Merge branch 'master' into ExportExceptionFixesForRoundTrip

Author: jcschaff

Dockerfile

@@ -67,8 +67,6 @@ COPY ./vcell-client/target/vcell-client-0.0.1-SNAPSHOT.jar \
      ./vcell-admin/target/maven-jars/*.jar \
      ./vcell-cli/target/vcell-cli-0.0.1-SNAPSHOT.jar \
      ./vcell-cli/target/maven-jars/*.jar \
-     ./non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
-     ./non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
      ./non-maven-java-libs/org/sbml/libcombine/libCombineLinux64/0.2.7/libCombineLinux64-0.2.7.jar \
      /usr/local/app/vcell/lib/
 

README_Debugging.md

@@ -3,7 +3,7 @@ If VCell client simulation list view says 'hasdata=no' but there is data
 -----Find sim id (click 'i' button when sim is selected) -> theSimID  
 -----log into vcell-node1 (or any node not in DMZ, not vcellapi or vcellapi-beta)  
 -----Check data exists, give cmd " ls /share/apps/vcell3/users/boris/SimID_theSimID* "  
------open oracle db tool (toad,sql,squirrel), log into vcell@vcell-db.cam.uchc.edu and do query " select * from vc_simulationjob where simref=theSimID; "  
+-----open oracle db tool (toad,sql,squirrel), log into vcell@vcell-oracle.cam.uchc.edu and do query " select * from vc_simulationjob where simref=theSimID; "  
 -----If the query column 'hasdata' is blank then do update " update vc_simulationJob set hasdata='Y' where simref=theSimID; "  and " commit; "  
 -----log into vcellapi(Rel) or vcellapi-beta(Alpha)  
 -----Restart VCell docker scheduler service  with cmd " sudo docker service update --force --detach=false vcell{rel,alpha}_sched "  
@@ -131,7 +131,7 @@ client local run  alpha
 -Dvcell.server.dbPassword=  
 -Dvcell.server.dbUserid=vcell  
 -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver  
--Dvcell.server.dbConnectURL=jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl  
+-Dvcell.server.dbConnectURL=jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521:ORCLPDB1  
 -Dvcell.server.id=alpha\_7.0.0\_51  
 -Dvcell.mongodb.database=TEST  
 -Dvcell.mongodb.host.internal=vcellapi-beta.cam.uchc.edu  

README_flow_control.md

@@ -55,7 +55,7 @@ all solvers call vcell-solver/VCellMessaging/src/SimulationMessaging.cpp.setWork
 --SimulationDispatcherEngine.onworkerEvent(...)  
 ---SimulationStateMachine.onWorkerEvent(...)  
 ----SimulationDatabaseDirect.updateSimulationJobStatus(...)  
------AdminDBToplevel.updateSimulationJobStatus(...)  (**updates Oracle** real database host vcell-db.cam.uchc.edu, NOT vcell-db container)  
+-----AdminDBToplevel.updateSimulationJobStatus(...)  (**updates Oracle** real database host vcell-oracle.cam.uchc.edu, NOT vcell-db container)  
 ----StatusMessage.sendToClient(...) (sends to AMQint container clientStatus topic)  
 **activemqint container**  
 -recieves sim status message on the 'clientStatus' topic  

README_orphan.md

@@ -79,21 +79,21 @@ vcellNagios.sh calls Rel web service https://vcellapi/health?check={login,sim}
 **DBBackupAndClean**  
 vcell-node1:/opt/build/frm/dbbackupclean  
 //Normal, without debug  
-java -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk vcell-db vcell /opt/build/frm/dbpw.txt  vcelldborcl.cam.uchc.edu /tmp /share/apps/vcell3/users  
+java -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk vcell-oracle vcell /opt/build/frm/dbpw.txt  ORCLPDB1 /tmp /share/apps/vcell3/users  
 
 //Normal, without debug, single user only  
-java -Xms200m -Xmx1500m -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk2 vcell-db vcell /opt/build/frm/dbpw.txt  vcelldborcl.cam.uchc.edu /tmp /share/apps/vcell3/users Juliajessica  
+java -Xms200m -Xmx1500m -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk2 vcell-oracle vcell /opt/build/frm/dbpw.txt  ORCLPDB1 /tmp /share/apps/vcell3/users Juliajessica  
 
