Re: Parsing GEXF in PHP

2011-06-05T07:29:02+01:00

I had a similar need and I used DOMXPath that works well. You have to register the namespaces with the xPath object:

CODE:

$xp->registerNamespace('gexf', 'http://www.gexf.net/1.1draft');$xp->registerNamespace('viz', 'http:///www.gexf.net/1.1draft/viz');

After that, queries give you all the attributes you want, but you have to explicit the namespaces:

CODE:

$nodesattributes = $xp->query("//gexf:graph[1]/gexf:attributes[@class='node']/gexf:attribute");

Here is all my code (stores the gexf in a database). I don't claim it's clean or well done, but it works and could help you...
NB: dbh is the database handler.

CODE:

load($file->get('path'));$xp = new DOMXPath($gexfDom);if($gexfDom->getElementsByTagName('gexf')->item(0)->getAttribute('xmlns') == "http://www.gephi.org/gexf"){# 'Old style' GEXF$xp->registerNamespace('gexf', 'http://www.gephi.org/gexf');$xp->registerNamespace('viz', 'http://www.gephi.org/gexf/viz');$this->dbh->beginTransaction();# Nodes table$nodesQuery = "CREATE TABLE nodes (id INTEGER PRIMARY KEY AUTOINCREMENT, importId TEXT, label TEXT, x REAL, y REAL, size REAL";# Nodes Attributes$nodesattributes = $xp->query("//gexf:graph[1]/gexf:attributes[@class='node']/gexf:attribute");$existingNames = array("id", "importId", "label", "x", "y", "size");foreach($nodesattributes as $attribute){$name = $attribute->getAttribute('id');$name = preg_replace('/[^a-z0-9_]*/i','',$name);while(in_array($name, $existingNames)){$name = "old_$name";}$existingNames[] = $name;$name = $this->dbh->quote($name);$title = $this->dbh->quote($attribute->getAttribute('title'));$default = $this->dbh->quote($attribute->getAttribute('default'));$truetype = strtolower($attribute->getAttribute('type'));if($truetype == "integer" || $truetype == "long"){$type = "INTEGER";$nodesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "double" || $truetype == "float"){$type = "REAL";$nodesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "boolean" || $truetype == "string" || $truetype == "anyuri"){$type = "TEXT";$nodesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "liststring"){$type = "TAGS";} else {die("Error (graph): unsupported attribute type ".strtolower($attribute->getAttribute('type')));}$truetype = $this->dbh->quote($truetype);$type = $this->dbh->quote($type);$this->dbh->exec(utf8_decode("INSERT INTO nodesattributes ('name', 'title', 'truetype', 'type', 'defaultvalue', 'viztype') VALUES ($name, $title, $truetype, $type, $default, 'unpublished')"));}$nodesQuery .= ")";$this->dbh->exec(utf8_decode($nodesQuery));$this->dbh->commit();$this->dbh->beginTransaction();# Edges table$edgesQuery = "CREATE TABLE edges (id INTEGER PRIMARY KEY AUTOINCREMENT, importId TEXT, source INTEGER, target INTEGER";# Edges Attributes$edgesattributes = $xp->query("//gexf:graph[1]/gexf:attributes[@class='edge']/gexf:attribute");$existingNames = array("id", "importId", "source", "target");foreach($edgesattributes as $attribute){$name = $attribute->getAttribute('id');$name = preg_replace('/[^a-z0-9_]*/i','',$name);while(in_array($name, $existingNames)){$name = "old_$name";}$existingNames[] = $name;$name = $this->dbh->quote($name);$title = $this->dbh->quote($attribute->getAttribute('title'));$default = $this->dbh->quote($attribute->getAttribute('default'));$truetype = strtolower($attribute->getAttribute('type'));if($truetype == "integer" || $truetype == "long"){$type = "INTEGER";$edgesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "double" || $truetype == "float"){$type = "REAL";$edgesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "boolean" || $truetype == "string" || $truetype == "anyuri"){$type = "TEXT";$edgesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "liststring"){$type = "TAGS";} else {die("Error (graph): unsupported attribute type ".strtolower($attribute->getAttribute('type')));}$truetype = $this->dbh->quote($truetype);$type = $this->dbh->quote($type);$this->dbh->exec(utf8_decode("INSERT INTO 'edgesattributes' ('name', 'title', 'truetype', 'type', 'defaultvalue', 'viztype') VALUES ($name, $title, $truetype, $type, $default, 'unpublished')"));}$edgesQuery .