Upgraded gcube-smartgears-bom version

.gitignore

@@ -1,3 +1,5 @@
 target
 .classpath
 .project
+/.DS_Store
+/bin/

CHANGELOG.md

@@ -2,10 +2,24 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 # Changelog for Smart Executor Service
 
+## [v3.2.1-SNAPSHOT]
+
+- Fixed bug on concurrent attempt to enter in a session while trying to schedule a second task #27319
+- Fixed bug on concurrent attempt to enter in a session while trying to execute another task #24116
+
+
+## [v3.2.0]
+
+- Fixed RequestFilter to avoid to remove info to Smartgears
+- Migrated code to reorganized E/R format [#24992]
+- Force guava version to 23.6-jre to meet requirements of new plugins
+
+
 ## [v3.1.0]
 
 - Ported service to authorization-utils [#22871]
 
+
 ## [v3.0.0] 
 
 - Switched smart-executor JSON management to gcube-jackson [#19647]
@@ -13,6 +27,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 - Redesigned HTTP APIs to comply with RESTful architectural style [#12997]
 - Added API to retrieve scheduled tasks [#10780]
 
+
 ## [v2.0.0] 
 
 - Removed SOAP APIs

docs/.gitignore

@@ -0,0 +1 @@
+/_build/

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/conf.py

@@ -0,0 +1,54 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Smart Executor Service'
+copyright = '2012, Luca Frosini (ISTI-CNR)'
+author = 'Luca Frosini (ISTI-CNR)'
+
+# The full version, including alpha/beta/rc tags
+release = '3.2.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = []
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinxdoc'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/index.rst

@@ -0,0 +1,103 @@
+
+***********************************************************
+Welcome to Smart Executor Service documentation
+***********************************************************
+
+Smart Executor is a RESTful application which exposes operations via REST-API.
+
+See the available `REST-API docs <../api-docs/index.html>`_.
+
+Authorization
+=============
+
+D4Science adopts state-of-the-art industry standards for authentication and authorization. 
+Specifically, the implementation fully adopts `OIDC (OpenID Connect) <https://openid.net/connect>`_ for authentication and UMA 2 (User-Managed Authorization) for authorization flows. 
+`JSON Web Token (JWT) Access token <https://jwt.io/>`_ are used for both authentication and authorization.
+
+Obtain your Bearer token here: https://dev.d4science.org/how-to-access-resources
+
+Service
+=======
+
+You can call the methods of the Web Service by writing your own REST client application or using existing REST client plugins.
+
+
+HTTP Statuses
+-------------
+
+Any successful operation returns *200 OK* HTTP status code.
+The create operation returns *201 Created*. 
+Any Background operation returns *202 Accepted*.
+Any operation which does not provide any content return *204 No Content*.
+
+
+
+The most common error status a client can obtain are:
+
+* **400 Bad Request** used to indicate a clients error `<https://tools.ietf.org/html/rfc7231#section-6.5.1>`_;
+* **401 Unauthorized** used to indicate that the client does not provide the authorization token in the HTTP Header or the client has not enough right to perform such request `<https://tools.ietf.org/html/rfc7235#section-3.1>`_;
+* **404 Not Found** used to indicate that the requested instance does not exist `<https://tools.ietf.org/html/rfc7231#section-6.5.4>`_;
+* **405 Method Not Allowed** the used HTTP method is not supported for the requested URL `<https://tools.ietf.org/html/rfc7231#section-6.5.5>`_.
+  The response contains the *Allow* HTTP Header indicating the supported HTTP method for such URL `<https://tools.ietf.org/html/rfc7231#section-7.4.1>`_;
+* **409 Conflict**  the request could not be completed due to a conflict with the current state of the target resource (e.g. the name of the resource already exists) `<https://tools.ietf.org/html/rfc7231#section-6.5.8>`_;
+* **500 Internal Server Error** indicate a server failure `<https://tools.ietf.org/html/rfc7231#section-6.6.1>`_.
+
+You can find a complete list of HTTP Status at `<https://httpstatuses.com/>`_
+
+If you get a *500 Internal Server Error*, please report it in the `gCube ticketing system <https://support.d4science.org>`_. 
+
+Please use this checklist before reporting an error:
+
+* Replicate the request;
+* The failure could be temporal due to network error, server issue and many other temporal issues. For this reason, please retry the request after a certain amount of time before reporting the issue;
+* indicate how to replicate the error;
+* indicate the time when the error occurred (this simplifies identifying the issue).
+
+HTTP Methods
+------------
+
+Smart Executor is a pure RESTful service. 
+
+
+
+Service Discovery on IS
+=======================
+
+The service can be discovered in the gCore IS as gCore Endpoint with the following parameter:
+
+.. code:: xml
+
+	<ServiceClass>org.gcube.vremanagement</ServiceClass>
+	<ServiceName>smart-executor</ServiceName>
+
+
+The service can be discovered in the Facet Based IS as EService with the following json query:
+
+.. code:: json
+
+	{
+		"@class": "EService",
+		"consistsOf": [
+			{
+				"@class": "IsIdentifiedBy",
+				"target": {
+					"@class": "SoftwareFacet",
+					"group": "org.gcube.vremanagement",
+					"name": "smart-executor"
+				}
+			}
+		]
+	}
+
+	
+	
+Service Maven Coordinates
+=========================
+	
+The maven coordinates of gCat service are:
+
+.. code:: xml
+
+	<groupId>org.gcube.vremanagement</groupId>
+	<artifactId>smart-executor</artifactId>
+	

