refactoring

libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/GraphArc.java

@@ -1,28 +0,0 @@
-package eu.dnetlib.manager.wf.model;
-
-import java.io.Serializable;
-
-public class GraphArc implements Serializable {
-
-	private static final long serialVersionUID = 7866138976929522262L;
-
-	private String name;
-	private String to;
-
-	public String getName() {
-		return name;
-	}
-
-	public void setName(final String name) {
-		this.name = name;
-	}
-
-	public String getTo() {
-		return to;
-	}
-
-	public void setTo(final String to) {
-		this.to = to;
-	}
-
-}

libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/GraphNode.java

@@ -1,65 +0,0 @@
-package eu.dnetlib.manager.wf.model;
-
-import java.io.Serializable;
-import java.util.List;
-
-public class GraphNode implements Serializable {
-
-	private static final long serialVersionUID = -3695762832959801906L;
-
-	private String name;
-	private String type;
-	private boolean isStart = false;
-	private boolean isJoin = false;
-	private List<GraphArc> arcs;
-	private List<GraphParameter> params;
-
-	public String getName() {
-		return name;
-	}
-
-	public void setName(final String name) {
-		this.name = name;
-	}
-
-	public String getType() {
-		return type;
-	}
-
-	public void setType(final String type) {
-		this.type = type;
-	}
-
-	public boolean isStart() {
-		return isStart;
-	}
-
-	public void setStart(final boolean isStart) {
-		this.isStart = isStart;
-	}
-
-	public boolean isJoin() {
-		return isJoin;
-	}
-
-	public void setJoin(final boolean isJoin) {
-		this.isJoin = isJoin;
-	}
-
-	public List<GraphArc> getArcs() {
-		return arcs;
-	}
-
-	public void setArcs(final List<GraphArc> arcs) {
-		this.arcs = arcs;
-	}
-
-	public List<GraphParameter> getParams() {
-		return params;
-	}
-
-	public void setParams(final List<GraphParameter> params) {
-		this.params = params;
-	}
-
-}

libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/GraphParameter.java

@@ -1,39 +0,0 @@
-package eu.dnetlib.manager.wf.model;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Map;
-
-public class GraphParameter extends GraphParameterValue implements Serializable {
-
-	private static final long serialVersionUID = 1894419948433994453L;
-
-	private String name;
-	private List<GraphParameterValue> values;
-	private Map<String, GraphParameterValue> map;
-
-	public String getName() {
-		return name;
-	}
-
-	public void setName(final String name) {
-		this.name = name;
-	}
-
-	public List<GraphParameterValue> getValues() {
-		return values;
-	}
-
-	public void setValues(final List<GraphParameterValue> values) {
-		this.values = values;
-	}
-
-	public Map<String, GraphParameterValue> getMap() {
-		return map;
-	}
-
-	public void setMap(final Map<String, GraphParameterValue> map) {
-		this.map = map;
-	}
-
-}

libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/GraphParameterValue.java

@@ -1,45 +0,0 @@
-package eu.dnetlib.manager.wf.model;
-
-import java.io.Serializable;
-
-public class GraphParameterValue implements Serializable {
-
-	private static final long serialVersionUID = 7815785723401725707L;
-
-	private String value;
-	private String ref;
-	private String property;
-	private String env;
-
-	public String getValue() {
-		return value;
-	}
-
-	public void setValue(final String value) {
-		this.value = value;
-	}
-
-	public String getRef() {
-		return ref;
-	}
-
-	public void setRef(final String ref) {
-		this.ref = ref;
-	}
-
-	public String getProperty() {
-		return property;
-	}
-
-	public void setProperty(final String property) {
-		this.property = property;
-	}
-
-	public String getEnv() {
-		return env;
-	}
-
-	public void setEnv(final String env) {
-		this.env = env;
-	}
-}

