/inputs/CTFS/CTFS_conversion_bci.php - Annotate - BIEN 3 - NCEAS Projects

1549

aaronmk

<html><body style="background-color:yellow;">

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<h1 style="text-align:center;"> CTFS to VegX conversion </h1>

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<?php

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$dbhost = 'localhost';

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$dbuser = 's_sramteke';

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$dbpass = 'S6a52mxX';

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echo date("m/d/y :H:i:s",time());

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$conn = mysql_connect($dbhost,$dbuser,$dbpass) or die ('Error');

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$dbname = 's_sramteke';

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mysql_select_db($dbname);

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//$sql = "SELECT * FROM `DFtemp`";

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//$result = mysql_query($sql);

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$xmlHandle = fopen("new_Xml_CTFS_row.xml","w");

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$writer = new XMLWriter();

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$writer->openMemory();

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$writer->setIndent(true);

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$writer->setIndentString("    ");

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$writer->startDocument('1.0', 'UTF-8');

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$writer->startElement('vegX');

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$writer->writeAttribute("xsi:noNamespaceSchemaLocation", "C:/Development/Utilities/LCR.Utilities.DataImport/LCR.Utilities.MappingTool/Resources/VEGX15~1.2/veg.xsd");

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$writer->writeAttribute("xmlns:acc", "eml://ecoinformatics.org/access-2.0.1");

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$writer->writeAttribute("xmlns:cov", "eml://ecoinformatics.org/coverage-2.0.1");

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$writer->writeAttribute("xmlns:doc", "eml://ecoinformatics.org/documentation-2.0.1");

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$writer->writeAttribute("xmlns:lit", "eml://ecoinformatics.org/literature-2.0.1");

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$writer->writeAttribute("xmlns:party","eml://ecoinformatics.org/party-2.0.1");

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$writer->writeAttribute("xmlns:proj","eml://ecoinformatics.org/project-2.0.1");

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$writer->writeAttribute("xmlns:res","eml://ecoinformatics.org/resource-2.0.1");

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$writer->writeAttribute("xmlns:txt","eml://ecoinformatics.org/text-2.0.1");

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$writer->writeAttribute("xmlns:dwe","http://rs.tdwg.org/dwc/dwelement/");

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$writer->writeAttribute("xmlns:dwg","http://rs.tdwg.org/dwc/geospatial/");

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$writer->writeAttribute("xmlns:misc","http://www.bfn.de/misc-1.0.1");

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$writer->writeAttribute("xmlns:org","http://www.bfn.de/organismobservation-1.0.1");

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$writer->writeAttribute("xmlns:plot","http://www.bfn.de/plot-1.0.1");

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$writer->writeAttribute("xmlns:obs","http://www.bfn.de/plotobservation-1.0.1");

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$writer->writeAttribute("xmlns:tcs","http://www.tdwg.org/schemas/tcs/1.01");

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$writer->writeAttribute("xmlns:xsi","http://www.w3.org/2001/XMLSchema-instance");

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$filename = "new_Xml_CTFS_row.xml";

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$file = $writer->outputMemory();

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file_put_contents($filename,$file);

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$i=0;

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/*while($row = mysql_fetch_row($result))

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$writer->startElement('projects');

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$writer->startElement('project');

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$writer->writeElement('title','Project 1');

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$writer->endElement();

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$writer->endElement();

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}*/

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$sql = "SELECT distinct `PlotID`, `Plot`, `QuadratID`, `QuadratName`, `gx`, `gy` FROM `DFtemp` WHERE plot = 'bci'";

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$result = mysql_query($sql);

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$writer->startElement('plots');

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while($row = mysql_fetch_row($result))

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$writer->startElement('plot');

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	$writer->writeElement('plotUniqueIdentifier',$row[0]);

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	$writer->writeElement('plotName',$row[1]);

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	$writer->startElement('geospatial');

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		$writer->writeElement('dwg:VerbatimLatitude',$row[4]);

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		$writer->writeElement('dwg:VerbatimLongitude',$row[5]);

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	$writer->endElement();

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$writer->endElement();

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$writer->startElement('plot');

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	$writer->writeElement('plotUniqueIdentifier',$row[2]);

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	$writer->writeElement('plotName',$row[3]);

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	$writer->startElement('relatedPlot');

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		$writer->startElement('relatedPlot');

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			$writer->writeElement('relatedPlotID',$row[0]);

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			$writer->writeElement('plotRelationship',"Quadrant");

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		$writer->endElement();

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	$writer->endElement();

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$writer->endElement();

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$i++;

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	if($i == 1000)

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		file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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		$i = 0;

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$writer->endElement();

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file_put_contents($filename, $writer->flush(true), FILE_APPEND);

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$i=0;

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$sql = "select MeasureID,CensusID,QuadratID, PlotCensusNumber, ExactDate,PLotID FROM `DFtemp` WHERE plot = 'bci'";

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$result = mysql_query($sql);