= ")";$this->dbh->exec(utf8_decode($edgesQuery));$this->dbh->commit();$this->loadAttributes();$tagQueries = array();# Fill nodes table$this->dbh->beginTransaction();$nodes = $xp->query("//gexf:graph[1]/gexf:nodes/gexf:node");foreach($nodes as $node){$query_insert = "INSERT INTO nodes ('importid', 'label', 'x', 'y', 'size'";$importid = $this->dbh->quote($node->getAttribute('id'));$label = $this->dbh->quote($node->getAttribute('label'));$x = rand(-100, 100);$y = rand(-100, 100);$size = 1;if($positionElement = $xp->query("//gexf:graph[1]/gexf:nodes/gexf:node[@id='".$node->getAttribute('id')."']/viz:position[1]")){$x = $this->dbh->quote($positionElement->item(0)->getAttribute('x'));$y = $this->dbh->quote($positionElement->item(0)->getAttribute('y'));}if($sizeElement = $xp->query("//gexf:graph[1]/gexf:nodes/gexf:node[@id='".$node->getAttribute('id')."']/viz:size[1]")){$size = $this->dbh->quote($sizeElement->item(0)->getAttribute('value'));}$query_values = "VALUES ($importid, $label, $x, $y, $size";if($node->getElementsByTagName('attvalues')->length > 0 && $node->getElementsByTagName('attvalues')->item(0)->getElementsByTagName('attvalue')->length > 0){foreach($node->getElementsByTagName('attvalues')->item(0)->getElementsByTagName('attvalue') as $value){$attId = $value->getAttribute('id') + 1;$attValue = $this->dbh->quote($value->getAttribute('value'));$att = $this->getNodeAttributeById($attId);$attName = $this->dbh->quote($att['name']);if($att['type'] == 'TAGS'){$tags = explode("|", $value->getAttribute('value'));foreach($tags as $tag){$tag = trim($tag);if($tag != ""){$tag = $this->dbh->quote($tag);$tagQueries[] = "INSERT INTO nodestags (attribute, node, value) SELECT $attId, n.id, $tag FROM nodes n WHERE n.importId=$importid";}}} else {$query_insert .= ", $attName";$query_values .= ", $attValue";}}}$this->dbh->exec(utf8_decode("$query_insert ) $query_values )"));}$this->dbh->commit();# Fill edges table$this->dbh->beginTransaction();$edges = $xp->query("//gexf:graph[1]/gexf:edges/gexf:edge");foreach($edges as $edge){$query_insert = "INSERT INTO 'edges' ('importid', 'source', 'target'";$importid = $this->dbh->quote($edge->getAttribute('id'));$source = $this->dbh->quote($edge->getAttribute('source'));$target = $this->dbh->quote($edge->getAttribute('target'));$query_select = "SELECT $importid, sourcenodes.id, targetnodes.id";$query_from = " FROM nodes sourcenodes, nodes targetnodes WHERE sourcenodes.importId=$source AND targetnodes.importId=$target";if($edge->getElementsByTagName('attvalues')->length > 0 && $edge->getElementsByTagName('attvalues')->item(0)->getElementsByTagName('attvalue')->length > 0){foreach($edge->getElementsByTagName('attvalues')->item(0)->getElementsByTagName('attvalue') as $value){$attId = $value->getAttribute('id') + 1;$attValue = $this->dbh->quote($value->getAttribute('value'));$att = $this->getNodeAttributeById($attId);$attName = $this->dbh->quote($att['name']);if($att['type'] == 'TAGS'){$tags = explode("|", $value->getAttribute('value'));foreach($tags as $tag){$tag = trim($tag);if($tag != ""){$tag = $this->dbh->quote($tag);$tagQueries[] = "INSERT INTO 'edgestags' (attribute, edge, value) SELECT $attId, e.id, $tag FROM edges e WHERE e.importId=$importid";}}} else {$query_insert .= ", $attName";$query_values .