libs/dnet-is-common/src/main/java/eu/dnetlib/manager/wf/model/WorkflowGraph.java

@@ -0,0 +1,270 @@
+package eu.dnetlib.manager.wf.model;
+
+import java.io.Serializable;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import java.util.stream.Collectors;
+
+import org.apache.commons.lang3.StringUtils;
+import org.springframework.core.env.Environment;
+
+public class WorkflowGraph implements Serializable {
+
+	private static final long serialVersionUID = 5919290887480115842L;
+
+	public List<WfParam> parameters;
+	public List<Node> graph;
+
+	public List<Node> getGraph() {
+		return graph;
+	}
+
+	public void setGraph(final List<Node> graph) {
+		this.graph = graph;
+	}
+
+	public List<WfParam> getParameters() {
+		return parameters;
+	}
+
+	public void setParameters(final List<WfParam> parameters) {
+		this.parameters = parameters;
+	}
+
+	class WfParam implements Serializable {
+
+		private static final long serialVersionUID = 5885589803738655166L;
+
+		private String name;
+		private String description;
+		private String type;
+		private String defaultValue;
+		private boolean required;
+
+		public String getName() {
+			return name;
+		}
+
+		public void setName(final String name) {
+			this.name = name;
+		}
+
+		public String getDescription() {
+			return description;
+		}
+
+		public void setDescription(final String description) {
+			this.description = description;
+		}
+
+		public String getType() {
+			return type;
+		}
+
+		public void setType(final String type) {
+			this.type = type;
+		}
+
+		public String getDefaultValue() {
+			return defaultValue;
+		}
+
+		public void setDefaultValue(final String defaultValue) {
+			this.defaultValue = defaultValue;
+		}
+
+		public boolean isRequired() {
+			return required;
+		}
+
+		public void setRequired(final boolean required) {
+			this.required = required;
+		}
+
+	}
+
+	public class Node implements Serializable {
+
+		private static final long serialVersionUID = -3695762832959801906L;
+
+		private static final String regExRef = "\\$\\{(\\w*)\\}";
+
+		private String name;
+		private String type;
+		private boolean isStart = false;
+		private boolean isJoin = false;
+		private List<Arc> arcs;
+		private List<NodeParam> input;
+
+		public String getName() {
+			return name;
+		}
+
+		public void setName(final String name) {
+			this.name = name;
+		}
+
+		public String getType() {
+			return type;
+		}
+
+		public void setType(final String type) {
+			this.type = type;
+		}
+
+		public boolean isStart() {
+			return isStart;
+		}
+
+		public void setStart(final boolean isStart) {
+			this.isStart = isStart;
+		}
+
+		public boolean isJoin() {
+			return isJoin;
+		}
+
+		public void setJoin(final boolean isJoin) {
+			this.isJoin = isJoin;
+		}
+
+		public List<Arc> getArcs() {
+			return arcs;
+		}
+
+		public void setArcs(final List<Arc> arcs) {
+			this.arcs = arcs;
+		}
+
+		public List<NodeParam> getInput() {
+			return input;
+		}
+
+		public void setInput(final List<NodeParam> input) {
+			this.input = input;
+		}
+
+		public Map<String, String> findEnvParams() {
+			return input.stream()
+				.filter(p -> StringUtils.isNotBlank(p.getEnv()))
+				.collect(Collectors.toMap(NodeParam::getName, NodeParam::getEnv));
+		}
+
+		public Map<String, Object> calculateInitialParams(final Map<String, String> globalParams, final Environment environment) {
+			final Map<String, Object> map = new HashMap<>();
+
+			input.stream()
+				.filter(p -> StringUtils.isBlank(p.getEnv()))
+				.forEach(p -> map.put(p.getName(), calculateSimpleValue(p, globalParams, environment)));
+
+			return map;
+		}
+
+		private Object calculateSimpleValue(final NodeParam p, final Map<String, String> globalParams, final Environment environment) {
+			String value = p.getValue();
+			final String ref = p.getRef();
+			final String prop = p.getProperty();
+
+			if (StringUtils.isNotBlank(ref) && StringUtils.isNotBlank(globalParams.get(ref))) {
+				return globalParams.get(ref);
+			} else if (StringUtils.isNotBlank(value)) {
+				final Matcher matcher = Pattern.compile(regExRef, Pattern.MULTILINE).matcher(value);
+				while (matcher.find()) {
+					final String rName = matcher.group(1);
+					final String rValue = globalParams.get(rName);
+					if (StringUtils.isBlank(rValue)) { return null; }
+					value = value.replaceAll(Pattern.quote(matcher.group(0)), rValue);
+					System.out.println("NEW VALUE " + value);
+				}
+				return value;
+			} else if (StringUtils.isNotBlank(prop)) {
+				return environment.getProperty(prop);
+			} else {
+				return null;
+			}
+
+		}
+
+	}
+
+	public class Arc implements Serializable {
+
+		private static final long serialVersionUID = 7866138976929522262L;
+
+		private String name;
+		private String to;
+
+		public String getName() {
+			return name;
+		}
+
+		public void setName(final String name) {
+			this.name = name;
+		}
+
+		public String getTo() {
+			return to;
+		}
+
+		public void setTo(final String to) {
+			this.to = to;
+		}
+
+	}
+
+	class NodeParam implements Serializable {
+
+		private static final long serialVersionUID = 7815785723401725707L;
+
+		private String name;
+		private String value;
+		private String ref;
+		private String property;
+		private String env;
+
+		public String getName() {
+			return name;
+		}
+
+		public void setName(final String name) {
+			this.name = name;
+		}
+
+		public String getValue() {
+			return value;
+		}
+
+		public void setValue(final String value) {
+			this.value = value;
+		}
+
+		public String getRef() {
+			return ref;
+		}
+
+		public void setRef(final String ref) {
+			this.ref = ref;
+		}
+
+		public String getProperty() {
+			return property;
+		}
+
+		public void setProperty(final String property) {
+			this.property = property;
+		}
+
+		public String getEnv() {
+			return env;
+		}
+
+		public void setEnv(final String env) {
+			this.env = env;
+		}
+
+	}
+
+}

libs/dnet-is-common/src/main/resources/sql/schema.sql

@@ -280,18 +280,6 @@ CREATE TABLE workflow_instances (
 	user_params             jsonb NOT NULL DEFAULT '{}'
 );
 