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$writer->startElement('plotObservations');

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while($row = mysql_fetch_row($result))

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$writer->startElement('plotObservation');

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	$writer->writeAttribute("id",$row[0]);

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	$writer->writeElement('plotUniqueIdentifierID',$row[5]);

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	$writer->writeElement('obsStartDate',$row[4]);

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	$writer->startElement('simpleUserdefined');

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		$writer->writeElement('name',"CensusID");

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		$writer->writeElement('value',$row[1]);

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		$writer->writeElement('methodID',"CensusID");

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	$writer->endElement();

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$writer->endElement();

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$writer->startElement('plotObservation');

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	$writer->writeAttribute("id",$row[2]);

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	$writer->writeElement('plotUniqueIdentifierID',$row[2]);

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	$writer->writeElement('obsStartDate',$row[4]);

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	$writer->startElement('simpleUserdefined');

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		$writer->writeElement('name',"CensusID");

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		$writer->writeElement('value',$row[1]);

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		$writer->writeElement('methodID',"CensusID");

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	$writer->endElement();

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$writer->endElement();

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$i++;

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	if($i == 1000)

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		file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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		$i = 0;

$writer->endElement();

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file_put_contents($filename, $writer->flush(true), FILE_APPEND);

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$i=0;

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$sql = " select Genus,Family,SpeciesName,GenusSpecies,SpeciesID,Mnemonic FROM `DFtemp` WHERE plot = 'bci'";

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$result = mysql_query($sql);

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$writer->startElement('taxonConcepts');

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while($row = mysql_fetch_row($result))

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$writer->startElement('taxonConcept');

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	$writer->writeAttribute("id",$row[0]);

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	$writer->writeElement('tcs:Name',$row[0]);

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	$writer->writeAttribute("scientific","false");

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	//$writer->endElement();

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	$writer->writeElement('tcs:Rank',"Genus");

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$writer->endElement();

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$writer->startElement('taxonConcept');

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	$writer->writeAttribute("id",$row[1]);

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	$writer->writeElement('tcs:Name',$row[1]);

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	$writer->writeAttribute("scientific","false");

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	//$writer->endElement();

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	$writer->writeElement('tcs:Rank',"Family");

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	$writer->startElement('tcs:TaxonRelationships');

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	$writer->startElement('tcs:TaxonRelationship');

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		$writer->writeAttribute("type","is child taxon of");

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		$writer->writeElement('tcs:ToTaxonConcept',$row[0]);

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	$writer->endElement();

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	$writer->endElement();

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$writer->endElement();

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$writer->startElement('taxonConcept');

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	$writer->writeAttribute("id",$row[2]);

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	$writer->startElement('tcs:Name');

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		$writer->startAttribute("scientific");

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			$writer->text("false");

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		$writer->endAttribute();

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		$writer->text($row[2]);

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	$writer->endElement();

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	$writer->writeElement('tcs:Rank',"Species");

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	$writer->startElement('tcs:TaxonRelationships');

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	$writer->startElement('tcs:TaxonRelationship');

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		$writer->writeAttribute("type","is child taxon of");

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		$writer->writeElement('tcs:ToTaxonConcept',$row[0]);

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	$writer->endElement();

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	$writer->startElement('tcs:TaxonRelationship');

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		$writer->writeAttribute("type","is child taxon of");

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		$writer->writeElement('tcs:ToTaxonConcept',$row[1]);

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	$writer->endElement();

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	$writer->endElement();

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$writer->endElement();

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$i++;

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	if($i == 1000)

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		file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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		$i = 0;

$writer->endElement();

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$i=0;

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file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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$sql = "select SpeciesID,Mnemonic FROM `DFtemp` WHERE plot = 'bci'";

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$result = mysql_query($sql);

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$writer->startElement('taxonNameUsageConcepts');

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while($row = mysql_fetch_row($result))

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$writer->startElement('taxonNameUsageConcept');

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	$writer->writeAttribute("id",$row[0]);

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	$writer->writeElement('authorName');

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	$writer->writeElement('authorCode',$row[1]);

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$writer->endElement();

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$i++;

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	if($i == 1000)

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		file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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		$i = 0;

$writer->endElement();

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$i=0;

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file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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$sql = "select MeasureID,PlotID,x,y,TreeID,Tag,StemId,StemTag,DBH,HOM,ListOfTSM,status FROM `DFtemp` WHERE plot = 'bci'";

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$result = mysql_query($sql);

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$writer->startElement('individualOrganismObservations');

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while($row = mysql_fetch_row($result))

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$writer->startElement('individualOrganismObservation');

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	$writer->writeAttribute("id",$row[0]);

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	$writer->writeElement('plotObservationID',$row[0]);

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	$writer->writeElement('individualOrganismID',$row[4]);

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	$writer->startElement('diameterBaseDistance');

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	$writer->startElement('diameter');

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	$writer->writeElement('value',$row[8]);

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	$writer->writeElement('attributeID',"DBH");

