Series of changes to get BSTS to approve of 7.7 Container

.github/workflows/bsts_local.yml

@@ -28,12 +28,12 @@ jobs:
 
       - name: Install Perl # for BioNetGen
         run: |
-          sudo apt-get update -y
-          sudo apt-get install -y --no-install-recommends perl
+          sudo apt update -y
+          sudo apt install -y --no-install-recommends perl
 
       - name: Install XPP
         run: |
-          sudo apt-get install -y --no-install-recommends xppaut
+          sudo apt install -y --no-install-recommends xppaut
 
       - name: Install Go (for Singularity)
         uses: actions/setup-go@v3
@@ -47,7 +47,7 @@ jobs:
           OS: linux
           ARCH: amd64
         run: |
-          sudo apt-get install -y --no-install-recommends \
+          sudo apt install -y --no-install-recommends \
             build-essential \
             libseccomp-dev \
             pkg-config \

.github/workflows/ci_cd.yml

@@ -107,7 +107,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Install hdf5 tools needed for testing
-        run: sudo apt-get -y update && sudo apt-get -y install hdf5-tools
+        run: sudo apt -y update && sudo apt -y install hdf5-tools
 
       - name: Set up Python
         uses: actions/setup-python@v5

docker/build/Dockerfile-admin-dev

@@ -10,17 +10,17 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM debian:buster-slim
+FROM debian:bullseye-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17
-RUN apt-get -y update && \
-    apt-get install -y curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu openssh-client && \
+RUN apt -y update && \
+    apt install -y curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu openssh-client && \
     mkdir -p /usr/local/app/lib 
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-api-dev

@@ -17,11 +17,11 @@ COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
 
-RUN apt-get -y update && \
-    apt-get install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu && \
+RUN apt -y update && \
+    apt install -y --no-install-recommends curl dnsutils apt-utils libfreetype6 fontconfig fonts-dejavu && \
     mkdir -p /usr/local/app/lib 
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-batch-dev

@@ -1,11 +1,11 @@
 FROM ghcr.io/virtualcell/vcell-solvers:v0.8.2
 
-RUN apt-get -y update && \
-    apt-get install -y  curl && \
-	apt-get install -y wget gdebi-core apt-utils libfreetype6 fontconfig fonts-dejavu && \
+RUN apt -y update && \
+    apt install -y  curl && \
+	apt install -y wget gdebi-core apt-utils libfreetype6 fontconfig fonts-dejavu && \
     pip3 install thrift
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-clientgen-dev

@@ -10,14 +10,14 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM debian:buster-slim
+FROM debian:bullseye-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install wget apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install wget apt-utils libfreetype6 fontconfig fonts-dejavu
 
 RUN mkdir /installer && cd /installer && \
     wget --quiet -O install4j_unix_10_0_5.tar.gz \

docker/build/Dockerfile-data-dev

@@ -17,14 +17,14 @@ COPY --from=jre-build /javaruntime $JAVA_HOME
 
 # now we have Java 17 and Python 3.9
 
-RUN apt-get -y update && \
-	apt-get -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu && \
+RUN apt -y update && \
+	apt -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu && \
     mkdir -p /usr/local/app
 
 RUN python3 -m pip install poetry &&  poetry config cache-dir "/poetry/.cache"
 ENV PATH="/root/.poetry/bin:/root/.local/bin:$PATH"
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-db-dev

@@ -10,16 +10,16 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM debian:buster-slim
+FROM debian:bullseye-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install screen apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install screen apt-utils libfreetype6 fontconfig fonts-dejavu
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-sched-dev

@@ -10,17 +10,17 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM debian:buster-slim
+FROM debian:bullseye-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install openssh-client curl screen apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install openssh-client curl screen apt-utils libfreetype6 fontconfig fonts-dejavu
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/build/Dockerfile-submit-dev

@@ -10,16 +10,16 @@ RUN $JAVA_HOME/bin/jlink \
          --output /javaruntime
 
 # Define base image and copy in jlink created minimal Java 17 environment
-FROM debian:buster-slim
+FROM debian:bullseye-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME
 
 RUN mkdir -p /usr/local/app && \
-	apt-get -y update && \
-    apt-get -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu
+	apt -y update && \
+    apt -y install openssh-client screen apt-utils libfreetype6 fontconfig fonts-dejavu
 
-RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN DEBIAN_FRONTEND=noninteractive apt install -y --no-install-recommends tzdata
 RUN unlink /etc/localtime || true
 RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 

docker/swarm/README_DockerSwarmConfig.md

@@ -25,8 +25,8 @@ install jq (utility for json processing)
 install poetry (for building/installing vcell-admin)
 
 ```bash
-sudo apt-get install -y jq
-sudo apt-get install -y python3-poetry
+sudo apt install -y jq
+sudo apt install -y python3-poetry
 ```
 
 ## Install singularity [more info linux](https://singularity.lbl.gov/install-linux)

pythonCopasiOpt/Dockerfile

@@ -1,7 +1,7 @@
-FROM python:3.10-slim-buster
+FROM python:3.10-slim-bullseye
 
 RUN apt -y update && apt -y upgrade &&  \
-    apt-get install -y curl
+    apt install -y curl
 
 RUN mkdir -p /usr/local/app/vcell/installDir && \
     mkdir -p /usr/local/app/vcell/installDir/python/vcell_opt

vcell-cli-utils/vcell_cli_utils/cli.py

@@ -1,16 +1,12 @@
-import glob
 import json
 import os
-import shutil
 import stat
 import sys
 import tempfile
-from dataclasses import dataclass
 from typing import List
 
 import biosimulators_utils.sedml.utils
 import fire
-import libsedml as lsed
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
@@ -23,12 +19,9 @@
 from biosimulators_utils.combine.validation import validate
 from biosimulators_utils.combine.data_model import CombineArchiveContentFormat
 
-# from biosimulators_utils.plot.data_model import PlotFormat  # noqa: F401
 from biosimulators_utils.report.data_model import DataSetResults, ReportResults, ReportFormat  # noqa: F401
-from biosimulators_utils.report.io import ReportWriter
-from biosimulators_utils.sedml.data_model import Report, Plot2D, Plot3D, DataSet
+from biosimulators_utils.sedml.data_model import Report, Plot2D, Plot3D, DataSet, SedDocument
 from biosimulators_utils.sedml.io import SedmlSimulationReader, SedmlSimulationWriter
-from libsedml import SedReport, SedPlot2D, SedDocument
 
 # Move status PY code here
 # Create temp directory
@@ -150,30 +143,29 @@ def get_all_dataref_and_curves(sedml_path):
     all_plot_curves = {}
     all_report_dataref = {}
 
-    sedml = lsed.readSedML(sedml_path)
+    sedml: SedDocument = SedmlSimulationReader().run(sedml_path)
 
-    for output in sedml.getListOfOutputs():
-        if type(output) == SedPlot2D:
+    for output in sedml.outputs:
+        if isinstance(output, Plot2D):
             all_curves = {}
-            for curve in output.getListOfCurves():
+            for curve in output.curves:
                 all_curves[curve.getId()] = {
                     'x': curve.getXDataReference(),
                     'y': curve.getYDataReference()
                 }
-            all_plot_curves[output.getId()] = all_curves
-        if type(output) == SedReport:
-            for dataset in output.getListOfDataSets():
+            all_plot_curves[output.id] = all_curves
+        if isinstance(output, Report):
+            for dataset in output.data_sets():
 
                 ######
-                if output.getId() in all_report_dataref:
-
-                    all_report_dataref[output.getId()].append({
+                if output.id in all_report_dataref:
+                    all_report_dataref[output.id].append({
                         'data_reference': dataset.getDataReference(),
                         'data_label': dataset.getLabel()
                     })
                 else:
-                    all_report_dataref[output.getId()] = []
-                    all_report_dataref[output.getId()].append({
+                    all_report_dataref[output.id] = []
+                    all_report_dataref[output.id].append({
                         'data_reference': dataset.getDataReference(),
                         'data_label': dataset.getLabel()
                     })
@@ -297,23 +289,22 @@ def gen_plots_for_sed2d_only_2(sedml_path, result_out_dir):
 def gen_plots_for_sed2d_only(sedml_path, result_out_dir):
     all_plot_curves = {}
 
-    sedml: SedDocument = lsed.readSedML(sedml_path)
+    sedml: SedDocument = SedmlSimulationReader().run(sedml_path)
 
