de.unirostock.sems.m2cat.graph

Class GraphModelDocument

java.lang.Object

de.unirostock.sems.m2cat.graph.GraphNode

de.unirostock.sems.m2cat.graph.GraphModelDocument

public class GraphModelDocument
extends GraphNode

The Class GraphDocument.

Author:

Martin Scharm

Field Summary

Fields inherited from class de.unirostock.sems.m2cat.graph.GraphNode

data, DB_ENTRY_EDGE_END, DB_ENTRY_EDGE_START, DB_ENTRY_EDGE_TYPE, DB_ENTRY_NODE_LABELS, DB_ENTRY_NODE_PROPERTIES, DB_ENTRY_NODE_SELF, dbEntry, TYPE_AUTHOR, TYPE_BIBENTRY, TYPE_COMMENT, TYPE_FILE, TYPE_INSTALLATION, TYPE_PLATFORM, TYPE_POST, TYPE_PUBLISHER, TYPE_REGISTERED, TYPE_TAG, TYPE_USER

Constructor Summary

Constructors

Constructor and Description
GraphModelDocument(org.json.simple.JSONObject data, GraphModel model) The Constructor.

Method Summary

Modifier and Type	Method and Description
void	addSimulationDescription(GraphSedmlDocument simulation) Adds the simulation description.
void	createCombineArchive(File f, String archiveName, User user) Creates an combine archive of this model.
String	getArchiveName() Gets the archive name.
void	getCurationResultPic(List<Resource> resources) Gets the reaction network.
Integer	getDocId() Gets the archive name.
String	getDocUri() Gets the URI to the document.
String	getFileName() Gets the file name.
GraphSedmlDocument	getFirstSimulationDescription() Gets the first simulation description.
GraphModel	getModel() Gets the model.
void	getReactionNetworkPic(List<Resource> resources) Gets the reaction network.
List<Resource>	getResources() Gets the resources.
boolean	isCellML() Checks if is cell ml.
boolean	isSimulationDescription() Checks if is simulation description.
List<Resource>	retrieveAdditionalResources() Gets the additional resources.
void	retrieveModelFiles() Retrieve model file.
String	toString()

Methods inherited from class de.unirostock.sems.m2cat.graph.GraphNode

getData, getFileUri, getId, getLabels, getNodeEntry, getRestProperties

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

GraphModelDocument

public GraphModelDocument(org.json.simple.JSONObject data,
                          GraphModel model)

The Constructor.

Parameters:

data - the data

model - the model

Method Detail

toString

public String toString()

Overrides:

toString in class Object

getResources

public List<Resource> getResources()

Gets the resources.

Returns:

the resources

getModel

public GraphModel getModel()

Gets the model.

Returns:

model

getDocUri

public String getDocUri()

Gets the URI to the document.

Returns:

the URI

getFileName

public String getFileName()

Gets the file name.

Returns:

the file name

retrieveModelFiles

public void retrieveModelFiles()
                        throws IOException,
                               URISyntaxException

Retrieve model file.

Throws:

IOException - the IO exception

URISyntaxException - the uRI syntax exception

addSimulationDescription

public void addSimulationDescription(GraphSedmlDocument simulation)

Adds the simulation description.

Parameters:

simulation - the simulation

isCellML

public boolean isCellML()

Checks if is cell ml.

Returns:

true, if checks if is cell ml

isSimulationDescription

public boolean isSimulationDescription()

Checks if is simulation description.

Returns:

true, if checks if is simulation description

getFirstSimulationDescription

public GraphSedmlDocument getFirstSimulationDescription()

Gets the first simulation description.

Returns:

the first simulation description

retrieveAdditionalResources

public List<Resource> retrieveAdditionalResources()
                                           throws org.apache.http.client.ClientProtocolException,
                                                  IOException,
                                                  URISyntaxException

Gets the additional resources.

Returns:

the additional resources

Throws:

org.apache.http.client.ClientProtocolException - the client protocol exception

IOException - Signals that an I/O exception has occurred.

URISyntaxException - the uRI syntax exception

getCurationResultPic

public void getCurationResultPic(List<Resource> resources)
                          throws org.apache.http.client.ClientProtocolException,
                                 IOException,
                                 URISyntaxException

Gets the reaction network.

Parameters:

resources - the resources

Throws:

org.apache.http.client.ClientProtocolException - the client protocol exception

IOException - Signals that an I/O exception has occurred.

URISyntaxException - the uRI syntax exception

getReactionNetworkPic

public void getReactionNetworkPic(List<Resource> resources)
                           throws org.apache.http.client.ClientProtocolException,
                                  IOException,
                                  URISyntaxException

Gets the reaction network.

Parameters:

resources - the resources

Throws:

org.apache.http.client.ClientProtocolException - the client protocol exception

IOException - Signals that an I/O exception has occurred.

URISyntaxException - the uRI syntax exception

createCombineArchive

public void createCombineArchive(File f,
                                 String archiveName,
                                 User user)
                          throws IOException,
                                 org.jdom2.JDOMException,
                                 ParseException,
                                 de.unirostock.sems.cbarchive.CombineArchiveException,
                                 TransformerException

Creates an combine archive of this model.

Parameters:

f - the file to write to

archiveName - the archive name

user - the user

Throws:

IOException - the IO exception

org.jdom2.JDOMException - the JDOM exception

ParseException - the parse exception

de.unirostock.sems.cbarchive.CombineArchiveException - the combine archive exception

TransformerException - the transformer exception

getDocId

public Integer getDocId()

Gets the archive name.

Returns:

the archive name

getArchiveName

public String getArchiveName()

Gets the archive name.

Returns:

the archive name