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	$writer->endElement();

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	$writer->startElement('baseDistance');

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	$writer->writeElement('value',$row[9]);

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	$writer->writeElement('attributeID',"HOM");

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	$writer->endElement();

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	$writer->endElement();

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	$writer->startElement("relatedIndividual");

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	$writer->startElement("relatedItem");

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	$writer->writeElement('relatedItemID',$row[6]);

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	$writer->writeElement('itemRelationship',"Stem");

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	$writer->endElement();

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	$writer->endElement();

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	$writer->startElement('relativePlotPosition');

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	$writer->writeElement('relativeX',$row[2]);

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	$writer->writeElement('relativeY',$row[3]);

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	$writer->endElement();

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	$str = $row[10];

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	while($str != "")

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		$pos = strpos($str,',');

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		if($pos === false)

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			$TSMcode = $str;

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			$str = "";

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		else

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			$TSMcode=substr($str,0,$pos);

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			$str = substr($str,$pos+1);

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		//echo $TSMcode;

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		$sqlt = "select status from attributes where attr = '" . $TSMcode . "'";

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		//echo $sqlt;

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		$resultt = mysql_query($sqlt);

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		$rowt = mysql_fetch_row($resultt);

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		//echo $rowt[0];

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		$writer->startElement('simpleUserdefined');

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		$writer->writeElement('name',$rowt[0]);

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		$writer->writeElement('value',$TSMcode);

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		$writer->writeElement('methodID',$TSMcode);

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		$writer->endElement();

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	$writer->writeElement('individualOrganismHealth',$row[11]);

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$writer->endElement();

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$i++;

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	if($i == 1000)

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		file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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		$i = 0;

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$writer->endElement();

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file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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$sql = "select SpeciesID,TreeID,Tag,StemId,StemTag FROM `DFtemp` WHERE plot = 'bci'";

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$i = 0;

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$result = mysql_query($sql);

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$writer->startElement('individualOrganisms');

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while($row = mysql_fetch_row($result))

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	$writer->startElement('individualOrganism');

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	$writer->writeAttribute("id",$row[1]);

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	$writer->writeElement('taxonNameUsageConceptID',$row[0]);

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	$writer->writeElement('identificationLabel',$row[2]);

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	$writer->endElement();

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	$writer->startElement('individualOrganism');

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	$writer->writeAttribute("id",$row[3]);

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	$writer->writeElement('taxonNameUsageConceptID',$row[0]);

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	$writer->writeElement('identificationLabel',$row[4]);

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	$writer->endElement();

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	$i++;

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	if($i == 1000)

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		file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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		$i = 0;

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$writer->endElement();

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file_put_contents('new_Xml_CTFS_row.xml', $writer->flush(true), FILE_APPEND);

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$writer->startElement('attributes');

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$writer->startElement('attribute');

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	$writer->writeAttribute("id","DBH");

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	$writer->startElement('quantitative');

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		$writer->writeElement('methodID');

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		$writer->writeElement('unit','m');

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		$writer->writeElement('precision','.01');

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		$writer->writeElement('upperBound',"10000");

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		$writer->writeElement('lowerBound',"0");

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	$writer->endElement();

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$writer->endElement();

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$writer->startElement('attribute');

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	$writer->writeAttribute("id","HOM");

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	$writer->startElement('quantitative');

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		$writer->writeElement('methodID');

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		$writer->writeElement('unit','m');

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		$writer->writeElement('precision','.01');

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		$writer->writeElement('upperBound',"10000");

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		$writer->writeElement('lowerBound',"0");

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	$writer->endElement();

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$writer->endElement();

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$writer->endElement();

$sql = "select attr,status from attributes";

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$result = mysql_query($sql);

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$writer->startElement('methods');

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$writer->startElement('method');

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	$writer->writeAttribute("id","CensusID");

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	$writer->writeElement('description',"Census information");

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	$writer->writeElement('name',"CensusID");

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$writer->endElement();

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while($row = mysql_fetch_row($result))

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$writer->startElement('method');

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	$writer->writeAttribute("id",$row[0]);

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	$writer->writeElement('description',$row[1]);

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	$writer->writeElement('name',$row[0]);

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$writer->endElement();

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$writer->endElement();

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$writer->endElement();

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$writer->endDocument();

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//header('Content-type: text/xml');

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//echo $writer->outputMemory();

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$filename = "new_Xml_CTFS_row.xml";

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//$file = $writer->outputMemory();

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file_put_contents($filename, $writer->flush(true), FILE_APPEND);

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//file_put_contents($filename,$file);

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echo "and Veg-X file for the uploaded csv file was created";

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echo date("m/d/y :H:i:s",time());

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?>

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<FORM METHOD="LINK" ACTION="new_Xml_CTFS_row.xml">

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<br/>

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<br/>

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<br/>

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<INPUT TYPE="submit" VALUE="Click to See the VegX file">

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</FORM>

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</body></html>

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