     # Generate all_plot_curves
-    for output in sedml.getListOfOutputs():
-        if not isinstance(output, SedPlot2D):
+    all_plot_curves = {}
+    for output in sedml.outputs:
+        if not isinstance(output, Plot2D):
             continue
-        sed_plot_2d: SedPlot2D = output
+        sed_plot_2d: Plot2D = output
         all_curves = {}
-        all_plot_curves = {}
-
 
-        for curve in sed_plot_2d.getListOfCurves():
-            all_curves[curve.getId()] = {
-                'x': curve.getXDataReference(),
-                'y': curve.getYDataReference()
+        for curve in sed_plot_2d.curves:
+            all_curves[curve.id] = {
+                'x': curve.x_data_generator,
+                'y': curve.y_data_generator
             }
-        all_plot_curves[sed_plot_2d.getId()] = all_curves
+        all_plot_curves[sed_plot_2d.id] = all_curves
 
 
     all_plots = dict(all_plot_curves)
@@ -348,8 +339,8 @@ def gen_plots_for_sed2d_only(sedml_path, result_out_dir):
 
         for curve_id, data in curve_dat_dict.items(): # data <--> (dict)all_curves.values()
             shouldLabel = True
-            for series_name in labelMap[data['y']]:
-                sns.lineplot(data=df, x=data['x'], y=series_name, ax=ax, label=(curve_id if shouldLabel else None))
+            for series_name in labelMap[data['y'].id]:
+                sns.lineplot(data=df, x=data['x'].id, y=series_name, ax=ax, label=(curve_id if shouldLabel else None))
                 ax.set_ylabel('')
                 shouldLabel = False
             plt.savefig(os.path.join(result_out_dir, plot_id + '.pdf'), dpi=300)

vcell-cli/src/main/java/org/vcell/cli/CLIPythonManager.java

@@ -72,7 +72,7 @@ public String callPython(String functionName, String... arguments) throws Python
      * @throws InterruptedException if the python process was interrupted
      * @throws IOException if there was a system IO failure
      */
-
+    @Deprecated
     public static void callNonSharedPython(String cliCommand, String sedmlPath, String resultOutDir)
             throws InterruptedException, IOException, PythonStreamException {
         if (lg.isWarnEnabled()) lg.warn("Using old style python invocation!");

vcell-cli/src/main/java/org/vcell/cli/run/OmexHandler.java

@@ -41,17 +41,18 @@ public OmexHandler(String omexPath, String outDir) throws IOException {
         int indexOfLastSlash = omexPath.lastIndexOf("/");
         this.omexName = omexPath.substring(indexOfLastSlash + 1);
         this.tempPath = RunUtils.getTempDir();
+        Path archiveTempDirPath = Files.copy(Paths.get(omexPath), Paths.get(RunUtils.getTempDir(), "archive_to_execute.omex"));
         try {
-            replaceMetadataRdfFiles(Paths.get(omexPath));
-            this.archive = new CombineArchive(new File(omexPath));
+            replaceMetadataRdfFiles(archiveTempDirPath);
+            this.archive = new CombineArchive(archiveTempDirPath.toFile());
             if (this.archive.hasErrors()){
                 String message = "Unable to initialise OMEX archive "+this.omexName+": "+this.archive.getErrors();
                 logger.error(message);
                 throw new IOException(message);
             }
         }catch (CombineArchiveException | JDOMException | ParseException e) {
             String message = String.format("Unable to initialise OMEX archive \"%s\", archive maybe corrupted", this.omexName);
-            logger.error(message+": "+e.getMessage(), e);
+            logger.error("{}: {}", message, e.getMessage());
             throw new IOException(e);
         }
     }

vcell-cli/src/main/java/org/vcell/cli/run/RunUtils.java

@@ -472,7 +472,7 @@ public static void zipResFiles(File dirPath) throws IOException {
 
     public static String getTempDir() throws IOException {
         String tempPath = String.valueOf(java.nio.file.Files.createTempDirectory(
-            RunUtils.VCELL_TEMP_DIR_PREFIX + UUID.randomUUID().toString()).toAbsolutePath());
+            RunUtils.VCELL_TEMP_DIR_PREFIX + UUID.randomUUID()).toAbsolutePath());
         logger.info("TempPath Created: " + tempPath);
         return tempPath;
     }