Merge branch 'master' into Container-deploy-fixes

# Conflicts: # vcell-core/src/main/java/cbit/vcell/export/server/JhdfUtils.java
virtualcell · Nov 14, 2024 · 8b72510 · 8b72510
2 parents 28764ae + b554cf0
commit 8b72510
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diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml
@@ -5,12 +5,12 @@ on:
   workflow_dispatch:
 
 env:
-  python-version: "3.9"
+  python-version: "3.10"
   poetry-version: "1.2.1"
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout Our Code
         uses: actions/checkout@v4

diff --git a/.github/workflows/ci_cd.yml b/.github/workflows/ci_cd.yml
@@ -10,7 +10,7 @@ on:
     types: [published, edited]
 
 env:
-  python-version: "3.9"
+  python-version: "3.10"
 
 jobs:
   CI-Build:

diff --git a/.github/workflows/create_bs_singularity.yml b/.github/workflows/create_bs_singularity.yml
@@ -8,12 +8,12 @@ on:
         default: 3ca1093da599a0ff4229b1130efe7a3924ff2b4c
 
 env:
-  python-version: "3.9"
+  python-version: "3.10"
 
 jobs:
   CD:
     name: CD
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
 
     steps:
       - uses: actions/checkout@v4

diff --git a/.github/workflows/nightly-model-testing.yml b/.github/workflows/nightly-model-testing.yml
@@ -6,12 +6,12 @@ on:
   workflow_dispatch:
 
 env:
-  python-version: "3.9"
+  python-version: "3.10"
   poetry-version: "1.2.1"
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - name: Checkout Our Code
         uses: actions/checkout@v4

diff --git a/docker/build/Dockerfile-batch-dev b/docker/build/Dockerfile-batch-dev
@@ -1,4 +1,4 @@
-FROM ghcr.io/virtualcell/vcell-solvers:v0.8.1.3
+FROM ghcr.io/virtualcell/vcell-solvers:v0.8.2
 
 RUN apt-get -y update && \
     apt-get install -y  curl && \

diff --git a/docker/build/Dockerfile-data-dev b/docker/build/Dockerfile-data-dev
@@ -10,7 +10,7 @@ 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 python:3.10.15-slim
 ENV JAVA_HOME=/opt/java/openjdk
 ENV PATH "${JAVA_HOME}/bin:${PATH}"
 COPY --from=jre-build /javaruntime $JAVA_HOME

diff --git a/pom.xml b/pom.xml
@@ -135,6 +135,7 @@
 		<jfreechart.version>1.5.0</jfreechart.version>
 		<jgrapht.version>1.3.0</jgrapht.version>
 		<jhdf.version>0.8.4</jhdf.version>
+		<jhdf5.cisd.version>19.04.1</jhdf5.cisd.version> <!-- deprecated -->
 		<jhdf5-2-10.version>2.9</jhdf5-2-10.version>
 		<jmatio.version>1.0</jmatio.version>
 		<joda-time.version>2.12.2</joda-time.version>

diff --git a/vcell-cli-utils/vcell_cli_utils/cli.py b/vcell-cli-utils/vcell_cli_utils/cli.py
@@ -28,7 +28,6 @@
 from biosimulators_utils.report.io import ReportWriter
 from biosimulators_utils.sedml.data_model import Report, Plot2D, Plot3D, DataSet
 from biosimulators_utils.sedml.io import SedmlSimulationReader, SedmlSimulationWriter
-from deprecated import deprecated
 from libsedml import SedReport, SedPlot2D, SedDocument
 
 # Move status PY code here
@@ -140,97 +139,6 @@ def gen_sedml_2d_3d(omex_file_path, base_out_path):
     return temp_path
 