--- TO DELETE 
-CREATE TABLE workflow_expected_params (
-	wf_id                   text REFERENCES resource(id),
-	name                    text,
-	description             text,
-	type                    text,
-	required                boolean,
-	default_value           text,
-	PRIMARY KEY (wf_id, name)
-);
--- END
-
 CREATE TABLE workflow_subscriptions (
 	wf_instance_id          text NOT NULL REFERENCES workflow_instances(id),
 	condition               text NOT NULL,

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/cron/ScheduledWorkflowLauncher.java

@@ -122,7 +122,9 @@ public class ScheduledWorkflowLauncher {
 	}
 
 	private boolean isNotRunning(final WorkflowInstance instance) {
-		for (final WorkflowProcess p : processRegistry.findProcsByOtherId(instance.getId())) {
+		final WorkflowProcess p = processRegistry.findProcsByInstanceId(instance.getId());
+
+		if (p != null) {
 			switch (p.getStatus()) {
 			case CREATED:
 				return false;
@@ -132,6 +134,7 @@ public class ScheduledWorkflowLauncher {
 				break;
 			}
 		}
+
 		return true;
 	}
 

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/GraphLoader.java

@@ -1,17 +1,10 @@
 package eu.dnetlib.manager.wf.workflows.graph;
 
-import java.util.HashMap;
 import java.util.HashSet;
-import java.util.List;
 import java.util.Map;
 import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.env.Environment;
 import org.springframework.stereotype.Service;
@@ -19,48 +12,41 @@ import org.springframework.stereotype.Service;
 import com.google.common.collect.Sets;
 
 import eu.dnetlib.errors.WorkflowManagerException;
-import eu.dnetlib.manager.wf.model.GraphArc;
+import eu.dnetlib.manager.wf.model.WorkflowGraph;
-import eu.dnetlib.manager.wf.model.GraphParameter;
-import eu.dnetlib.manager.wf.model.GraphParameterValue;
 import eu.dnetlib.manager.wf.workflows.util.NodeHelper;
 
 @Service
 public class GraphLoader {
 
-	private static final Log log = LogFactory.getLog(GraphLoader.class);
-
-	private final String regExRef = "\\$\\{(\\w*)\\}";
-
-	final Pattern pattern = Pattern.compile(regExRef, Pattern.MULTILINE);
-
 	@Autowired
 	private NodeHelper nodeHelper;
 
 	@Autowired
-	private Environment env;
+	private Environment environment;
 
-	public Graph loadGraph(final List<eu.dnetlib.manager.wf.model.GraphNode> workflowGraph, final Map<String, String> globalParams)
+	public Graph loadGraph(final WorkflowGraph workflowGraph, final Map<String, String> globalParams)
 		throws WorkflowManagerException {
 		final Graph graph = new Graph();
 
-		for (final eu.dnetlib.manager.wf.model.GraphNode node : workflowGraph) {
+		for (final WorkflowGraph.Node node : workflowGraph.getGraph()) {
 			final String nodeName = node.getName();
 			final String nodeType = node.getType();
 			final boolean isStart = node.isStart();
 			final boolean isJoin = node.isJoin();
 
-			final Map<String, GraphNodeParameter> params = calculateParamsForNode(node, globalParams);
+			final Map<String, Object> params = node.calculateInitialParams(globalParams, environment);
+			final Map<String, String> envParams = node.findEnvParams();
 
 			if (isStart) {
-				graph.addNode(GraphNode.newStartNode(nodeName, nodeType, params));
+				graph.addNode(GraphNode.newStartNode(nodeName, nodeType, params, envParams));
 			} else if (isJoin) {
-				graph.addNode(GraphNode.newJoinNode(nodeName, nodeType, params));
+				graph.addNode(GraphNode.newJoinNode(nodeName, nodeType, params, envParams));
 			} else {
-				graph.addNode(GraphNode.newNode(nodeName, nodeType, params));
+				graph.addNode(GraphNode.newNode(nodeName, nodeType, params, envParams));
 			}
 
-			if (graph.getArcs() != null) {
+			if (node.getArcs() != null) {
-				for (final GraphArc a : node.getArcs()) {
+				for (final WorkflowGraph.Arc a : node.getArcs()) {
 					final String arcName = a.getName();
 					final String to = a.getTo();
 					graph.addArc(new Arc(StringUtils.isNotBlank(arcName) ? arcName : Arc.DEFAULT_ARC, nodeName, to));
@@ -75,75 +61,6 @@ public class GraphLoader {
 		return graph;
 	}
 