 //With debug  (note: eclipse debug config: vcell-server,vcell-node1,30301)  
-java  -agentlib:jdwp=transport=dt_socket,server=y,address=30301,suspend=y  -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk vcell-db vcell /opt/build/frm/dbpw.txt  vcelldborcl.cam.uchc.edu /tmp /share/apps/vcell3/users  
+java  -agentlib:jdwp=transport=dt_socket,server=y,address=30301,suspend=y  -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk vcell-oracle vcell /opt/build/frm/dbpw.txt  ORCLPDB1 /tmp /share/apps/vcell3/users  
 
-//DBBackupAndClean Scheduled Task (vcell-db.cam.uchc.edu->'scheduled task'->'Task Scheduler Library'->cleanAndBackupDB->properties->Actions->'Edit...')
+//DBBackupAndClean Scheduled Task (vcell-oracle.cam.uchc.edu->'scheduled task'->'Task Scheduler Library'->cleanAndBackupDB->properties->Actions->'Edit...')
 Program/script: "C:\Program Files (x86)\Java\jre1.8.0_121\bin\java.exe"
-Add arguments: -jar DBBackupAndClean_Ampli.jar cleanandbackup vcell-db vcell cbittech vcelldborcl.cam.uchc.edu \\cfs05\vcell\temp \\cfs03\shared\archive\vcell\VCDBdumps
+Add arguments: -jar DBBackupAndClean_Ampli.jar cleanandbackup vcell-oracle vcell password ORCLPDB1 \\cfs05\vcell\temp \\cfs03\shared\archive\vcell\VCDBdumps
 Start in: C:\fromDBS3
 
 
-**Delete large listener.log file**  
+**Delete large listener.log file - obsolete - oracle now containerized running on vcell-oracle machine **  
 log in to vcell-db (a windows host) as admin user using 'Remote Desktop Connection'  
 start 'cmd' window as system administrator (start->'command prompt->'rt-click, 'run as administrator')  
 //make sure of path to listener log  
@@ -130,22 +130,22 @@ NOTE: enter following after 'java' for debug (-agentlib:jdwp=transport=dt_socket
 4a. Run to generate .csv report, expects vcellDB password to be enetered on console  
 
     java -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar  
-       cbit.vcell.tools.IonItems 'jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl' '/share/apps/vcell3/users' publicmodelwithsims false | tee ./pubModelsSimIdOnly.txt  
+       cbit.vcell.tools.IonItems 'jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521:ORCLPDB1' '/share/apps/vcell3/users' publicmodelwithsims false | tee ./pubModelsSimIdOnly.txt  
 
 4b. Run to save vcml of published modesl with sims that have no data or exceptions removed from vcml  
 
     java -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar:./maven-  jars/jhdf5_2.10-2.9.jar  
-      -Djava.library.path="./natlibs"  cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" "/share/apps/vcell3/users" publishedmodelvcml   /share/apps/vcell3/users/ionvcml 0 0  
+      -Djava.library.path="./natlibs"  cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521:ORCLPDB1" "/share/apps/vcell3/users" publishedmodelvcml   /share/apps/vcell3/users/ionvcml 0 0  
 
 4c. Run to read vcml saved from 4b and compare to vcml from db and print the sims that had to be removed  
 
     java -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar:./maven-jars/jhdf5_2.10-2.9.jar  
-      -Djava.library.path="./natlibs"  cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl" /share/apps/vcell3/users/ionvcml publishedmodelvcmldiff  
+      -Djava.library.path="./natlibs"  cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521:ORCLPDB1" /share/apps/vcell3/users/ionvcml publishedmodelvcmldiff  
       
 4d.  Run to save vcml from TestSuit
 
     java  -cp ./dbbackupclean/ojdbc6-11.2.0.4.jar:./dbbackupclean/ucp-11.2.0.4.jar:./dbbackupclean/vcell-oracle-0.0.1-SNAPSHOT.jar:./cbit_vcell_tools_IonItems.jar:./maven-jars/jhdf5_2.10-2.9.jar  
-    -Djava.library.path="./natlibs"  cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-db.cam.uchc.edu:1521:vcelldborcl"  /share/apps/vcell3/users/ionts testsuitemodelvcml
+    -Djava.library.path="./natlibs"  cbit.vcell.tools.IonItems "jdbc:oracle:thin:@vcell-oracle.cam.uchc.edu:1521:ORCLPDB1"  /share/apps/vcell3/users/ionts testsuitemodelvcml
 
