Merge pull request #1228 from virtualcell/remove-unused-services

remove unused vcell-web and SimDataWebService, consolidate native HDF5
virtualcell · Apr 26, 2024 · b67c799 · b67c799
2 parents 04be7b9 + 389bd5d
commit b67c799
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Showing 61 changed files with 1,868 additions and 5,011 deletions.
diff --git a/docker/build/Dockerfile-api-dev b/docker/build/Dockerfile-api-dev
@@ -65,7 +65,6 @@ ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
 	smtp_port="smtp-port-not-set" \
 	smtp_emailaddress="smtp-emailaddress-not-set" \
     simdataCacheSize="simdataCacheSize-not-set" \
-    webDataPort="webDataPort-not-set" \
 	ssl_ignoreHostMismatch=true \
 	ssl_ignoreCertProblems=false \
 	serverPrefixV0="server-path-prefix-v0-not-set" \
@@ -115,7 +114,6 @@ ENTRYPOINT java \
 	-Dvcellapi.keystore.pswdfile="${keystorepswdfile}" \
 	-Dvcell.smtp.hostName="${smtp_hostname}" \
 	-Dvcell.smtp.port="${smtp_port}" \
-	-Dvcelldata.web.server.port=${webDataPort} \
 	-Dvcell.smtp.emailAddress="${smtp_emailaddress}" \
 	-Dvcell.ssl.ignoreHostMismatch="${ssl_ignoreHostMismatch}" \
 	-Dvcell.ssl.ignoreCertProblems="${ssl_ignoreCertProblems}" \

diff --git a/docker/build/Dockerfile-data-dev b/docker/build/Dockerfile-data-dev
@@ -58,7 +58,6 @@ ENV softwareVersion=SOFTWARE-VERSION-NOT-SET \
     export_baseurl="export-baseurl-not-set" \
     simdatadir_external=/path/to/external/simdata/ \
     simdataCacheSize="simdataCacheSize-not-set" \
-    webDataPort="webDataPort-not-set" \
     servertype="servertype-not-set" \
     s3ProxyPortExternal="80" \
     s3export_baseURL="s3-export-baseurl-not-set"
@@ -110,6 +109,5 @@ ENTRYPOINT java \
 	-Dvcell.mongodb.host.internal=${mongodb_host_internal} \
 	-Dvcell.mongodb.port.internal=${mongodb_port_internal} \
 	-Dvcell.mongodb.database=${mongodb_database} \
-	-Dvcelldata.web.server.port=${webDataPort} \
 	-cp "./lib/*" cbit.vcell.message.server.data.SimDataServerMain \
 	"${servertype}"
diff --git a/docker/build/Dockerfile-web-dev b/docker/build/Dockerfile-web-dev
diff --git a/docker/build/vcell-web.log4j.xml b/docker/build/vcell-web.log4j.xml
diff --git a/docker/kustomize/config/devjim/api.env b/docker/kustomize/config/devjim/api.env
@@ -1,7 +1,5 @@
 simdataCacheSize=10000000
 
-webDataPort=55556
-
 smtp_emailaddress=[email protected]
 smtp_hostname=vdsmtp.cam.uchc.edu
 smtp_port=25

diff --git a/docker/kustomize/config/devjim/data.env b/docker/kustomize/config/devjim/data.env
@@ -1,7 +1,5 @@
 simdataCacheSize=10000000
 
-webDataPort=55556
-
 s3ProxyPortExternal=8089
 s3export_baseURL=https://localhost
 

diff --git a/docker/kustomize/config/stage/api.env b/docker/kustomize/config/stage/api.env
@@ -1,6 +1,5 @@
 simdataCacheSize=10000000
 
-webDataPort=55556
 serverPrefixV0=/api/v0
 
 smtp_emailaddress=[email protected]

diff --git a/docker/kustomize/config/stage/data.env b/docker/kustomize/config/stage/data.env
@@ -1,7 +1,5 @@
 simdataCacheSize=10000000
 
