annotate db2dbRestClient.php @ 3:d4e959143115 draft

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\f0\fs22 \cf2 <?php\cf0 \
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\cf3 //$client = new SoapClient("http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl");\cf0 \
\cf3 /*\cf0 \
\cf3 $input = 'Ensembl Gene ID';\cf0 \
\cf3 $inputValues = 'ENSG00000121410, ENSG00000171428';\cf0 \
\cf3 $outputs = 'Gene Symbol, Ensembl Protein ID';\cf0 \
\cf3 $taxonId = '9606';\cf0 \
\cf3 $methods = array(\cf0 \
\cf3 			'getInputs',\cf0 \
\cf3 			'getOutputsForInput',XML: http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getoutputsforinput&input=genesymbol\cf0 \
\cf3 			'getDirectOutputsForInput',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getdirectoutputsforinput&input=genesymbol&directOutput=1\cf0 \
\cf3 			'getPathways', http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=ncipid,kegg&taxonId=9606\cf0 \
\cf3 			'db2db',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=db2db&input=geneid&inputValues=1,3&outputs=genesymbol,affyid&taxonId=9606&format=row\cf0 \
\cf3 			'dbReport',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbreport&input=geneid&inputValues=1,3&taxonId=9606&format=row\cf0 \
\cf3 			'dbWalk',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbwalk&inputValues=A1BG,MYC&dbPath=genesymbol-%3Egeneid-%3Eaffyid&taxonId=9606&format=row\cf0 \
\cf3 			'dbFind',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbfind&inputValues=A1BG,MYC,1,3&output=geneid&taxonId=9606&format=row\cf0 \
\cf3 			'dbOrtho',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbortho&input=geneid&inputValues=1,3&inputTaxon=9606&outputTaxon=10090&output=genesymbol&format=row\cf0 \
\cf3 			'dbAnnot'http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=dbannot&inputValues=1,MYC,MTOR_HUMAN&taxonId=9606&annotations=Genes,Pathways&format=row\cf0 \
\cf3 			)\cf0 \
\cf3 */\cf0 \
\
$taxonId = \cf4 ""\cf0 ;\
\
\
\cf3 //format='row' input='ensemblgeneid' inputValues='ENSG00000121410' outputs='genesymbol' taxonId='9606'\cf0 \
\cf3 //&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606";\cf0 \
\cf3 //$biodbnetRestApiCall = "http://biodbnet.abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getinputs";\cf0 \
\
\
\cf3 //print_r($argv);\cf0 \
\
$biodbnetRestApiCall = \cf4 ''\cf0 ;\
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\cf5 foreach \cf0 ($argv \cf5 as \cf0 $val)\
\{\
	$arr = preg_split(\cf4 "/=/"\cf0 , $val);\
	\cf5 if \cf0 (strcmp(\cf4 'input'\cf0 , $arr[0]) == 0)\
	\{\
		$input = $arr[1];\
		$biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&input=" \cf0 . $input;\
	\}\
	\cf5 else if \cf0 (strcmp(\cf4 'taxonId'\cf0 , $arr[0]) == 0)\
	\{\
		$taxonId = $arr[1];\
		$biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&taxonId=" \cf0 . $taxonId;\
	\}\
	\cf5 else if \cf0 (strcmp(\cf4 'inputValues'\cf0 , $arr[0]) == 0)\
	\{\
		$inputValues = $arr[1];\
		$biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&inputValues=" \cf0 . $inputValues;\
	\}\
	\cf5 else if \cf0 (strcmp(\cf4 'outputs'\cf0 , $arr[0]) == 0)\
	\{\
		$outputs = $arr[1];\
		$biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&outputs=" \cf0 . $outputs;\
	\}\
	\cf5 else if \cf0 (strcmp(\cf4 'fileType'\cf0 , $arr[0]) == 0)\
	\{\
		$fileType = strtolower($arr[1]);\
		\cf5 if \cf0 ($fileType == \cf4 'xml'\cf0 )\{\
			$biodbnetRestApiCallCore = \cf4 "http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.xml?method=db2db"\cf0 ;\
		\}\
		\cf5 else\cf0 \{\
			$biodbnetRestApiCallCore = \cf4 "http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db"\cf0 ;\
		\}\
		\cf5 if \cf0 ($fileType == \cf4 'table'\cf0 )\{\
			$biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&format=row"\cf0 ;\
		\}\
	\}\
\}\
$restApiCall =  $biodbnetRestApiCallCore . $biodbnetRestApiCall;\
$response = file_get_contents($restApiCall);\
\cf5 if \cf0 ($fileType == \cf4 'xml' \cf0 || $fileType == \cf4 'json'\cf0 )\{\
	print_r($response);\
\}\cf5 elseif \cf0 ($fileType == \cf4 'table'\cf0 )\{\
	\
	$formattedResponse = json_decode($response, \cf5 true\cf0 );\
	\cf3 //print_r($formattedResponse);\cf0 \
	\
	\cf5 echo \cf4 "<html>\\n"\cf0 ;\
	\cf5 echo \cf4 "<br/><br/><b>bioDBnet: db2db results</b><br/>"\cf0 ;\
	\cf5 echo \cf4 "<table border=1>\\n"\cf0 ;\
	$colNames = array_keys($formattedResponse[0]);\
	\cf5 echo \cf4 "<tr>"\cf0 ;\
	\cf5 foreach \cf0 ($colNames \cf5 as \cf0 $col)\
	\{\
		\cf5 if \cf0 ($col == \cf4 'InputValue'\cf0 )\
			$col = $input;\
		\cf5 echo \cf4 "<th>\cf0 $col\cf4 </th>"\cf0 ;\
	\}\
	\cf5 echo \cf4 "</tr>\\n"\cf0 ;\
	\cf5 foreach \cf0 ($formattedResponse \cf5 as \cf0 $row)\
	\{\
		\cf5 echo \cf4 "<tr>"\cf0 ;\
		\cf5 foreach \cf0 ($row \cf5 as \cf0 $key => $col)\
		\{\
			\cf5 echo \cf4 "<td>\cf0 $col\cf4 </td>"\cf0 ;\
		\}\
		\cf5 echo \cf4 "</tr>\\n"\cf0 ;\
	\}\
	\
	\cf5 echo \cf4 "</table>\\n"\cf0 ;\
	\cf5 echo \cf4 "</html>\\n"\cf0 ;\
\}\
\
\
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\cf2 ?>}