java

@@ -1116,6 +1116,9 @@ private boolean isEqual(MiriamResource aThis, MiriamResource aThat) {
 	@SuppressWarnings("unchecked")
 	private void initializeComboBoxURI() {
 //		jComboBoxURI = getJComboBoxURI();
+		if (selectedObject == null && vcMetaData == null){
+			return;
+		}
 		Identifiable entity = getIdentifiable(selectedObject);
 		defaultComboBoxModelURI.removeAllElements();
 		List<String> tooltips = new ArrayList<> ();

vcell-core/src/main/java/cbit/vcell/solver/MathOverrides.java

@@ -14,15 +14,13 @@
 import cbit.vcell.math.*;
 import cbit.vcell.model.common.VCellErrorMessages;
 import cbit.vcell.parser.*;
-import jscl.math.function.Exp;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.util.*;
 import org.vcell.util.Issue.IssueCategory;
 import org.vcell.util.IssueContext.ContextType;
 
 import java.util.*;
-import java.util.function.BiPredicate;
 import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -353,7 +351,7 @@ public Expression getActualExpression(String key, int index){
             for(int i = 0; i < names.length; i++){
                 bounds[i] = getConstantArraySpec(names[i]).getNumValues() - 1;
             }
-            int[] coordinates = BeanUtils.indexToCoordinate(index, bounds);
+            int[] coordinates = BeanUtils.jobIndexToScanParameterCoordinate(index, bounds);
             int localIndex = coordinates[java.util.Arrays.binarySearch(names, key)];
             return getConstantArraySpec(key).getConstants()[localIndex].getExpression();
         }