-	public Map<String, GraphNodeParameter> calculateParamsForNode(final eu.dnetlib.manager.wf.model.GraphNode node, final Map<String, String> globalParams) {
-
-		final Map<String, GraphNodeParameter> params = new HashMap<>();
-
-		if (node.getParams() != null) {
-			for (final GraphParameter p : node.getParams()) {
-
-				final String pName = p.getName();
-
-				final GraphNodeParameter pValue = calculateSimpleValue(p, globalParams);
-
-				if (pValue != null) {
-					params.put(pName, pValue);
-				} else if (p.getMap() != null) {
-
-					final Map<String, GraphNodeParameter> map = p.getMap()
-						.entrySet()
-						.stream()
-						.collect(Collectors.toMap(e -> e.getKey(), e -> {
-							final GraphNodeParameter gnp = calculateSimpleValue(e.getValue(), globalParams);
-							if (gnp == null) {
-								final String msg = String.format("missing value for param: \"%s\"", e.getKey());
-								log.debug(msg);
-								return GraphNodeParameter.newNullParam();
-							}
-							return gnp;
-						}));
-					params.put(pName, GraphNodeParameter.newMapParam(map));
-				} else if (p.getValues() != null) {
-					final List<GraphNodeParameter> list = p.getValues()
-						.stream()
-						.map(e -> calculateSimpleValue(e, globalParams))
-						.collect(Collectors.toList());
-					params.put(pName, GraphNodeParameter.newListParam(list));
-				}
-			}
-		}
-
-		return params;
-	}
-
-	private GraphNodeParameter calculateSimpleValue(final GraphParameterValue graphValue, final Map<String, String> globalParams) {
-		String value = graphValue.getValue();
-		final String ref = graphValue.getRef();
-		final String prop = graphValue.getProperty();
-		final String envRef = graphValue.getEnv();
-
-		if (StringUtils.isNotBlank(ref) && StringUtils.isNotBlank(globalParams.get(ref))) {
-			return GraphNodeParameter.newSimpleParam(globalParams.get(ref));
-		} else if (StringUtils.isNotBlank(envRef)) {
-			return GraphNodeParameter.newEnvParam(envRef);
-		} else if (StringUtils.isNotBlank(value)) {
-			final Matcher matcher = pattern.matcher(value);
-			while (matcher.find()) {
-				final String rName = matcher.group(1);
-				final String rValue = globalParams.get(rName);
-				if (StringUtils.isBlank(rValue)) { return null; }
-				value = value.replaceAll(Pattern.quote(matcher.group(0)), rValue);
-				System.out.println("NEW VALUE " + value);
-			}
-			return GraphNodeParameter.newSimpleParam(value);
-		} else if (StringUtils.isNotBlank(prop)) {
-			return GraphNodeParameter.newSimpleParam(env.getProperty(prop));
-		} else {
-			return null;
-		}
-
-	}
-
 	private void checkValidity(final Graph graph) throws WorkflowManagerException {
 
 		final Set<String> nodesFromArcs = new HashSet<>();

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/GraphNode.java

@@ -2,9 +2,7 @@ package eu.dnetlib.manager.wf.workflows.graph;
 
 import java.io.StringWriter;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
-import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
@@ -19,42 +17,48 @@ public class GraphNode {
 	private final boolean isStart;
 	private final boolean isJoin;
 	private final boolean isSucessNode;
-	private final Map<String, GraphNodeParameter> nodeParams;
+	private final Map<String, Object> params;
+	private final Map<String, String> envParams;
 
 	private GraphNode(final String name,
 		final String type,
 		final boolean isStart,
 		final boolean isJoin,
 		final boolean isSuccessNode,
-		final Map<String, GraphNodeParameter> nodeParams) {
+		final Map<String, Object> params,
+		final Map<String, String> envParams) {
 		this.name = name;
 		this.type = type;
 		this.isStart = isStart;
 		this.isJoin = isJoin;
 		this.isSucessNode = isSuccessNode;
-		this.nodeParams = nodeParams;
+		this.params = params;
+		this.envParams = envParams;
 	}
 
 	public static GraphNode newNode(final String name,
 		final String type,
-		final Map<String, GraphNodeParameter> nodeParams) {
+		final Map<String, Object> params,
-		return new GraphNode(name, type, false, false, false, nodeParams);
+		final Map<String, String> envParams) {
+		return new GraphNode(name, type, false, false, false, params, envParams);
 	}
 
 	public static GraphNode newStartNode(final String name,
 		final String type,
-		final Map<String, GraphNodeParameter> nodeParams) {
+		final Map<String, Object> params,
-		return new GraphNode(name, type, true, false, false, nodeParams);
+		final Map<String, String> envParams) {
+		return new GraphNode(name, type, true, false, false, params, envParams);
 	}
 
 	public static GraphNode newJoinNode(final String name,
 		final String type,
-		final Map<String, GraphNodeParameter> nodeParams) {
+		final Map<String, Object> params,
-		return new GraphNode(name, type, false, true, false, nodeParams);
+		final Map<String, String> envParams) {
+		return new GraphNode(name, type, false, true, false, params, envParams);
 	}
 
 	public static GraphNode newSuccessNode() {
-		return new GraphNode(SUCCESS_NODE, null, false, true, true, null);
+		return new GraphNode(SUCCESS_NODE, null, false, true, true, new HashMap<>(), new HashMap<>());
 	}
 
 	public String getName() {
@@ -96,54 +100,30 @@ public class GraphNode {
 		return sw.toString();
 	}
 
-	public Map<String, GraphNodeParameter> getNodeParams() {
+	public Map<String, Object> getParams() {
-		return this.nodeParams;
+		return this.params;
+	}
+
+	public Map<String, String> getEnvParams() {
+		return this.envParams;
 	}
 
 	public Map<String, Object> resolveParamsWithNoEnv() {
 		return resolveParams(null);
 	}
 