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

gcube/extra-resources/WEB-INF/gcube-app.xml

@@ -5,4 +5,6 @@
 	<group>${project.groupId}</group>
 	<version>${project.version}</version>
 	<description>${project.description}</description>
+	<exclude>/api-docs.*</exclude>
+	<exclude>/docs.*</exclude>
 </application>

pom.xml

@@ -11,7 +11,7 @@
 
 	<groupId>org.gcube.vremanagement</groupId>
 	<artifactId>smart-executor</artifactId>
-	<version>3.1.0</version>
+	<version>3.2.1-SNAPSHOT</version>
 	<name>SmartExecutor</name>
 	<description>Smart Executor Service allows to launch recurrent tasks such as task for infrastructure management, healthy monitoring etc.</description>
 	<packaging>war</packaging>
@@ -20,6 +20,7 @@
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 		<webappDirectory>${project.basedir}${file.separator}src${file.separator}main${file.separator}webapp${file.separator}WEB-INF</webappDirectory>
 		<orientdb.version>3.1.12</orientdb.version>
+		<enunciate.version>2.14.0</enunciate.version>
 	</properties>
 
 	<scm>
@@ -33,7 +34,7 @@
 			<dependency>
 				<groupId>org.gcube.distribution</groupId>
 				<artifactId>gcube-smartgears-bom</artifactId>
-				<version>2.2.0</version>
+				<version>2.5.1-SNAPSHOT</version>
 				<type>pom</type>
 				<scope>import</scope>
 			</dependency>
@@ -104,29 +105,63 @@
 			<artifactId>smart-executor-client</artifactId>
 			<version>[3.0.0, 4.0.0-SNAPSHOT)</version>
 		</dependency>
-
-
-		<!-- Jersey -->
+		
 		<dependency>
-			<groupId>javax.ws.rs</groupId>
-			<artifactId>javax.ws.rs-api</artifactId>
+			<groupId>com.google.guava</groupId>
+			<artifactId>guava</artifactId>
+			<version>23.6-jre</version>
 		</dependency>
+
+
 		<dependency>
 			<groupId>org.glassfish.jersey.containers</groupId>
 			<artifactId>jersey-container-servlet</artifactId>
 		</dependency>
 		<dependency>
-			<groupId>javax.servlet</groupId>
-			<artifactId>javax.servlet-api</artifactId>
-			<version>3.0.1</version>
+		    <groupId>javax.ws.rs</groupId>
+		    <artifactId>javax.ws.rs-api</artifactId>
+		</dependency>
+
+		<!-- Added to support Java 11 JDK -->
+		<dependency>
+    		<groupId>javax.xml.ws</groupId>
+    		<artifactId>jaxws-api</artifactId>
+    		<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.projectlombok</groupId>
+			<artifactId>lombok</artifactId>
 			<scope>provided</scope>
 		</dependency>
-		<!-- END Jersey -->
-
+		<!-- END Added to support Java 11 JDK -->
+		
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-api</artifactId>
 		</dependency>
+		
+		<!-- Required for Enunciate plugin -->
+		<dependency>
+			<groupId>com.webcohesion.enunciate</groupId>
+			<artifactId>enunciate-core-annotations</artifactId>
+			<version>${enunciate.version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.webcohesion.enunciate</groupId>
+			<artifactId>enunciate-rt-util</artifactId>
+			<version>${enunciate.version}</version>
+			<scope>provided</scope>
+		</dependency>
