From e9cce591f200c954e2941e1ecc66889ca9f724f1 Mon Sep 17 00:00:00 2001
From: Maximiliano Osorio <maxiosorio@gmail.com>
Date: Tue, 13 Jun 2023 16:58:38 -0400
Subject: [PATCH] fix: save

---
 planner/.classpath                            | 11 ++++
 portal/pom.xml                                |  2 +-
 wings-docker/config/default/portal.properties | 52 ------------------
 .../config/local-mosorio/portal.properties    | 54 -------------------
 .../config/local-mosorio/wings-portal.xml     |  5 --
 wings-docker/config/pegasus/portal.properties | 53 ------------------
 wings-docker/docker/default/Dockerfile        |  1 -
 7 files changed, 12 insertions(+), 166 deletions(-)
 delete mode 100644 wings-docker/config/default/portal.properties
 delete mode 100644 wings-docker/config/local-mosorio/portal.properties
 delete mode 100644 wings-docker/config/local-mosorio/wings-portal.xml
 delete mode 100644 wings-docker/config/pegasus/portal.properties

diff --git a/planner/.classpath b/planner/.classpath
index 94fadc55..9fdde8b4 100644
--- a/planner/.classpath
+++ b/planner/.classpath
@@ -54,5 +54,16 @@
 			<attribute name="test" value="true"/>
 		</attributes>
 	</classpathentry>
+	<classpathentry kind="src" path=".apt_generated">
+		<attributes>
+			<attribute name="optional" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path=".apt_generated_tests">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="target/classes"/>
 </classpath>
diff --git a/portal/pom.xml b/portal/pom.xml
index 978c993e..9cdcf2f4 100644
--- a/portal/pom.xml
+++ b/portal/pom.xml
@@ -21,7 +21,7 @@
 		<servlet-api.version>2.5</servlet-api.version>
 		<httpclient.version>4.5.2</httpclient.version>
 		<jersey.version>2.27</jersey.version>
-		<jackson.version>2.8.6</jackson.version>
+		<jackson.version>2.14.0-rc2</jackson.version>
 		<javax.validation.version>1.1.0.Final</javax.validation.version>
 		<commons-fileupload.version>1.3.3</commons-fileupload.version>
 	</properties>
diff --git a/wings-docker/config/default/portal.properties b/wings-docker/config/default/portal.properties
deleted file mode 100644
index dace1762..00000000
--- a/wings-docker/config/default/portal.properties
+++ /dev/null
@@ -1,52 +0,0 @@
-{
-    storage =
-    {
-        local = /opt/wings/storage/default;
-        tdb = /opt/wings/storage/default/TDB;
-    }
-
-    server = http://localhost:8080;
-    graphviz = /usr/bin/dot;
-    light-reasoner = false;
-    ontology = 
-    {
-        data = http://www.wings-workflows.org/ontology/data.owl;
-        component = http://www.wings-workflows.org/ontology/component.owl;
-        workflow = http://www.wings-workflows.org/ontology/workflow.owl;
-        execution = http://www.wings-workflows.org/ontology/execution.owl;
-    }
-
-    execution = 
-    {
-        engine = 
-        {
-            name = Local;
-            implementation = edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
-            type = BOTH;
-        }
-
-        engine = 
-        {
-            name = Distributed;
-            implementation = edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
-            type = BOTH;
-        }
-    }
-
-    publisher =
-    {
-        url = "https://publisher.mint.isi.edu";
-        name = "exportTest"
-        upload-server =
-        {
-            url = "https://publisher.mint.isi.edu";
-            username = "user";
-            password = "password";
-        }
-        triple-store = {
-            publish = http://ontosoft.isi.edu:3030/provenance/data;
-            query = http://ontosoft.isi.edu:3030/provenance/sparql;
-            domains-directory = /opt/wings/storage/default;
-        }
-    }
-}
diff --git a/wings-docker/config/local-mosorio/portal.properties b/wings-docker/config/local-mosorio/portal.properties
deleted file mode 100644
index 1ec6f442..00000000
--- a/wings-docker/config/local-mosorio/portal.properties
+++ /dev/null
@@ -1,54 +0,0 @@
-{
-
-
-    storage = 
-    {
-        local = /Users/mosorio/Downloads/tomcat/wings/storage/default;
-        tdb = /Users/mosorio/Downloads/tomcat/wings/storage/default/TDB;
-    }
-
-    server = http://localhost:8080;