-	@SuppressWarnings("unchecked")
 	public Map<String, Object> resolveParams(final Env env) {
-		final Map<String, Object> params = new HashMap<>();
+		final Map<String, Object> map = new HashMap<>();
 
-		if (this.nodeParams != null) {
+		if (this.params != null) {
-
+			this.params.forEach((k, v) -> map.put(k, v));
-			for (final Map.Entry<String, GraphNodeParameter> e : this.nodeParams.entrySet()) {
-				final String pName = e.getKey();
-				final GraphNodeParameter param = e.getValue();
-
-				if (param.isEnvParam()) {
-					params.put(pName, resolveFromEnv(param, env));
-				} else if (param.isMap()) {
-
-					final Map<String, Object> map = new HashMap<>();
-
-					for (final Map.Entry<String, GraphNodeParameter> e1 : ((Map<String, GraphNodeParameter>) param.getValue()).entrySet()) {
-						map.put(e1.getKey(), e1.getValue().isEnvParam() ? resolveFromEnv(e1.getValue(), env) : e1.getValue().getValue());
-					}
-
-					params.put(pName, map);
-
-				} else if (param.isList()) {
-					params.put(pName, ((List<GraphNodeParameter>) param.getValue())
-						.stream()
-						.map(p -> p.isEnvParam() ? resolveFromEnv(p, env) : p.getValue())
-						.collect(Collectors.toList()));
-
-				} else {
-					params.put(pName, param.getValue());
-				}
-
-			}
 		}
 
-		return params;
+		if (this.envParams != null && env != null) {
-	}
+			this.envParams.forEach((k, v) -> map.put(k, env.getAttribute(v)));
+		}
 
-	private Object resolveFromEnv(final GraphNodeParameter param, final Env env) {
+		return map;
-		return env != null ? env.getAttribute(param.getEnvVariable()) : "[this value will be resolved using the runtime ENV]";
 	}
 
 }

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/graph/GraphNodeParameter.java

@@ -1,56 +0,0 @@
-package eu.dnetlib.manager.wf.workflows.graph;
-
-import java.util.List;
-import java.util.Map;
-
-public class GraphNodeParameter {
-
-	private final Object value;
-	private final String envVariable;
-
-	private GraphNodeParameter(final Object value, final String envVariable) {
-		this.value = value;
-		this.envVariable = envVariable;
-	}
-
-	public static GraphNodeParameter newNullParam() {
-		return new GraphNodeParameter(null, null);
-	}
-
-	public static GraphNodeParameter newSimpleParam(final Object value) {
-		return new GraphNodeParameter(value, null);
-	}
-
-	public static GraphNodeParameter newMapParam(final Map<String, GraphNodeParameter> map) {
-		return new GraphNodeParameter(map, null);
-	}
-
-	public static GraphNodeParameter newListParam(final List<GraphNodeParameter> list) {
-		return new GraphNodeParameter(list, null);
-	}
-
-	public static GraphNodeParameter newEnvParam(final String envVariable) {
-		return new GraphNodeParameter(null, envVariable);
-	}
-
-	public Object getValue() {
-		return this.value;
-	}
-
-	public boolean isEnvParam() {
-		return this.envVariable != null;
-	}
-
-	public String getEnvVariable() {
-		return this.envVariable;
-	}
-
-	public boolean isMap() {
-		return this.value != null && (this.value instanceof Map);
-	}
-
-	public boolean isList() {
-		return this.value != null && (this.value instanceof List);
-	}
-
-}

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/ProcessFactory.java

@@ -3,7 +3,6 @@ package eu.dnetlib.manager.wf.workflows.procs;
 import java.time.LocalDateTime;
 import java.time.format.DateTimeFormatter;
 import java.util.HashMap;
-import java.util.List;
 import java.util.Map;
 
 import org.apache.commons.logging.Log;
@@ -12,8 +11,10 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 import eu.dnetlib.errors.WorkflowManagerException;
-import eu.dnetlib.manager.wf.model.GraphNode;
+import eu.dnetlib.is.model.resource.SimpleResource;
+import eu.dnetlib.manager.wf.model.WorkflowGraph;
 import eu.dnetlib.manager.wf.model.WorkflowInstance;
+import eu.dnetlib.manager.wf.workflows.graph.Graph;
 import eu.dnetlib.manager.wf.workflows.graph.GraphLoader;
 import eu.dnetlib.manager.wf.workflows.util.ProcessCallback;
 
@@ -29,30 +30,19 @@ public class ProcessFactory {
 	@Autowired
 	private GraphLoader graphLoader;
 
-	public WorkflowProcess newProcess(final String wfId,
+	public WorkflowProcess newProcess(final SimpleResource wfMetadata,
-		final String wfName,
+		final WorkflowGraph wfGraph,
-		final String wfFamily,
+		final WorkflowInstance wfInstance,
-		final List<GraphNode> graph,
-		final WorkflowInstance instance,
 		final ProcessCallback processCallback,
 		final String parent) throws WorkflowManagerException {
 
 		final Map<String, String> globalParams = new HashMap<>();
-		globalParams.putAll(instance.getSystemParams());
+		globalParams.putAll(wfInstance.getSystemParams());
-		globalParams.putAll(instance.getUserParams());
+		globalParams.putAll(wfInstance.getUserParams());
 
