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comparison db2dbRestClient.php @ 2:ae43e2d7f68a draft

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author cheanney
date Tue, 07 Jul 2015 13:01:27 -0400
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1:6c2176813df3 2:ae43e2d7f68a
1 {\rtf1\ansi\ansicpg1252\cocoartf1344\cocoasubrtf720
2 {\fonttbl\f0\fnil\fcharset0 Monaco;}
3 {\colortbl;\red255\green255\blue255;\red255\green0\blue0;\red85\green127\blue95;\red0\green0\blue192;
4 \red127\green0\blue85;}
5 \margl1440\margr1440\vieww21520\viewh8280\viewkind0
6 \deftab720
7 \pard\pardeftab720
8
9 \f0\fs22 \cf2 <?php\cf0 \
10 \pard\pardeftab720
11 \cf3 //$client = new SoapClient("http://biodbnet.abcc.ncifcrf.gov/webServices/bioDBnet.wsdl");\cf0 \
12 \cf3 /*\cf0 \
13 \cf3 $input = 'Ensembl Gene ID';\cf0 \
14 \cf3 $inputValues = 'ENSG00000121410, ENSG00000171428';\cf0 \
15 \cf3 $outputs = 'Gene Symbol, Ensembl Protein ID';\cf0 \
16 \cf3 $taxonId = '9606';\cf0 \
17 \cf3 $methods = array(\cf0 \
18 \cf3 'getInputs',\cf0 \
19 \cf3 'getOutputsForInput',XML: http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getoutputsforinput&input=genesymbol\cf0 \
20 \cf3 'getDirectOutputsForInput',http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getdirectoutputsforinput&input=genesymbol&directOutput=1\cf0 \
21 \cf3 'getPathways', http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi?method=getpathways&pathways=ncipid,kegg&taxonId=9606\cf0 \
22 \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 \
23 \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 \
24 \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 \
25 \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 \
26 \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 \
27 \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 \
28 \cf3 )\cf0 \
29 \cf3 */\cf0 \
30 \
31 $taxonId = \cf4 ""\cf0 ;\
32 \
33 \
34 \cf3 //format='row' input='ensemblgeneid' inputValues='ENSG00000121410' outputs='genesymbol' taxonId='9606'\cf0 \
35 \cf3 //&format=row&input=genesymbol&inputValues=MYC,MTOR&outputs=geneid,affyid&taxonId=9606";\cf0 \
36 \cf3 //$biodbnetRestApiCall = "http://biodbnet.abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=getinputs";\cf0 \
37 \
38 \
39 \cf3 //print_r($argv);\cf0 \
40 \
41 $biodbnetRestApiCall = \cf4 ''\cf0 ;\
42 \pard\pardeftab720
43 \cf5 foreach \cf0 ($argv \cf5 as \cf0 $val)\
44 \{\
45 $arr = preg_split(\cf4 "/=/"\cf0 , $val);\
46 \cf5 if \cf0 (strcmp(\cf4 'input'\cf0 , $arr[0]) == 0)\
47 \{\
48 $input = $arr[1];\
49 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&input=" \cf0 . $input;\
50 \}\
51 \cf5 else if \cf0 (strcmp(\cf4 'taxonId'\cf0 , $arr[0]) == 0)\
52 \{\
53 $taxonId = $arr[1];\
54 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&taxonId=" \cf0 . $taxonId;\
55 \}\
56 \cf5 else if \cf0 (strcmp(\cf4 'inputValues'\cf0 , $arr[0]) == 0)\
57 \{\
58 $inputValues = $arr[1];\
59 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&inputValues=" \cf0 . $inputValues;\
60 \}\
61 \cf5 else if \cf0 (strcmp(\cf4 'outputs'\cf0 , $arr[0]) == 0)\
62 \{\
63 $outputs = $arr[1];\
64 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&outputs=" \cf0 . $outputs;\
65 \}\
66 \cf5 else if \cf0 (strcmp(\cf4 'fileType'\cf0 , $arr[0]) == 0)\
67 \{\
68 $fileType = strtolower($arr[1]);\
69 \cf5 if \cf0 ($fileType == \cf4 'xml'\cf0 )\{\
70 $biodbnetRestApiCallCore = \cf4 "http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.xml?method=db2db"\cf0 ;\
71 \}\
72 \cf5 else\cf0 \{\
73 $biodbnetRestApiCallCore = \cf4 "http://fr-s-bsg-bdb-0.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json?method=db2db"\cf0 ;\
74 \}\
75 \cf5 if \cf0 ($fileType == \cf4 'table'\cf0 )\{\
76 $biodbnetRestApiCall = $biodbnetRestApiCall . \cf4 "&format=row"\cf0 ;\
77 \}\
78 \}\
79 \}\
80 $restApiCall = $biodbnetRestApiCallCore . $biodbnetRestApiCall;\
81 $response = file_get_contents($restApiCall);\
82 \cf5 if \cf0 ($fileType == \cf4 'xml' \cf0 || $fileType == \cf4 'json'\cf0 )\{\
83 print_r($response);\
84 \}\cf5 elseif \cf0 ($fileType == \cf4 'table'\cf0 )\{\
85 \
86 $formattedResponse = json_decode($response, \cf5 true\cf0 );\
87 \cf3 //print_r($formattedResponse);\cf0 \
88 \
89 \cf5 echo \cf4 "<html>\\n"\cf0 ;\
90 \cf5 echo \cf4 "<br/><br/><b>bioDBnet: db2db results</b><br/>"\cf0 ;\
91 \cf5 echo \cf4 "<table border=1>\\n"\cf0 ;\
92 $colNames = array_keys($formattedResponse[0]);\
93 \cf5 echo \cf4 "<tr>"\cf0 ;\
94 \cf5 foreach \cf0 ($colNames \cf5 as \cf0 $col)\
95 \{\
96 \cf5 if \cf0 ($col == \cf4 'InputValue'\cf0 )\
97 $col = $input;\
98 \cf5 echo \cf4 "<th>\cf0 $col\cf4 </th>"\cf0 ;\
99 \}\
100 \cf5 echo \cf4 "</tr>\\n"\cf0 ;\
101 \cf5 foreach \cf0 ($formattedResponse \cf5 as \cf0 $row)\
102 \{\
103 \cf5 echo \cf4 "<tr>"\cf0 ;\
104 \cf5 foreach \cf0 ($row \cf5 as \cf0 $key => $col)\
105 \{\
106 \cf5 echo \cf4 "<td>\cf0 $col\cf4 </td>"\cf0 ;\
107 \}\
108 \cf5 echo \cf4 "</tr>\\n"\cf0 ;\
109 \}\
110 \
111 \cf5 echo \cf4 "</table>\\n"\cf0 ;\
112 \cf5 echo \cf4 "</html>\\n"\cf0 ;\
113 \}\
114 \
115 \
116 \pard\pardeftab720
117 \cf2 ?>}