-webDataPort=55556
-
 s3ProxyPortExternal=8089
 s3export_baseURL=https://localhost
 

diff --git a/docker/swarm/docker-compose-small.yml b/docker/swarm/docker-compose-small.yml
@@ -22,8 +22,6 @@ services:
       - mongodb_port_internal=27017
       - mongodb_database=test
 
-      - webDataPort=${VCELL_WEB_DATA_PORT}
-
       - smtp_hostname=${VCELL_SMTP_HOSTNAME}
       - smtp_port=${VCELL_SMTP_PORT}
       - smtp_emailaddress=${VCELL_SMTP_EMAILADDRESS}
@@ -118,8 +116,6 @@ services:
       - s3ProxyPortExternal=${VCELL_S3PROXY_PORT_EXTERNAL}
       - s3export_baseURL=${VCELL_S3_EXPORT_BASEURL}
 
-      - webDataPort=${VCELL_WEB_DATA_PORT}
-
       - servertype=CombinedData
     ports:
       - "127.0.0.1:${VCELL_DEBUG_PORT_VCELL_DATA}:8000" # java remote debugging

diff --git a/docker/swarm/docker-compose.yml b/docker/swarm/docker-compose.yml
@@ -24,8 +24,6 @@ services:
       - mongodb_port_internal=27017
       - mongodb_database=test
 
-      - webDataPort=${VCELL_WEB_DATA_PORT}
-
       - smtp_hostname=${VCELL_SMTP_HOSTNAME}
       - smtp_port=${VCELL_SMTP_PORT}
       - smtp_emailaddress=${VCELL_SMTP_EMAILADDRESS}
@@ -284,8 +282,6 @@ services:
       - s3ProxyPortExternal=${VCELL_S3PROXY_PORT_EXTERNAL}
       - s3export_baseURL=${VCELL_S3_EXPORT_BASEURL}
 
-      - webDataPort=${VCELL_WEB_DATA_PORT}
-
       - servertype=CombinedData
     ports:
       - "${VCELL_DEBUG_PORT_VCELL_DATA}:8000" # java remote debugging

diff --git a/docker/swarm/localconfig_mockslurm-not-used.sh b/docker/swarm/localconfig_mockslurm-not-used.sh
@@ -120,7 +120,6 @@ VCELL_EXPORTDIR_HOST=/Volumes/vcell/export/
 VCELL_MAX_JOBS_PER_SCAN=100
 VCELL_MAX_ODE_JOBS_PER_USER=100
 VCELL_MAX_PDE_JOBS_PER_USER=40
-VCELL_WEB_DATA_PORT=55556
 VCELL_SSH_CMD_TIMEOUT=10000
 VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 
@@ -193,6 +192,5 @@ VCELL_TAG=$VCELL_TAG
 VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
 VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
 VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
-VCELL_WEB_DATA_PORT=$VCELL_WEB_DATA_PORT
 EOF
 
diff --git a/docker/swarm/localconfig_realslurm_oracle.sh b/docker/swarm/localconfig_realslurm_oracle.sh
@@ -145,7 +145,6 @@ VCELL_EXPORTDIR_HOST=/Volumes/vcell/export/
 VCELL_MAX_JOBS_PER_SCAN=100
 VCELL_MAX_ODE_JOBS_PER_USER=100
 VCELL_MAX_PDE_JOBS_PER_USER=40
-VCELL_WEB_DATA_PORT=55556
 VCELL_SSH_CMD_TIMEOUT=10000
 VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 
@@ -235,6 +234,5 @@ VCELL_TAG=$VCELL_TAG
 VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
 VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
 VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
-VCELL_WEB_DATA_PORT=$VCELL_WEB_DATA_PORT
 EOF
 
diff --git a/docker/swarm/localconfig_realslurm_oracle_zeke.sh b/docker/swarm/localconfig_realslurm_oracle_zeke.sh
@@ -148,7 +148,6 @@ VCELL_EXPORTDIR_HOST=/media/zeke/DiskDrive/Home/Work/CCAM/TempStorage/export
 VCELL_MAX_JOBS_PER_SCAN=100
 VCELL_MAX_ODE_JOBS_PER_USER=100
 VCELL_MAX_PDE_JOBS_PER_USER=40
-VCELL_WEB_DATA_PORT=55556
 VCELL_SSH_CMD_TIMEOUT=10000
 VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 
@@ -257,6 +256,6 @@ VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
 
 VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
 VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
-VCELL_WEB_DATA_PORT=$VCELL_WEB_DATA_PORT
+
 EOF
 
diff --git a/docker/swarm/localconfig_realslurm_postgres.sh b/docker/swarm/localconfig_realslurm_postgres.sh
@@ -145,7 +145,6 @@ VCELL_EXPORTDIR_HOST=/Volumes/vcell/export/
 VCELL_MAX_JOBS_PER_SCAN=100
 VCELL_MAX_ODE_JOBS_PER_USER=100
 VCELL_MAX_PDE_JOBS_PER_USER=40
-VCELL_WEB_DATA_PORT=55556
 VCELL_SSH_CMD_TIMEOUT=10000
 VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 
@@ -235,6 +234,5 @@ VCELL_TAG=$VCELL_TAG
 VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
 VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
 VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
-VCELL_WEB_DATA_PORT=$VCELL_WEB_DATA_PORT
 EOF
 
diff --git a/docker/swarm/serverconfig-uch.sh b/docker/swarm/serverconfig-uch.sh
@@ -167,7 +167,6 @@ VCELL_EXPORTDIR_HOST=/opt/vcelldata/export/
 VCELL_MAX_JOBS_PER_SCAN=100
 VCELL_MAX_ODE_JOBS_PER_USER=100
 VCELL_MAX_PDE_JOBS_PER_USER=40
-VCELL_WEB_DATA_PORT=55555
 VCELL_SSH_CMD_TIMEOUT=10000
 VCELL_SSH_CMD_RESTORE_TIMEOUT=5
 
@@ -258,6 +257,5 @@ VCELL_TAG=$VCELL_TAG
 VCELL_UPDATE_SITE=http://vcell.org/webstart/${_site_camel}
 VCELL_VERSION_NUMBER=$VCELL_VERSION_NUMBER
 VCELL_VERSION=${_site_camel}_Version_${VCELL_VERSION_NUMBER}_build_${VCELL_BUILD_NUMBER}
-VCELL_WEB_DATA_PORT=$VCELL_WEB_DATA_PORT
 EOF
 
diff --git a/pom.xml b/pom.xml
@@ -64,7 +64,6 @@
 		<module>vcell-util</module>
 		<module>vcell-vmicro</module>
 		<module>vcell-cli</module>
-		<module>vcell-web</module>
 		<module>vcell-rest</module>
         <module>vcell-restclient</module>
     </modules>

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecuteImpl.java
@@ -2,7 +2,6 @@
 
 import cbit.vcell.parser.ExpressionException;
 import cbit.vcell.solver.ode.ODESolverResultSet;
-import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.vcell.cli.CLIRecordable;
@@ -22,6 +21,8 @@
 import java.util.List;
 import java.util.Map;
 
+import static org.vcell.cli.run.hdf5.BiosimulationsHdf5Writer.BiosimulationsHdfWriterException;
+
 public class ExecuteImpl {
 
     private final static Logger logger = LogManager.getLogger(ExecuteImpl.class);
@@ -65,7 +66,7 @@ public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRec
                     if (inputFileName.endsWith("omex"))
                         runSingleExecOmex(inputFile, outputDir, cliLogger,
                                 bKeepTempFiles, bExactMatchOnly, bSmallMeshOverride);
-                } catch (ExecutionException | RuntimeException | HDF5Exception e){
+                } catch (ExecutionException e){
                     logger.error("Error caught executing batch mode", e);
                     Tracer.failure(e, "Error caught executing batch mode");
                     failedFiles.add(inputFileName);
@@ -105,7 +106,7 @@ public static void batchMode(File dirOfArchivesToProcess, File outputDir, CLIRec
 