 ***----------------------------------------------------------------------------------------------------------***
 

docker/README_Oracle.md

@@ -0,0 +1,71 @@
+# grab dump from VCell-db.cam.uchc.edu, windows 2008, Oracle 11g enterprise
+### character set is WE8MSWIN1252
+
+### export from vcell-db using datapump for vcell schema
+in vcell-db database, named directory ```E_DATA_PUMP_DIR``` maps to ```e:\db```
+
+scn = 1430710053 (compute from sql below)
+```sql 
+select current_scn from v$database
+```
+expdp system/<<password>>@vcelldborcl directory=E_DATA_PUMP_DIR dumpfile=vcelldb_dump_2023_08_19.dmp logfile=vcelldb_dump_2023_08_19.log schemas=vcell flashback_scn=1430710053
+
+# build new oracle database image on vcell-oracle.cam.uchc.edu
+
+### check out github repo for oracle docker containers
+### download ```LINUX.X64_193000_db_home.zip``` and install in ./19.3.0/ directory
+### build the container (from docker-images/OracleDatabase/SingleInstance/)
+
+```bash
+./buildContainerImage.sh -s -v 19.3.0 -o '--build-arg SLIMMING=false'
+```
+### tag and push image to container repository
+```bash
+docker tag <<image name>> ghcr.io/virtualcell/oracle-database:19.3.0-se2
+docker push ghcr.io/virtualcell/oracle-database:19.3.0-se2
+```
+
+## create /data/oradata, /data/backup directories and set permissions to allow container oracle/dba rw access.
+
+## running the container on vcell-oracle (for the first time)
+```bash
+sudo docker run --detach --restart=always \
+    --name oracle-database \
+    -p 1521:1521 -p 5500:5500 \
+    --ulimit nofile=1024:65536 --ulimit nproc=2047:16384 --ulimit stack=10485760:33554432 --ulimit memlock=3221225472 \
+    -e ORACLE_SID=ORCLCDB \
+    -e ORACLE_PDB=ORCLPDB1 \
+    -e ORACLE_PWD=<<password>> \
+    -e INIT_CPU_COUNT=4 \
+    -e ORACLE_EDITION=standard \
+    -e ENABLE_TCPS=false \
+    -e ORACLE_CHARACTERSET=WE8MSWIN1252 \
+    -e ENABLE_ARCHIVELOG=true \
+    -v /data/oradata:/opt/oracle/oradata \
+    -v /data/backup:/opt/oracle/backup \
+    ghcr.io/virtualcell/oracle-database:19.3.0-se2
+```
+
+```bash
+sudo docker logs -f oracle-database
+```
+
+## register directory object EXT_DATA_PUMP_DIR for /opt/oracle/backup (host /data/backup)
+```sql
+create or replace directory EXT_DATA_PUMP_DIR as '/opt/oracle/backup';
+```
+
+## add user vcell (((Command doesn't work)))
+sqlplus system/<<password>>@ORCLPDB1
+```sql
+create directory EXT_DATA_PUMP_DIR as '/opt/oracle/backup';
+```
+
+## run the import
+```bash
+docker exec -it oracle-database /bin/bash
+impdp system/<<password>>@ORCLPDB1 schemas=vcell table_exists_action=REPLACE directory=EXT_DATA_PUMP_DIR dumpfile=FRMDEV2ORCL_VCELL_2023_08_19_17_05_08.DMP logfile=FRMDEV2ORCL_VCELL_2023_08_19_17_05_08.log
+
+impdp system/<<password>>@ORCLPDB1 schemas=vcell table_exists_action=REPLACE directory=EXT_DATA_PUMP_DIR dumpfile=FRMDEV2ORCL_VCELL_2023_08_19_17_05_08.DMP logfile=FRMDEV2ORCL_VCELL_2023_08_19_17_05_08.log.3
+```
+