-		return new WorkflowProcess(generateProcessId(),
+		final Graph graph = graphLoader.loadGraph(wfGraph, globalParams);
-			wfName,
+
-			wfFamily,
+		return new WorkflowProcess(generateProcessId(), wfMetadata, wfInstance, graph, globalParams, processCallback, parent);
-			instance.getDsId(),
-			instance.getDsName(),
-			instance.getApiId(),
-			graphLoader.loadGraph(graph, globalParams),
-			instance.getPriority(),
-			wfId,
-			instance.getId(),
-			globalParams,
-			processCallback, parent);
 
 	}
 

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/ProcessRegistry.java

@@ -1,11 +1,10 @@
 package eu.dnetlib.manager.wf.workflows.procs;
 
 import java.time.LocalDateTime;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashMap;
 import java.util.Map;
-import java.util.Set;
+import java.util.Optional;
 import java.util.concurrent.PriorityBlockingQueue;
 
 import org.apache.commons.logging.Log;
@@ -13,18 +12,16 @@ import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.stereotype.Service;
 
-import com.google.common.collect.BiMap;
-import com.google.common.collect.HashBiMap;
-
 import eu.dnetlib.errors.WorkflowManagerException;
+import eu.dnetlib.manager.wf.model.WorkflowInstance;
 import eu.dnetlib.manager.wf.workflows.util.WorkflowsConstants;
 
 @Service
 public class ProcessRegistry {
 
 	private static final Log log = LogFactory.getLog(ProcessRegistry.class);
-	private final BiMap<String, WorkflowProcess> procs = HashBiMap.create();
+	private final Map<String, WorkflowProcess> procs = new HashMap<>();
-	private final Map<String, Collection<WorkflowProcess>> byOtherId = new HashMap<>();
+	private final Map<String, WorkflowProcess> byInstanceId = new HashMap<>();
 
 	private final PriorityBlockingQueue<WorkflowProcess> pendingProcs = new PriorityBlockingQueue<>();
 
@@ -46,18 +43,15 @@ public class ProcessRegistry {
 		return this.procs.get(procId);
 	}
 
-	public Set<WorkflowProcess> listProcesses() {
+	public Collection<WorkflowProcess> listProcesses() {
 		return this.procs.values();
 	}
 
-	public Collection<WorkflowProcess> findProcsByOtherId(final String id) {
+	public WorkflowProcess findProcsByInstanceId(final String id) {
-		synchronized (this) {
+		return this.byInstanceId.get(id);
-			final Collection<WorkflowProcess> res = this.byOtherId.get(id);
-			return res != null ? res : new ArrayList<>();
-		}
 	}
 
-	public String registerProcess(final WorkflowProcess process, final String... ids) throws WorkflowManagerException {
+	public String registerProcess(final WorkflowProcess process, final WorkflowInstance wfInstance) throws WorkflowManagerException {
 		if (this.procs.containsValue(process) || this.procs.containsKey(process.getId())) {
 			log.error("Already registerd process: " + process);
 			throw new WorkflowManagerException("Already registerd process: " + process);
@@ -68,14 +62,7 @@ public class ProcessRegistry {
 		}
 
 		this.procs.put(process.getId(), process);
-		for (final String id : ids) {
+		this.byInstanceId.put(wfInstance.getId(), process);
-			synchronized (this) {
-				if (!this.byOtherId.containsKey(id)) {
-					this.byOtherId.put(id, new ArrayList<WorkflowProcess>());
-				}
-				this.byOtherId.get(id).add(process);
-			}
-		}
 
 		synchronized (this.pendingProcs) {
 			if (this.pendingProcs.size() > WorkflowsConstants.MAX_PENDING_PROCS_SIZE) {
@@ -116,8 +103,13 @@ public class ProcessRegistry {
 		synchronized (this) {
 			final WorkflowProcess process = this.procs.remove(procId);
 			if (process != null) {
-				for (final Collection<WorkflowProcess> processes : this.byOtherId.values()) {
+				final Optional<String> instanceId = this.byInstanceId.entrySet()
-					processes.remove(process);
+					.stream()
+					.filter(e -> e.getValue().getId().equals(process.getId()))
+					.map(e -> e.getKey())
+					.findFirst();
+				if (instanceId.isPresent()) {
+					this.byInstanceId.remove(instanceId, process);
 				}
 			}
 		}

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/WorkflowExecutor.java

@@ -1,8 +1,7 @@
 package eu.dnetlib.manager.wf.workflows.procs;
 
-import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.List;
+import java.util.Objects;
 import java.util.UUID;
 import java.util.concurrent.Executors;
 import java.util.concurrent.TimeUnit;
@@ -14,7 +13,6 @@ import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dsm.DsmService;
@@ -22,7 +20,7 @@ import eu.dnetlib.errors.DsmException;
 import eu.dnetlib.errors.WorkflowManagerException;
 import eu.dnetlib.is.model.resource.SimpleResource;
 import eu.dnetlib.is.resource.repository.SimpleResourceRepository;
-import eu.dnetlib.manager.wf.model.GraphNode;
+import eu.dnetlib.manager.wf.model.WorkflowGraph;
 import eu.dnetlib.manager.wf.model.WorkflowInstance;
 import eu.dnetlib.manager.wf.repository.WorkflowInstanceRepository;
 import eu.dnetlib.manager.wf.workflows.util.ProcessCallback;
@@ -111,38 +109,34 @@ public class WorkflowExecutor implements Stoppable {
 		return startWorkflowInstance(instance, processCallback, parent);
 	}
 