     private static void runSingleExecOmex(File inputFile, File outputDir, CLIRecordable cliLogger, boolean bKeepTempFiles,
                                           boolean bExactMatchOnly, boolean bSmallMeshOverride)
-            throws IOException, ExecutionException, PythonStreamException, HDF5Exception, InterruptedException {
+            throws IOException, ExecutionException, PythonStreamException, InterruptedException, BiosimulationsHdfWriterException {
         String bioModelBaseName = inputFile.getName().substring(0, inputFile.getName().indexOf(".")); // ".omex"??
         Files.createDirectories(Paths.get(outputDir.getAbsolutePath() + File.separator + bioModelBaseName)); // make output subdir
         final boolean bEncapsulateOutput = true;
@@ -230,7 +231,7 @@ public static void singleExecVcml(File vcmlFile, File outputDir, CLIRecordable c
 
     private static void singleExecOmex(File inputFile, File rootOutputDir, CLIRecordable cliRecorder,
             boolean bKeepTempFiles, boolean bExactMatchOnly, boolean bEncapsulateOutput, boolean bSmallMeshOverride, boolean bBioSimMode)
-            throws ExecutionException, PythonStreamException, IOException, InterruptedException, HDF5Exception {
+            throws ExecutionException, PythonStreamException, IOException, InterruptedException, BiosimulationsHdfWriterException {
 
         ExecutionJob requestedExecution = new ExecutionJob(inputFile, rootOutputDir, cliRecorder,
             bKeepTempFiles, bExactMatchOnly, bEncapsulateOutput, bSmallMeshOverride);

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java b/vcell-cli/src/main/java/org/vcell/cli/run/ExecutionJob.java
@@ -1,25 +1,22 @@
 package org.vcell.cli.run;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.vcell.cli.CLIRecordable;
 import org.vcell.cli.PythonStreamException;
 import org.vcell.cli.exceptions.ExecutionException;
+import org.vcell.cli.run.hdf5.BiosimulationsHdf5Writer;
 import org.vcell.cli.run.hdf5.HDF5ExecutionResults;
-import org.vcell.cli.run.hdf5.Hdf5DataContainer;
 import org.vcell.util.FileUtils;
 
-import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
-
-import org.vcell.cli.run.hdf5.Hdf5Writer;
-
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
-
 import java.io.File;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.List;
 
+import static org.vcell.cli.run.hdf5.BiosimulationsHdf5Writer.BiosimulationsHdfWriterException;
+
 /**
  * Contains the code necessary to execute an Omex archive in VCell
  */
@@ -124,7 +121,7 @@ public void preprocessArchive() throws PythonStreamException, IOException {
      * @throws IOException if there are system I/O issues
      * @throws ExecutionException if an execution specfic error occurs
      */
-    public void executeArchive(boolean isBioSimSedml) throws HDF5Exception, PythonStreamException, ExecutionException {
+    public void executeArchive(boolean isBioSimSedml) throws BiosimulationsHdfWriterException, PythonStreamException, ExecutionException {
         try {
             HDF5ExecutionResults masterHdf5File = new HDF5ExecutionResults(isBioSimSedml);
             this.queueAllSedml();
@@ -145,7 +142,7 @@ public void executeArchive(boolean isBioSimSedml) throws HDF5Exception, PythonSt
                 if (hasSucceeded) logger.info("Processing of SedML succeeded.\n" + stats.toString());
                 else logger.error("Processing of SedML has failed.\n" + stats.toString());
             }
-            Hdf5Writer.writeHdf5(masterHdf5File, new File(this.outputDir));
+            BiosimulationsHdf5Writer.writeHdf5(masterHdf5File, new File(this.outputDir));
 
         } catch(PythonStreamException e){
             logger.error("Python-processing encountered fatal error. Execution is unable to properly continue.", e);