+		<dependency>
+		    <groupId>javax.servlet</groupId>
+		    <artifactId>javax.servlet-api</artifactId>
+		    <version>3.1.0</version>
+		    <scope>provided</scope>
+		</dependency>
+		<!-- END Required for Enunciate plugin -->
+		
+		
 		<!-- Tests -->
 		<dependency>
 			<groupId>junit</groupId>
@@ -141,4 +176,80 @@
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
+	
+	
+		<build>
+       	<plugins>
+			<!-- Sphinx plugin' -->
+			<plugin>
+				<groupId>kr.motd.maven</groupId>
+				<artifactId>sphinx-maven-plugin</artifactId>
+				<version>2.10.0</version>
+				<configuration>
+					<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}/docs</outputDirectory>
+					<builder>html</builder>
+					<configDirectory>${basedir}/docs</configDirectory>
+					<sourceDirectory>${basedir}/docs</sourceDirectory>
+				</configuration>
+				<executions>
+					<execution>
+						<phase>process-resources</phase>
+						<goals>
+							<goal>generate</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			
+			<!-- Enunciate Maven plugin -->
+			<plugin>
+				<groupId>com.webcohesion.enunciate</groupId>
+				<artifactId>enunciate-maven-plugin</artifactId>
+				<version>${enunciate.version}</version>
+				<executions>
+					<execution>
+		            	<id>assemble</id>
+		            	<goals>
+		                	<goal>assemble</goal>
+		            	</goals>
+		        	</execution>
+		    	</executions>
+			</plugin>
+			<!-- Copy Enunciate Documentation from your-application/api-docs into your war -->
+			<plugin>
+			    <groupId>org.apache.maven.plugins</groupId>
+			    <artifactId>maven-resources-plugin</artifactId>
+			    <executions>
+			        <execution>
+			            <id>copy-enunciate-docs</id>
+			            <phase>process-resources</phase>
+			            <goals>
+			                <goal>copy-resources</goal>
+			            </goals>
+			            <configuration>
+			                <outputDirectory>target</outputDirectory>
+			                <resources>
+			                    <resource>
+			                        <targetPath>${project.build.directory}/${project.artifactId}-${project.version}/api-docs</targetPath>
+			                        <directory>${project.build.directory}/api-docs</directory>
+			                        <filtering>true</filtering>
+			                    </resource>
+			                </resources>
+			            </configuration>
+			        </execution>
+			    </executions>
+			</plugin>
+			
+			
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-war-plugin</artifactId>
+				<configuration>
+					<attachClasses>true</attachClasses>
+				</configuration>
+			</plugin>
+			
+		</plugins>
+	</build>
+	
 </project>

src/main/java/org/gcube/vremanagement/executor/SmartExecutorInitializator.java

@@ -148,24 +148,27 @@ public class SmartExecutorInitializator implements ApplicationManager {
 						Secret secret = SecretUtility.getSecretByTokenString(scheduledTasktoken);
 						
