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Commit message:
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added:
db2dbRestClient.php |
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| diff -r 6c2176813df3 -r ae43e2d7f68a db2dbRestClient.php --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/db2dbRestClient.php Tue Jul 07 13:01:27 2015 -0400 |
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| @@ -0,0 +1,117 @@ +{\rtf1\ansi\ansicpg1252\cocoartf1344\cocoasubrtf720 +{\fonttbl\f0\fnil\fcharset0 Monaco;} +{\colortbl;\red255\green255\blue255;\red255\green0\blue0;\red85\green127\blue95;\red0\green0\blue192; +\red127\green0\blue85;} +\margl1440\margr1440\vieww21520\viewh8280\viewkind0 +\deftab720 +\pard\pardeftab720 + +\f0\fs22 \cf2 <?php\cf0 \ +\pard\pardeftab720 +\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 \ +\ +$biodbnetRestApiCall = \cf4 ''\cf0 ;\ +\pard\pardeftab720 +\cf5 foreach \cf0 ($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 ;\ +\}\ +\ +\ +\pard\pardeftab720 +\cf2 ?>} \ No newline at end of file |