docker/README_serviceInfo.md

@@ -107,7 +107,7 @@ nmym8qspowiu1d850ok9vwtk2     vcell-node4.cam.uchc.edu     Ready               A
 kn3y3t1rw8skyua80j841ohng     vcellapi-beta.cam.uchc.edu   Ready               Active              Reachable           18.03.0-ce
 ```
 
-## vcell-db.cam.uchc.edu, NOT Docker, (VCell database)  
+## vcell-oracle.cam.uchc.edu, NOT Docker, (VCell database)  
 Oracle database, has all models, sim status, all user data,  everything  
 
 ## vcell-docker.cam.uchc.edu, NOT Swarm node, (VCell docker registry) [details](build/README_Registry.md)

docker/build/Dockerfile-admin-dev

@@ -3,15 +3,17 @@ FROM ubuntu:18.04
 RUN apt-get -y update && \
     apt-get install -y curl openjdk-8-jre dnsutils && \
     mkdir -p /usr/local/app/lib 
-	
+
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN unlink /etc/localtime || true
+RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
+
 WORKDIR /usr/local/app
 
 COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
      ./vcell-server/target/maven-jars/*.jar \
      ./vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
      ./vcell-oracle/target/maven-jars/*.jar \
-     ./non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
-     ./non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
      ./vcell-api/target/vcell-api-0.0.1-SNAPSHOT.jar \
      ./vcell-api/target/maven-jars/*.jar \
      ./vcell-admin/target/vcell-admin-0.0.1-SNAPSHOT.jar \

docker/build/Dockerfile-api-dev

@@ -3,15 +3,17 @@ FROM ubuntu:18.04
 RUN apt-get -y update && \
     apt-get install -y curl openjdk-8-jre dnsutils && \
     mkdir -p /usr/local/app/lib 
-	
+
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN unlink /etc/localtime || true
+RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
+
 WORKDIR /usr/local/app
 
 COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
      ./vcell-server/target/maven-jars/*.jar \
      ./vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
      ./vcell-oracle/target/maven-jars/*.jar \
-     ./non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
-     ./non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
      ./vcell-api/target/vcell-api-0.0.1-SNAPSHOT.jar \
      ./vcell-api/target/maven-jars/*.jar \
      ./lib/
@@ -62,6 +64,7 @@ ENTRYPOINT java \
 	-Dvcell.server.dbDriverName="${dbdriver}" \
 	-Dvcell.server.dbUserid="${dbuser}" \
 	-Dvcell.db.pswdfile="${dbpswdfile}" \
+	-Duser.timezone="${userTimezone}" \
 	-Dvcell.jms.int.host.internal="${jmshost_int_internal}" \
 	-Dvcell.jms.int.port.internal="${jmsport_int_internal}" \
 	-Dvcell.jms.blobMessageUseMongo=true \

docker/build/Dockerfile-batch-dev

@@ -86,6 +86,10 @@ RUN apt-get -y update && \
 #	wget --no-check-certificate https://download.opensuse.org/repositories/home:/fbergman:/COPASI/xUbuntu_17.10/amd64/python-copasi_4.22.170-1_amd64.deb && \
 #	gdebi -n -q python-copasi_4.22.170-1_amd64.deb
 
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends tzdata
+RUN unlink /etc/localtime || true
+RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
+
 RUN mkdir -p /usr/local/app/localsolvers && ln -s /vcellbin  /usr/local/app/localsolvers/linux64
 WORKDIR /usr/local/app
 

docker/build/Dockerfile-data-dev

@@ -58,16 +58,18 @@ RUN mkdir -p /usr/local/app && \
 	apk update && \
 	apk add --no-cache ttf-dejavu && \
     apk add openssh-client && \
-    apk add screen
+    apk add screen tzdata
+
+ENV TZ=America/New_York
+RUN unlink /etc/localtime || true
+RUN ln -s /usr/share/zoneinfo/America/New_York /etc/localtime
 
 WORKDIR /usr/local/app
 
 COPY ./vcell-server/target/vcell-server-0.0.1-SNAPSHOT.jar \
      ./vcell-server/target/maven-jars/*.jar \
      ./vcell-oracle/target/vcell-oracle-0.0.1-SNAPSHOT.jar \
      ./vcell-oracle/target/maven-jars/*.jar \
-     ./non-maven-java-libs/com/oracle/ojdbc6/11.2.0.4/ojdbc6-11.2.0.4.jar \
-     ./non-maven-java-libs/com/oracle/ucp/11.2.0.4/ucp-11.2.0.4.jar \
      ./lib/