-	public String startWorkflowInstance(final WorkflowInstance instance, final ProcessCallback processCallback, final String parent)
+	public String startWorkflowInstance(final WorkflowInstance wfInstance, final ProcessCallback processCallback, final String parent)
 		throws WorkflowManagerException {
 
-		if (!instance.isEnabled() || !instance.isConfigured()) {
+		if (!wfInstance.isEnabled() || !wfInstance.isConfigured()) {
-			log.warn("Wf instance " + instance.getId() + " is not ready to start");
+			log.warn("Wf instance " + wfInstance.getId() + " is not ready to start");
-			throw new WorkflowManagerException("Wf instance " + instance.getId() + " is not ready to start");
+			throw new WorkflowManagerException("Wf instance " + wfInstance.getId() + " is not ready to start");
 		}
 
-		final SimpleResource wf = simpleResourceRepository
+		final SimpleResource wfMetadata = simpleResourceRepository
-			.findById(instance.getWorkflow())
+			.findById(wfInstance.getWorkflow())
 			.filter(r -> r.getType().equals("workflows"))
-			.orElseThrow(() -> new WorkflowManagerException("WF not found: " + instance.getWorkflow()));
+			.orElseThrow(() -> new WorkflowManagerException("WF not found: " + wfInstance.getWorkflow()));
 
-		final List<GraphNode> graph = simpleResourceRepository.findContentById(wf.getId())
+		final WorkflowGraph wfGraph = simpleResourceRepository.findContentById(wfMetadata.getId())
 			.map(s -> {
-				final ObjectMapper mapper = new ObjectMapper();
-				final TypeReference<List<GraphNode>> type = new TypeReference<List<GraphNode>>() {};
-				final List<GraphNode> list = new ArrayList<>();
 				try {
-					list.addAll(mapper.readValue(s, type));
+					return new ObjectMapper().readValue(s, WorkflowGraph.class);
 				} catch (final Exception e) {
-					log.error("Error parsing json", e);
+					return (WorkflowGraph) null;
 				}
-				return list;
 			})
-			.filter(list -> !list.isEmpty())
+			.filter(Objects::nonNull)
-			.orElseThrow(() -> new WorkflowManagerException("Invalid wf: " + wf.getId()));
+			.orElseThrow(() -> new WorkflowManagerException("Invalid wf: " + wfMetadata.getId()));
 
 		final WorkflowProcess process =
-			processFactory.newProcess(wf.getId(), wf.getName(), wf.getSubtype(), graph, instance, processCallback, parent);
+			processFactory.newProcess(wfMetadata, wfGraph, wfInstance, processCallback, parent);
 
-		return processRegistry.registerProcess(process, instance.getId());
+		return processRegistry.registerProcess(process, wfInstance);
 	}
 
 	@Override

libs/dnet-wf-service/src/main/java/eu/dnetlib/manager/wf/workflows/procs/WorkflowProcess.java

@@ -8,6 +8,8 @@ import java.util.concurrent.CopyOnWriteArrayList;
 
 import org.apache.commons.lang3.math.NumberUtils;
 
+import eu.dnetlib.is.model.resource.SimpleResource;
+import eu.dnetlib.manager.wf.model.WorkflowInstance;
 import eu.dnetlib.manager.wf.workflows.graph.Graph;
 import eu.dnetlib.manager.wf.workflows.util.ProcessCallback;
 
@@ -16,104 +18,96 @@ import eu.dnetlib.manager.wf.workflows.util.ProcessCallback;
  */
 public class WorkflowProcess implements Comparable<WorkflowProcess> {
 
+	public enum Status {
+		CREATED,
+		EXECUTING,
+		SUCCESS,
+		FAILURE,
+		KILLED;
+	}
+
+	public enum StartMode {
+		AUTO,
+		MANUAL,
+		DISABLED
+	}
+
 	private final String id;
-	private final String name;
+	private final SimpleResource wfMetadata;
-	private final String family;
+	private final WorkflowInstance wfInstance;
-	private String dsId;
-	private String dsName;
-	private String dsInterface;
 	private final Graph graph;
 	private final ProcessCallback callback;
-	private final int priority;
 	private final Env env;
 	private final List<Token> tokens = new CopyOnWriteArrayList<>();
 	private LocalDateTime lastActivityDate;
 	private Status status;
 	private LocalDateTime startDate = LocalDateTime.MIN;
 	private LocalDateTime endDate = LocalDateTime.MIN;
-	private final String wfId;
+	private final Map<String, List<Token>> pausedJoinNodeTokens = new HashMap<>();
-	private final String wfInstanceId;
+	private final Map<String, String> globalParams;
-	private Map<String, List<Token>> pausedJoinNodeTokens = new HashMap<>();
-	private Map<String, String> globalParams;
 	private String error;
 	private String errorStacktrace;
-	private Map<String, String> outputParams = new HashMap<>();
+	private final Map<String, String> outputParams = new HashMap<>();
-	private String parentProfileId;
+	private final String parentProfileId;
 