 						SecretManager secretManager = SecretManagerProvider.instance.get();
-						try {
-							secretManager.startSession(secret);
-							SmartExecutorScheduler smartExecutorScheduler = SmartExecutorSchedulerFactory.getSmartExecutorScheduler();
-							// A new Scheduled Task will be persisted due to launch. Removing it 
-							smartExecutorPersistenceConnector.removeScheduledTask(scheduledTask);
-							smartExecutorScheduler.schedule(launchParameter, scheduledTask.getUUID());
-						} catch (Exception e) {
-							logger.error("({}) Error while trying to relaunch scheduled task.", context, e);
+						synchronized (secretManager) {
 							try {
-								smartExecutorPersistenceConnector.addScheduledTask(scheduledTask);
-							} catch (Exception ex) {
-								logger.error("({}) Unable to add back scheduled task {}", context, taskAsString);
+								logger.trace("Starting a Secret Manager session (synchronized block)...");
+								secretManager.startSession(secret);
+								SmartExecutorScheduler smartExecutorScheduler = SmartExecutorSchedulerFactory.getSmartExecutorScheduler();
+								// A new Scheduled Task will be persisted due to launch. Removing it 
+								smartExecutorPersistenceConnector.removeScheduledTask(scheduledTask);
+								smartExecutorScheduler.schedule(launchParameter, scheduledTask.getUUID());
+							} catch (Exception e) {
+								logger.error("({}) Error while trying to relaunch scheduled task.", context, e);
+								try {
+									smartExecutorPersistenceConnector.addScheduledTask(scheduledTask);
+								} catch (Exception ex) {
+									logger.error("({}) Unable to add back scheduled task {}", context, taskAsString);
+								}
+							}finally {
+								secretManager.endSession();
+								logger.trace("Secret Manager session terminated (synchronized block).");
 							}
-						}finally {
-							secretManager.endSession();
 						}
 						
-						
 					}
 					
 				};

src/main/java/org/gcube/vremanagement/executor/ispublisher/RestISPublisher.java

@@ -9,7 +9,6 @@ import java.util.Map;
 import java.util.UUID;
 
 import org.gcube.informationsystem.base.reference.Direction;
-import org.gcube.informationsystem.model.impl.properties.HeaderImpl;
 import org.gcube.informationsystem.model.impl.properties.PropagationConstraintImpl;
 import org.gcube.informationsystem.model.reference.entities.Facet;
 import org.gcube.informationsystem.model.reference.entities.Resource;
@@ -151,7 +150,7 @@ public class RestISPublisher extends ISPublisher {
 	protected RunningPlugin publishRunningPluginWithRelations(Plugin plugin, UUID pluginUUID) throws Exception {
 		
 		RunningPlugin runningPlugin = new RunningPluginImpl();
-		runningPlugin.setHeader(new HeaderImpl(pluginUUID));
+		runningPlugin.setID(pluginUUID);
 		
 		SoftwareFacet softwareFacet = new SoftwareFacetImpl();
 		softwareFacet.setGroup(plugin.getGroup());
@@ -240,7 +239,7 @@ public class RestISPublisher extends ISPublisher {
 				runningPlugin = publishRunningPluginWithRelations(plugin, pluginUUID);
 			} catch (AvailableInAnotherContextException e) {
 				runningPlugin = new RunningPluginImpl();
-				runningPlugin.setHeader(new HeaderImpl(pluginUUID));
+				runningPlugin.setID(pluginUUID);
 				resourceRegistryPublisher.addToCurrentContext(runningPlugin, false);
 			} catch (ResourceRegistryException e) {
 				throw e;

src/main/java/org/gcube/vremanagement/executor/pluginmanager/RunnablePlugin.java

@@ -75,7 +75,7 @@ public class RunnablePlugin<T extends Plugin> implements Runnable {
 	