= ", $attValue";}}}$this->dbh->exec(utf8_decode("$query_insert ) $query_select $query_from"));}$this->dbh->commit();# Execute the tag queries$this->dbh->beginTransaction();foreach($tagQueries as $query){$this->dbh->exec(utf8_decode($query));}$this->dbh->commit();} else if($gexfDom->getElementsByTagName('gexf')->item(0)->getAttribute('xmlns') == "http://www.gexf.net/1.1draft"){# 1.1 draft GEXF$xp->registerNamespace('gexf', 'http://www.gexf.net/1.1draft');$xp->registerNamespace('viz', 'http:///www.gexf.net/1.1draft/viz');$this->dbh->beginTransaction();# Nodes table$nodesQuery = "CREATE TABLE nodes (id INTEGER PRIMARY KEY AUTOINCREMENT, importid TEXT, label TEXT, x REAL, y REAL, size REAL";# Nodes Attributes$nodesattributes = $xp->query("//gexf:graph[1]/gexf:attributes[@class='node']/gexf:attribute");$existingNames = array("id", "importid", "label", "x", "y", "size");foreach($nodesattributes as $attribute){$name = "attr_".$attribute->getAttribute('id');$name = preg_replace('/[^a-z0-9_]*/i','',$name);while(in_array($name, $existingNames)){$name = "old_$name";}$existingNames[] = $name;$name = $this->dbh->quote($name);$title = $this->dbh->quote($attribute->getAttribute('title'));$default = $this->dbh->quote($attribute->getAttribute('default'));$truetype = strtolower($attribute->getAttribute('type'));if($truetype == "int" || $truetype == "integer" || $truetype == "long"){$type = "INTEGER";$nodesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "double" || $truetype == "float"){$type = "REAL";$nodesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "boolean" || $truetype == "string" || $truetype == "anyuri"){$type = "TEXT";$nodesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "liststring"){$type = "TAGS";} else {die("Error (graph): unsupported attribute type ".strtolower($attribute->getAttribute('type')));}$truetype = $this->dbh->quote($truetype);$type = $this->dbh->quote($type);$this->dbh->exec(utf8_decode("INSERT INTO nodesattributes ('name', 'title', 'truetype', 'type', 'defaultvalue', 'viztype') VALUES ($name, $title, $truetype, $type, $default, 'unpublished')"));}$nodesQuery .= ")";$this->dbh->exec(utf8_decode($nodesQuery));$this->dbh->commit();$this->dbh->beginTransaction();# Edges table$edgesQuery = "CREATE TABLE edges (id INTEGER PRIMARY KEY AUTOINCREMENT, importid TEXT, source INTEGER, target INTEGER";# Edges Attributes$edgesattributes = $xp->query("//gexf:graph[1]/gexf:attributes[@class='edge']/gexf:attribute");$existingNames = array("id", "importid", "source", "target", "weight");foreach($edgesattributes as $attribute){$name = "attr_".$attribute->getAttribute('id');$name = preg_replace('/[^a-z0-9_]*/i','',$name);while(in_array($name, $existingNames)){$name = "old_$name";}$existingNames[] = $name;$name = $this->dbh->quote($name);$title = $this->dbh->quote($attribute->getAttribute('title'));$default = $this->dbh->quote($attribute->getAttribute('default'));$truetype = strtolower($attribute->getAttribute('type'));if($truetype == "int" || $truetype == "integer" || $truetype == "long"){$type = "INTEGER";$edgesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "double" || $truetype == "float"){$type = "REAL";$edgesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "boolean" || $truetype == "string" || $truetype == "anyuri"){$type = "TEXT";$edgesQuery .= ", $name $type DEFAULT $default";} else if($truetype == "liststring"){$type = "TAGS";} else {die("Error (graph): unsupported attribute type ".strtolower($attribute->getAttribute('type')));}$truetype = $this->dbh->quote($truetype);$type = $this->dbh->quote($type);$this->dbh->exec(utf8_decode("INSERT INTO 'edgesattributes' ('name', 'title', 'truetype', 'type', 'defaultvalue', 'viztype') VALUES ($name, $title, $truetype, $type, $default, 'unpublished')"));}$edgesQuery .