Merge pull request #1121 from virtualcell/biosimulators_upload_fixes

Biosimulators upload fixes

.github/workflows/ci_cd.yml

@@ -15,7 +15,7 @@ env:
 jobs:
   CI-Build:
     name: CI-build
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: ${{ github.event_name == 'push' }}
     steps:
       - uses: actions/checkout@v3
@@ -84,7 +84,7 @@ jobs:
         if: ${{ failure() }}
 
   CI-Test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         test-group: [Fast, MathGen_IT, SBML_IT, SEDML_SBML_IT, SEDML_VCML_IT, BSTS_IT]
@@ -156,7 +156,7 @@ jobs:
 
   CD:
     name: CD
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: ${{ github.event_name == 'release' }}
 
     steps:

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:17 as jre-build
+FROM eclipse-temurin:17-jammy as jre-build
 
 # Create a custom Java runtime
 RUN $JAVA_HOME/bin/jlink \
@@ -10,13 +10,12 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM python:3.9.7-slim
+FROM ubuntu:jammy
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
-
 ARG SIMULATOR_VERSION="7.5.0.11"
 ARG MAX_JAVA_MEM=0
 # Make sure you don't sap all of docker's memory when you set this.
@@ -47,8 +46,11 @@ LABEL \
     about.tags="rule-based modeling,kinetic modeling,dynamical simulation,systems biology,BNGL,SED-ML,COMBINE,OMEX" \
     maintainer="BioSimulators Team <[email protected]>"
 
-RUN apt-get -y update
-RUN apt-get install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu
+ENV DEBIAN_FRONTEND noninteractive
+RUN apt -y update && apt install -y software-properties-common
+RUN add-apt-repository ppa:deadsnakes/ppa -y
+RUN apt install -y --no-install-recommends curl python3.9-full python3-pip build-essential dnsutils \
+    apt-utils libfreetype6 fontconfig fonts-dejavu
 
 RUN mkdir -p /usr/local/app/vcell/lib && \
     mkdir -p /usr/local/app/vcell/simulation && \

vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsExecTest.java

@@ -173,8 +173,9 @@ public void testBiosimulationsProject(String testCaseProjectID) throws Exception
 					computedH5File.toAbsolutePath().toString()
 			});
 			command.start(new int[] { 0, 1 });
-			assertFalse(command.getStdoutString().contains("position"), "H5 files have significant differences: " +
-					command.getStdoutString().substring(0, 300));
+			String stdOutString = command.getStdoutString();
+			assertFalse(stdOutString.contains("position"), "H5 files have significant differences: " +
+					stdOutString.substring(0, Math.min(300, stdOutString.length())));
 
 		} catch (Exception | AssertionError e){
 			FAULT fault = this.determineFault(e);

vcell-core/pom.xml

@@ -656,7 +656,7 @@
 										<goal>wget</goal>
 									</goals>
 									<configuration>
-										<url>https://github.com/virtualcell/vcell-solvers/releases/download/v0.0.40/linux64.tgz</url>
+										<url>https://github.com/virtualcell/vcell-solvers/releases/download/v0.0.44-dev2/linux64.tgz</url>
 										<unpack>true</unpack>
 										<outputDirectory>${project.build.directory}/../../localsolvers/linux64</outputDirectory>
 									</configuration>