From 8234cf9c9cbee9c7eda0028843620733eba640aa Mon Sep 17 00:00:00 2001
From: GMarupilla <marupilla@mail.com>
Date: Wed, 31 Mar 2021 15:52:36 -0400
Subject: [PATCH 1/5] Revert "Fix the issue when importing nested SED document"

This reverts commit dbf96caa64c6c6d3eed5cb9fa186a3a16bc0d037.
---
 .../jlibsedml/execution/ArchiveModelResolver.java | 15 ++-------------
 1 file changed, 2 insertions(+), 13 deletions(-)

diff --git a/vcell-core/src/main/java/org/jlibsedml/execution/ArchiveModelResolver.java b/vcell-core/src/main/java/org/jlibsedml/execution/ArchiveModelResolver.java
index 64dea85df3..db71a88ea0 100644
--- a/vcell-core/src/main/java/org/jlibsedml/execution/ArchiveModelResolver.java
+++ b/vcell-core/src/main/java/org/jlibsedml/execution/ArchiveModelResolver.java
@@ -1,10 +1,8 @@
 package org.jlibsedml.execution;
 
-import java.io.File;
 import java.net.URI;
 import java.util.List;
 
-import cbit.vcell.resource.OperatingSystemInfo;
 import org.jlibsedml.ArchiveComponents;
 import org.jlibsedml.IModelContent;
 
@@ -14,19 +12,10 @@ public ArchiveModelResolver(ArchiveComponents ac) {
         this.ac=ac;
     }
     public String getModelXMLFor(URI modelURI) {
-        String rc = null;
-        // Considering the import for nested SED-ML document
-        String regExp = null;
+        String rc=null;
         List<IModelContent> children = ac.getModelFiles();
         for (IModelContent imc: children) {
-            if (OperatingSystemInfo.getInstance().isWindows()) {
-                regExp = "\\\\";
-            } else {
-                regExp = "/";
-            }
-            String[] splitURI = modelURI.toString().split(regExp);
-            String filename = splitURI[splitURI.length-1];
-            if(imc.getName().equals(filename)){
+            if(imc.getName().equals(modelURI.toString())){
                 rc= imc.getContents();
             }
         }

From bc2f80a91f34e8cdaf96f1b9787154c25e8c1ef3 Mon Sep 17 00:00:00 2001
From: GMarupilla <marupilla@mail.com>
Date: Thu, 1 Apr 2021 15:21:45 -0400
Subject: [PATCH 2/5] CLI-Handling simulations which has Multiple Tasks Per Sed
 Document

---
 vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java b/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java
index 9cea5116b3..fcd0816ad2 100644
--- a/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java
+++ b/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java
@@ -1002,7 +1002,9 @@ public void vetoableChange(java.beans.PropertyChangeEvent evt) throws java.beans
 		for (int i=0;i<simulations.length-1;i++){
 			for (int j=i+1;j<simulations.length;j++){
 				if (simulations[i].getName().equals(simulations[j].getName())){
-					throw new PropertyVetoException(VCellNames.getName(simulations[i])+" with name "+simulations[i].getName()+" already exists",evt);
+					// Note: Exception is not being handled to support multiple tasks with same simulation(in SED-ML)
+					// throw new PropertyVetoException(VCellNames.getName(simulations[i])+" with name "+simulations[i].getName()+" already exists",evt);
+					System.err.println(VCellNames.getName(simulations[i])+" with name `"+simulations[i].getName()+"` already exists");
 				}
 			}
 		}

From 46cc95933f6fc1f5b76144f238de3fb81bf53d86 Mon Sep 17 00:00:00 2001
From: GMarupilla <marupilla@uchc.edu>
Date: Thu, 1 Apr 2021 18:47:23 -0400
Subject: [PATCH 3/5] Update ci_cd.yml

---
 .github/workflows/ci_cd.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci_cd.yml b/.github/workflows/ci_cd.yml
index 51c6f8968c..f0e2925aa8 100644
--- a/.github/workflows/ci_cd.yml
+++ b/.github/workflows/ci_cd.yml
@@ -6,6 +6,7 @@ on:
       - '*'
       - '*/*'
       - '**'
+      - validate
   release:
     types: [published, edited]
 

From 71a6ed54eaa19dbdb49f22b3b37e8f74b8e494bc Mon Sep 17 00:00:00 2001
From: GMarupilla <marupilla@mail.com>
Date: Wed, 7 Apr 2021 13:30:22 -0400
Subject: [PATCH 4/5] Revert "CLI-Handling simulations which has Multiple Tasks
 Per Sed Document"

This reverts commit bc2f80a91f34e8cdaf96f1b9787154c25e8c1ef3.
---
 vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java b/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java
index fcd0816ad2..9cea5116b3 100644
--- a/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java
+++ b/vcell-core/src/main/java/cbit/vcell/biomodel/BioModel.java
@@ -1002,9 +1002,7 @@ public void vetoableChange(java.beans.PropertyChangeEvent evt) throws java.beans
 		for (int i=0;i<simulations.length-1;i++){
 			for (int j=i+1;j<simulations.length;j++){
 				if (simulations[i].getName().equals(simulations[j].getName())){
-					// Note: Exception is not being handled to support multiple tasks with same simulation(in SED-ML)
-					// throw new PropertyVetoException(VCellNames.getName(simulations[i])+" with name "+simulations[i].getName()+" already exists",evt);
-					System.err.println(VCellNames.getName(simulations[i])+" with name `"+simulations[i].getName()+"` already exists");
+					throw new PropertyVetoException(VCellNames.getName(simulations[i])+" with name "+simulations[i].getName()+" already exists",evt);
 				}
 			}
 		}

From 374316ab69b0417f2ad8c1fc24d406c325f58ab6 Mon Sep 17 00:00:00 2001
From: GMarupilla <marupilla@mail.com>
Date: Wed, 7 Apr 2021 13:31:32 -0400
Subject: [PATCH 5/5] Revert "Update ci_cd.yml"

This reverts commit 46cc95933f6fc1f5b76144f238de3fb81bf53d86.
---
 .github/workflows/ci_cd.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/ci_cd.yml b/.github/workflows/ci_cd.yml
index f0e2925aa8..51c6f8968c 100644
--- a/.github/workflows/ci_cd.yml
+++ b/.github/workflows/ci_cd.yml
@@ -6,7 +6,6 @@ on:
       - '*'
       - '*/*'
       - '**'
-      - validate
   release:
     types: [published, edited]