-    graphviz = /usr/bin/dot;
-    light-reasoner = false;
-    ontology = 
-    {
-        data = http://www.wings-workflows.org/ontology/data.owl;
-        component = http://www.wings-workflows.org/ontology/component.owl;
-        workflow = http://www.wings-workflows.org/ontology/workflow.owl;
-        execution = http://www.wings-workflows.org/ontology/execution.owl;
-    }
-
-    execution = 
-    {
-        engine = 
-        {
-            name = Local;
-            implementation = edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
-            type = BOTH;
-        }
-
-        engine = 
-        {
-            name = Distributed;
-            implementation = edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
-            type = BOTH;
-        }
-    }
-
-    publisher =
-    {
-        url = "http://ontosoft.isi.edu:7071";
-        name = "exportTest"
-        upload-server =
-        {
-            url = "http://ontosoft.isi.edu:7071";
-            username = "user";
-            password = "password";
-        }
-        triple-store = {
-            publish = http://ontosoft.isi.edu:3030/provenance/data;
-            query = http://ontosoft.isi.edu:3030/provenance/sparql;
-            domains-directory = /Users/mosorio/Downloads/tomcat/wings/storage/default;
-        }
-    }
-}
diff --git a/wings-docker/config/local-mosorio/wings-portal.xml b/wings-docker/config/local-mosorio/wings-portal.xml
deleted file mode 100644
index 272e5c07..00000000
--- a/wings-docker/config/local-mosorio/wings-portal.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<Context debug="0" reloadable="true" crossContext="true">
-   <Parameter name="config.file" value="/etc/wings/portal.properties" />
-   <ResourceLink name="users" global="UserDatabase" type="org.apache.catalina.UserDatabase" />
-</Context>
diff --git a/wings-docker/config/pegasus/portal.properties b/wings-docker/config/pegasus/portal.properties
deleted file mode 100644
index c05f48bc..00000000
--- a/wings-docker/config/pegasus/portal.properties
+++ /dev/null
@@ -1,53 +0,0 @@
-{
-    storage = 
-    {
-        local = /lfs/wings/storage/default;
-        tdb = /lfs/wings/storage/default/TDB;
-    }
-
-    server = http://localhost:8080;
-    graphviz = /usr/bin/dot;
-    light-reasoner = false;
-    ontology = 
-    {
-        data = http://www.wings-workflows.org/ontology/data.owl;
-        component = http://www.wings-workflows.org/ontology/component.owl;
-        workflow = http://www.wings-workflows.org/ontology/workflow.owl;
-        execution = http://www.wings-workflows.org/ontology/execution.owl;
-    }
-
-    execution = 
-    {
-        engine = 
-        {
-            name = Local;
-            implementation = edu.isi.wings.execution.engine.api.impl.local.LocalExecutionEngine;
-            type = BOTH;
-        }
-
-        engine = 
-        {
-            name = Distributed;
-            implementation = edu.isi.wings.execution.engine.api.impl.distributed.DistributedExecutionEngine;
-            type = BOTH;
-        }
-
-
-        engine =
-        {
-            name = Pegasus;
-            implementation = edu.isi.wings.execution.engine.api.impl.pegasus.PegasusExecutionEngine;
-            type = BOTH;
-            properties =
-            {
-                pegasus =
-                {
-                    home         = /usr;
-                    storage-dir  = /lfs/pegasus/storage;
-                    site-catalog = /etc/pegasus/local.sites.xml
-                    site         = local;
-                }
-            }
-        }
-    }
-}
diff --git a/wings-docker/docker/default/Dockerfile b/wings-docker/docker/default/Dockerfile
index fd9f3fee..a1738c90 100644
--- a/wings-docker/docker/default/Dockerfile
+++ b/wings-docker/docker/default/Dockerfile
@@ -49,6 +49,5 @@ RUN jar -xvf wings-portal-*.war
 
 # Add wings context file to the wings portal webapp
 COPY ./wings-docker/config/default/wings-portal.xml /usr/local/tomcat/webapps/wings-portal/META-INF/context.xml
-COPY ./wings-docker/config/default/portal.properties /etc/wings/portal.properties
 
 WORKDIR /usr/local/tomcat