 	public WorkflowProcess(
 		final String id,
-		final String name,
+		final SimpleResource wfMetadata,
-		final String family,
+		final WorkflowInstance wfInstance,
-		final String dsId,
-		final String dsName,
-		final String dsInterface,
 		final Graph graph,
-		final int priority,
-		final String wfId,
-		final String wfInstanceId,
 		final Map<String, String> globalParams,
 		final ProcessCallback callback,
 		final String parentProfileId) {
 		this.id = id;
-		this.name = name;
+		this.wfMetadata = wfMetadata;
-		this.family = family;
+		this.wfInstance = wfInstance;
-		this.dsId = dsId;
-		this.dsName = dsName;
-		this.dsInterface = dsInterface;
 		this.graph = graph;
-		this.priority = priority;
 		this.callback = callback;
 		this.status = Status.CREATED;
 		this.env = new Env();
-		this.wfId = wfId;
-		this.wfInstanceId = wfInstanceId;
 		this.globalParams = globalParams;
 		this.lastActivityDate = LocalDateTime.now();
 		this.parentProfileId = parentProfileId;
 	}
 
-	public void setParentProfileId(final String parentProfileId) {
-		this.parentProfileId = parentProfileId;
-	}
-
-	public String getDsId() {
-		return dsId;
-	}
-
-	public void setDsId(final String dsId) {
-		this.dsId = dsId;
-	}
-
-	public String getDsName() {
-		return dsName;
-	}
-
-	public void setDsName(final String dsName) {
-		this.dsName = dsName;
-	}
-
-	public String getDsInterface() {
-		return dsInterface;
-	}
-
-	public void setDsInterface(final String dsInterface) {
-		this.dsInterface = dsInterface;
-	}
-
-	public Map<String, List<Token>> getPausedJoinNodeTokens() {
-		return pausedJoinNodeTokens;
-	}
-
-	public void setPausedJoinNodeTokens(final Map<String, List<Token>> pausedJoinNodeTokens) {
-		this.pausedJoinNodeTokens = pausedJoinNodeTokens;
-	}
-
 	public String getId() {
 		return id;
 	}
 
 	public String getName() {
-		return name;
+		return wfMetadata.getName();
+	}
+
+	public String getFamily() {
+		return wfMetadata.getSubtype();
+	}
+
+	public String getWfId() {
+		return wfMetadata.getId();
+	}
+
+	public String getWfInstanceId() {
+		return wfInstance.getId();
+	}
+
+	public int getPriority() {
+		return wfInstance.getPriority();
+	}
+
+	public String getDsId() {
+		return wfInstance.getId();
+	}
+
+	public String getDsName() {
+		return wfInstance.getDsName();
+	}
+
+	public String getDsInterface() {
+		return wfInstance.getApiId();
+	}
+
+	public Map<String, List<Token>> getPausedJoinNodeTokens() {
+		return pausedJoinNodeTokens;
 	}
 
 	public Env getEnv() {
@@ -144,10 +138,6 @@ public class WorkflowProcess implements Comparable<WorkflowProcess> {
 		return callback;
 	}
 
-	public int getPriority() {
-		return priority;
-	}
-
 	public boolean isTerminated() {
 		switch (status) {
 		case SUCCESS:
@@ -169,7 +159,7 @@ public class WorkflowProcess implements Comparable<WorkflowProcess> {
 
 	@Override
 	public String toString() {
-		return String.format("[process id='%s' name='%s']", id, name);
+		return String.format("[process id='%s' name='%s']", id, wfMetadata.getName());
 	}
 
 	@Override
@@ -181,22 +171,6 @@ public class WorkflowProcess implements Comparable<WorkflowProcess> {
 		return globalParams;
 	}
 
-	public void setGlobalParams(final Map<String, String> globalParams) {
-		this.globalParams = globalParams;
-	}
-
-	public String getFamily() {
-		return family;
-	}
-
-	public String getWfId() {
-		return wfId;
-	}
-
-	public String getWfInstanceId() {
-		return wfInstanceId;
-	}
-
 	public void setStartDate(final LocalDateTime startDate) {
 		this.startDate = startDate;
 	}
@@ -213,20 +187,6 @@ public class WorkflowProcess implements Comparable<WorkflowProcess> {
 		return endDate;
 	}
 
-	public enum Status {
-		CREATED,
-		EXECUTING,
-		SUCCESS,
-		FAILURE,
-		KILLED;
-	}
-
-	public enum StartMode {
-		AUTO,
-		MANUAL,
-		DISABLED
-	}
-
 	public String getError() {
 		return error;
 	}
@@ -243,10 +203,6 @@ public class WorkflowProcess implements Comparable<WorkflowProcess> {
 		this.errorStacktrace = errorStacktrace;
 	}
 
-	public void setOutputParams(final Map<String, String> outputParams) {
-		this.outputParams = outputParams;
-	}
-
 	public Map<String, String> getOutputParams() {
 		return outputParams;
 	}