= ")";$this->dbh->exec(utf8_decode($edgesQuery));$this->dbh->commit();$this->loadAttributes();$tagQueries = array();# Fill nodes table$this->dbh->beginTransaction();$nodes = $xp->query("//gexf:graph[1]/gexf:nodes/gexf:node");foreach($nodes as $node){$query_insert = "INSERT INTO nodes ('importid', 'label', 'x', 'y', 'size'";$importid = $this->dbh->quote($node->getAttribute('id'));$label = $this->dbh->quote($node->getAttribute('label'));$x = rand(-100, 100);$y = rand(-100, 100);$size = 1;if($positionElement = $xp->query("//gexf:graph[1]/gexf:nodes/gexf:node[@id='".$node->getAttribute('id')."']/viz:position[1]")){$x = $this->dbh->quote($positionElement->item(0)->getAttribute('x'));$y = $this->dbh->quote($positionElement->item(0)->getAttribute('y'));}if($sizeElement = $xp->query("//gexf:graph[1]/gexf:nodes/gexf:node[@id='".$node->getAttribute('id')."']/viz:size[1]")){$size = $this->dbh->quote($sizeElement->item(0)->getAttribute('value'));}$query_values = "VALUES ($importid, $label, $x, $y, $size";foreach($node->getElementsByTagName('attvalue') as $value){$attName = "attr_".preg_replace('/[^a-z0-9_]*/i','',$value->getAttribute('for'));$attValue = $this->dbh->quote($value->getAttribute('value'));$att = $this->getNodeAttributeByName($attName);$attName = $this->dbh->quote($att['name']);if($att['type'] == 'TAGS'){$tags = explode("|", $value->getAttribute('value'));foreach($tags as $tag){$tag = $this->dbh->quote($tag);$tagQueries[] = "INSERT INTO nodestags (attribute, node, value) SELECT a.id, n.id, $tag FROM nodes n, nodesattributes a WHERE n.importid=$importid AND a.name=$attName";}} else {$query_insert .= ", $attName";$query_values .= ", $attValue";}}$this->dbh->exec(utf8_decode("$query_insert ) $query_values )"));}$this->dbh->commit();# Fill edges table$this->dbh->beginTransaction();$edges = $xp->query("//gexf:graph[1]/gexf:edges/gexf:edge");foreach($edges as $edge){$query_insert = "INSERT INTO 'edges' ('importid', 'source', 'target'";$importid = $this->dbh->quote($edge->getAttribute('id'));$source = $this->dbh->quote($edge->getAttribute('source'));$target = $this->dbh->quote($edge->getAttribute('target'));$query_select = "SELECT $importid, sourcenodes.id, targetnodes.id";$query_from = " FROM nodes sourcenodes, nodes targetnodes WHERE sourcenodes.importid=$source AND targetnodes.importid=$target";foreach($edge->getElementsByTagName('attvalue') as $value){$attName = "attr_".preg_replace('/[^a-z0-9_]*/i','',$value->getAttribute('for'));$attValue = $this->dbh->quote($value->getAttribute('value'));$att = $this->getEdgeAttributeByName($attName);$attName = $this->dbh->quote($att['name']);if($attName != "''"){if($att['type'] == 'TAGS'){$tags = explode("|", $attValue);foreach($tags as $tag){$tag = $this->dbh->quote($tag);$tagQueries[] = "INSERT INTO 'edgestags' (attribute, node, value) SELECT $attId, e.id, $tag FROM edges e WHERE e.importid=$importid";}} else {$query_insert .= ", $attName";$query_select .= ", $attValue";}}}$this->dbh->exec(utf8_decode("$query_insert ) $query_select $query_from"));}$this->dbh->commit();# Execute the tag queries$this->dbh->beginTransaction();foreach($tagQueries as $query){$this->dbh->exec(utf8_decode($query));}$this->dbh->commit();} else {die("unsupported version of GEXF format");}

Statistics:Posted by jacomyma — 05 Jun 2011 07:29

[SOLVED] Parsing GEXF in PHP

2011-06-05T04:22:01+01:00

I'm using PHP to translate a .gexf output to JSON to look into representation of Gephi output in Protovis/D3 but I'm having a bear of a time accessing the viz: attributes of a node. For some reason, when I check the children of node, I see "attvalues" but I don't see viz:size, viz:position or viz:color. I'm just using simplexml_load_file so if someone has a better process or a built parser, let me know.

Of course, the real thing to do is build a Protovis/D3 exporter (unfortunately, it doesn't parse id values for source/target but instead treats the id value as the order of the node in the JSON) which I suppose I should do.

Statistics:Posted by elijah — 05 Jun 2011 04:22

Gephi forums

Re: Parsing GEXF in PHP

[SOLVED] Parsing GEXF in PHP