 	
 	@Override
-	public void run(){
+	public synchronized void run(){
 		String pluginName = plugin.getName(); 
 		
 		logger.info("{} : {} is going to be launched (UUID={}, iterationNumber={}) with the following inputs {}", 
@@ -85,10 +85,10 @@ public class RunnablePlugin<T extends Plugin> implements Runnable {
 		JobUsageRecord jobUsageRecord = new JobUsageRecord();
 		
 		long startTime = actualStateEvolution.getTimestamp();
+		Secret secret = SecretUtility.getSecretByTokenString(token);
 		SecretManager secretManager = SecretManagerProvider.instance.get();
 		
 		try {
-			Secret secret = SecretUtility.getSecretByTokenString(token);
 			secretManager.startSession(secret);
 			
 			setState(PluginState.RUNNING);

src/main/java/org/gcube/vremanagement/executor/rest/RequestFilter.java

@@ -32,7 +32,7 @@ public class RequestFilter implements ContainerRequestFilter, ContainerResponseF
 	public void filter(ContainerRequestContext requestContext) throws IOException {
 		logger.trace("PreMatching RequestFilter");
 		
-		SecretManagerProvider.instance.reset();
+		SecretManagerProvider.instance.remove();
 		SecretManager secretManager = new SecretManager();
 		
 		String token = AccessTokenProvider.instance.get();
@@ -48,14 +48,13 @@ public class RequestFilter implements ContainerRequestFilter, ContainerResponseF
 		}
 		
 		SecretManagerProvider.instance.set(secretManager);
-		
 	}
 
 	@Override
 	public void filter(ContainerRequestContext requestContext, ContainerResponseContext responseContext)
 			throws IOException {
 		logger.trace("ResponseFilter");
-		SecretManagerProvider.instance.reset();
+		SecretManagerProvider.instance.remove();
 	}
 
 }

src/main/webapp/WEB-INF/web.xml

@@ -4,6 +4,14 @@
 	<servlet>
     	<servlet-name>org.gcube.vremanagement.executor.ResourceInitializer</servlet-name>
     </servlet>
+    <servlet-mapping>
+2		<servlet-name>default</servlet-name>
+3		<url-pattern>/docs/*</url-pattern>
+4	</servlet-mapping>
+    <servlet-mapping>
+2		<servlet-name>default</servlet-name>
+3		<url-pattern>/api-docs/*</url-pattern>
+4	</servlet-mapping>
     <servlet-mapping>
         <servlet-name>org.gcube.vremanagement.executor.ResourceInitializer</servlet-name>
         <url-pattern>/*</url-pattern>

src/main/webapp/docs/css/d4science_enunciate_custom.css

@@ -0,0 +1,25 @@
+.d4science_intro {
+	top: 0;
+	z-index: 2000;
+	position: fixed;
+	display: block ruby;
+	padding: 10px;
+	background: white;
+	width: 100%;
+}
+
+.navbar-fixed-top {
+	top: 100px !important;
+}
+
+.sidebar {
+	top: 160px !important;
+}
+
+.navbar {
+	margin-bottom: 40px !important;
+}
+
+.main {
+	top: 90px;
+}

src/test/java/org/gcube/vremanagement/executor/ispublisher/RestISPublisherTest.java

@@ -6,7 +6,7 @@ import java.util.UUID;
 import javax.servlet.ServletContext;
 
 import org.gcube.common.events.Hub;
-import org.gcube.informationsystem.utils.ElementMapper;
+import org.gcube.informationsystem.serialization.ElementMapper;
 import org.gcube.resourcemanagement.model.impl.entities.facets.AccessPointFacetImpl;
 import org.gcube.resourcemanagement.model.reference.entities.facets.AccessPointFacet;
 import org.gcube.smartgears.configuration.application.ApplicationConfiguration;