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Templates

The plugin supports parameterized cypher query templates and a configurable mapping. The template is specified in an xml file, the user can select the template in the user interface: Apps -> Cypher Queries -> Import Stored Cypher Query.

XML

The xml contains a query, parameters and a mapping specification. There are two mapping options, a default strategy 'copy all', it just copies all nodes and edges from Neo4j to cytoscape. Or the user can specify an explicit mapping.

cytemplate (1)

The root element for the temlae

query (1)

Cyher query (typically in a CDATA element)

parameters (0..1)

List of parameters

parameter (0..n)

A parameter has a name and a type, it is as a parameter in the cypher query. Attributes:

    • name, the parameter name, string
    • type, a valid java type like (java.lang.String or java.lang.Integer, ...)

mapping (0..1)

The mapping specifies how nodes and edge are imported in cytoscape. It contains two elements: node and edge.

node (0..1)

Attributes:

  • referenceIdColumn, the name of the column where the node id is copied into to.
column (0..n)

Attributes:

  • type, a java type like java.lang.String
  • name, the name of the column the value is copied into
expression (0..1)

The value of column is calculate by evaluating a javascript expression. The variable 'node' of type 'nl.corwur.cytoscape.neo4j.internal.graph.GraphNode' is passed into the expression.

id (0..1)

The id of the Neo4j node is copied into the column

property (0..1)

The property of the node is copied into the column. Attributes:

  • key, the name of the Neo4j property.
label (0..1)

The label of the node is copied into the column. Attributes:

  • match, a regular expression that matches a label.

edge (0..1)

An edge is mapped to columns.

column (0..n)

Attributes:

  • type (java type like java.lang.String)
  • name (string)
id

Copy the id of the Neo4j edge into the column

edgeType

Copy the id of the Neo4j edge into the column

copyall

Use a copy all mapping strategy, all nodes and relations form the query are copied. Attributes:

  • referenceIdColumn (string), the name of the column where the id is stored.

Example

<?xml version="1.0" encoding="UTF-8" ?>
<cytemplate name="test-query">
    <query><![CDATA[MATCH p=(n:gene) - [r:order*] - (m:gene) WHERE n.geneID=$from AND m.geneID=$to RETURN p]]></query>
    <parameters>
        <parameter name="from" type="java.lang.String" />
        <parameter name="to" type="java.lang.String" />
    </parameters>
    <mapping>
        <node referenceIdColumn="refid">
            <column type="java.lang.String" name="name">
                <expression>node.labels[0] + node.getProperty('geneID')</expression>
            </column>
            <column type="java.lang.Long" name="refId">
                <id/>
            </column>
            <column type="java.lang.String" name="geneID">
                <property key="geneID" />
            </column>
            <column type="java.lang.Long" name="start">
                <property key="start" />
            </column>
            <column type="java.lang.Long" name="end">
                <property key="end" />
            </column>
            <column type="java.lang.String" name="nodeType">
                <label match=".*"/>
            </column>
        </node>
        <edge referenceIdColumn="refid">
            <column type="java.lang.Long" name="refid" >
                <id/>
            </column>
            <column type="java.lang.String" name="linkType">
                <edgeType/>
            </column>
        </edge>
    </mapping>
</cytemplate>

XSD

<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<xs:schema version="1.0" xmlns:xs="http://www.w3.org/2001/XMLSchema">

  <xs:element name="cytemplate" type="queryTemplate"/>

  <xs:complexType name="columnMapping">
    <xs:sequence>
      <xs:element name="node" type="nodeMapping" minOccurs="0"/>
      <xs:element name="edge" type="edgeMapping" minOccurs="0"/>
    </xs:sequence>
  </xs:complexType>

  <xs:complexType name="nodeMapping">
    <xs:sequence>
      <xs:element name="column" type="nodeColumn" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:attribute name="referenceIdColumn" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="nodeColumn">
    <xs:sequence>
      <xs:element name="property" type="property" minOccurs="0"/>
      <xs:element name="id" type="id" minOccurs="0"/>
      <xs:element name="expression" type="expression" minOccurs="0"/>
      <xs:element name="label" type="label" minOccurs="0"/>
    </xs:sequence>
    <xs:attribute name="type" type="xs:string"/>
    <xs:attribute name="name" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="property">
    <xs:sequence/>
    <xs:attribute name="key" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="id">
    <xs:sequence/>
  </xs:complexType>

  <xs:simpleType name="expression">
    <xs:restriction base="xs:string"/>
  </xs:simpleType>

  <xs:complexType name="label">
    <xs:sequence/>
    <xs:attribute name="match" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="edgeMapping">
    <xs:sequence>
      <xs:element name="column" type="edgeColumn" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
    <xs:attribute name="referenceIdColumn" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="edgeColumn">
    <xs:sequence>
      <xs:element name="property" type="property" minOccurs="0"/>
      <xs:element name="id" type="id" minOccurs="0"/>
      <xs:element name="edgetype" type="edgeType" minOccurs="0"/>
      <xs:element name="expression" type="expression" minOccurs="0"/>
    </xs:sequence>
    <xs:attribute name="type" type="xs:string"/>
    <xs:attribute name="name" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="edgeType">
    <xs:sequence/>
  </xs:complexType>

  <xs:complexType name="copyAll">
    <xs:sequence/>
    <xs:attribute name="referenceIdColumn" type="xs:string"/>
    <xs:attribute name="network" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="parameter">
    <xs:sequence/>
    <xs:attribute name="name" type="xs:string"/>
    <xs:attribute name="type" type="xs:string"/>
  </xs:complexType>

  <xs:complexType name="parameters">
    <xs:sequence>
      <xs:element name="parameter" type="parameter" minOccurs="0" maxOccurs="unbounded"/>
    </xs:sequence>
  </xs:complexType>

  <xs:complexType name="queryTemplate">
    <xs:sequence>
      <xs:element name="query" type="xs:string" minOccurs="0"/>
      <xs:element name="parameters" type="parameters" minOccurs="0"/>
      <xs:choice minOccurs="0">
        <xs:element name="mapping" type="columnMapping"/>
        <xs:element name="copyall" type="copyAll"/>
      </xs:choice>
    </xs:sequence>
    <xs:attribute name="name" type="xs:string"/>
  </xs:complexType>
</xs:schema>