 
-@deprecated("This method is no longer used")
-def exec_sed_doc(omex_file_path, base_out_path):
-    # defining archive
-    config = Config(VALIDATE_OMEX_MANIFESTS=False)
-    archive = CombineArchiveReader().run(in_file=omex_file_path, out_dir=tmp_dir,
-                                         config=config)
-
-    # determine files to execute
-    sedml_contents = get_sedml_contents(archive)
-
-    report_results = ReportResults()
-    for i_content, content in enumerate(sedml_contents):
-        content_filename = os.path.join(tmp_dir, content.location)
-
-        doc = SedmlSimulationReader().run(content_filename)
-
-        for report_filename in glob.glob(os.path.join(base_out_path, content.location, '*.csv')):
-            report_id = os.path.splitext(os.path.basename(report_filename))[0]
-
-            # read report from CSV file produced by VCell
-            data_set_df = pd.read_csv(report_filename).transpose()
-            data_set_df.columns = data_set_df.iloc[0]
-            data_set_df = data_set_df.drop(data_set_df.iloc[0].name)
-            data_set_df = data_set_df.reset_index()
-            data_set_df = data_set_df.rename(
-                columns={'index': data_set_df.columns.name})
-            data_set_df = data_set_df.transpose()
-            data_set_df.index.name = None
-
-            report = next(
-                report for report in doc.outputs if report.id == report_id)
-
-            data_set_results = DataSetResults()
-
-            # print("report: ", report, file=sys.stderr)
-            # print("report Type: ", type(report), file=sys.stderr)
-            # print("Plot Type: ", Plot2D, file=sys.stderr)
-            if type(report) != Plot2D and type(report) != Plot3D:
-                # Considering the scenario where it has the datasets in sedml
-                for data_set in report.data_sets:
-                    data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(
-                        dtype='float64')
-                    # print("DF for report: ", data_set_results[data_set.id], file=sys.stderr)
-                    # print("df.types: ", data_set_results[data_set.id].dtype, file=sys.stderr)
-            else:
-                data_set_df = pd.read_csv(report_filename, header=None).T
-                data_set_df.columns = data_set_df.iloc[0]
-                data_set_df.drop(0, inplace=True)
-                data_set_df.reset_index(inplace=True)
-                data_set_df.drop('index', axis=1, inplace=True)
-                # print("DF for plot: ", data_set_df, file=sys.stderr)
-                # Considering the scenario where it doesn't have datasets in sedml (pseudo sedml for plots)
-                for col in list(data_set_df.columns):
-                    data_set_results[col] = data_set_df[col].values
-
-            # append to data structure of report results
-            report_results[report_id] = data_set_results
-
-            # save file in desired BioSimulators format(s)
-            # for report_format in report_formats:
-            # print("HDF report: ", report, file=sys.stderr)
-            # print("HDF dataset results: ", data_set_results, file=sys.stderr)
-            # print("HDF base_out_path: ", base_out_path,file=sys.stderr)
-            # print("HDF path: ", os.path.join(content.location, report.id), file=sys.stderr)
-
-            rel_path = os.path.join(content.location, report.id)
-
-            if len(rel_path.split("./")) > 1:
-                rel_path = rel_path.split("./")[1]
-
-            if type(report) != Plot2D and type(report) != Plot3D:
-                ReportWriter().run(report,
-                                   data_set_results,
-                                   base_out_path,
-                                   rel_path,
-                                   format='h5')
-            else:
-                datasets = []
-                for col in list(data_set_df.columns):
-                    datasets.append(DataSet(id=col, label=col, name=col))
-                report.data_sets = datasets
-                ReportWriter().run(report,
-                                   data_set_results,
-                                   base_out_path,
-                                   rel_path,
-                                   format='h5')
-
-    # Remove temp directory
-    shutil.rmtree(tmp_dir)
-
-
 def transpose_vcml_csv(csv_file_path: str):
     df = pd.read_csv(csv_file_path, header=None)
     cols = list(df.columns)
@@ -451,7 +359,6 @@ def gen_plots_for_sed2d_only(sedml_path, result_out_dir):
     fire.Fire({
         'genSedml2d3d': gen_sedml_2d_3d,
         'genPlotsPseudoSedml': gen_plots_for_sed2d_only,
-        'execSedDoc': exec_sed_doc,
         'transposeVcmlCsv': transpose_vcml_csv,
         'genPlotPdfs': gen_plot_pdfs,
     })
diff --git a/vcell-cli-utils/vcell_cli_utils/wrapper.py b/vcell-cli-utils/vcell_cli_utils/wrapper.py
@@ -2,7 +2,6 @@
 import sys
 import glob
 import os
-from deprecated import deprecated
 from pathlib import Path
 if __name__ == "__main__":
     from vcell_cli_utils import cli, status
@@ -35,7 +34,7 @@ def genSedml2d3d(omexFilePath : str, baseOutPath : str) -> None:
 def genPlotsPseudoSedml(sedmlPath : str, resultOutDir : str) -> None:
     cli.gen_plots_for_sed2d_only(sedmlPath, resultOutDir)
 
-@deprecated("This method is no longer used") 
+# this function is no longer used
 def execSedDoc(omexFilePath : str, baseOutPath : str) -> None:
     cli.exec_sed_doc(omexFilePath, baseOutPath)
 

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/PythonCalls.java b/vcell-cli/src/main/java/org/vcell/cli/run/PythonCalls.java
@@ -72,20 +72,6 @@ public static void setExceptionMessage(String sedmlAbsolutePath, String entityId
         cliPythonManager.parsePythonReturn(results, "", "Failed updating task status YAML\n");
     }
 
-    public void convertCSVtoHDF(String omexFilePath, String outputDir, CLIPythonManager cliPythonManager) throws PythonStreamException {
-
-        // Convert CSV to HDF5
-        /*
-        Usage: cli.py SEDML_FILE_PATH WORKING_DIR BASE_OUT_PATH CSV_DIR <flags>
-                    optional flags:        --rel_out_path | --apply_xml_model_changes |
-                         --report_formats | --plot_formats | --log | --indent
-        * */
-        // handle exceptions here
-        logger.trace("Dialing Python function execSedDoc");
-        String results = cliPythonManager.callPython("execSedDoc", omexFilePath, outputDir);
-        cliPythonManager.parsePythonReturn(results, "HDF conversion successful\n","HDF conversion failed\n");
-    }
-
     // Sample STATUS YML
     /*
     sedDocuments:

diff --git a/vcell-core/pom.xml b/vcell-core/pom.xml
@@ -404,11 +404,27 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-		<dependency>
+		<dependency> <!-- deprecated -->
 			<groupId>org.scala-saddle</groupId>
 			<artifactId>jhdf5_2.10</artifactId>
 			<version>${jhdf5-2-10.version}</version>
 		</dependency>
+		<!-- https://mvnrepository.com/artifact/cisd/jhdf5 -->
+		<dependency>
+			<groupId>cisd</groupId>
+			<artifactId>jhdf5</artifactId>
+			<version>${jhdf5.cisd.version}</version>
+			<exclusions>
+				<exclusion>
+					<groupId>org.apache.commons</groupId>
+					<artifactId>commons-lang3</artifactId>
+				</exclusion>
+				<exclusion>
+					<groupId>commons-io</groupId>
+					<artifactId>commons-io</artifactId>
+				</exclusion>
+			</exclusions>
+		</dependency>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>