Encode query with Python

    Encode query with Python

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    Contents

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        1 Summary

        2 Description

        3 Sample program

        4 Link

    Summary

    Result may not be able to be retrieved normally, if query including non alphanumeric character is used with Python.

    Description

    You have to encode your query. If qPath is a query to be encoded, please do as follows.

    import urllib

    urllib.urlencode({'<parameter_name>':qPath,})

    Sample program

    This tutorial introduces a example that retrieve entries which feature-key is 'rRNA', qualifier name is 'product' and has '16s ribosomal RNA' in qualifier value with searchByXMLPath of ARSA.

    Download this program

    import socket

    import urllib

    #set server

    host = "xml.nig.ac.jp"

    port =  80

    #set API server

    url = "/rest/Invoke"

    qPath = "/ENTRY/DDBJ/feature-table/feature/f_key=='rRNA' AND "

    qPath = qPath + "(/ENTRY/DDBJ/feature-table/feature{/f_key=='rRNA' AND "

    qPath = qPath + "/f_quals/qualifier{/q_name=='product' AND /q_value='16S ribosomal RNA'}}) "

    rPath = "/ENTRY/DDBJ/primary-accession,/ENTRY/DDBJ/definition"

    offset = "1";

    count = "10";

    query = urllib.urlencode({'queryPath':qPath,'returnPath':rPath,'offset':offset,'count':count});

    #set parameter

    query = "service=ARSA&method=searchByXMLPath&"+ query;

    #make connection

    sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)

    try:

    sock.connect((host, port))

    sock.send("POST " + url + " HTTP/1.0\n")

    sock.send("Content-Type: application/x-www-form-urlencoded\n")

    sock.send("User-Agent: python/socket\n")

    sock.send("Content-Length:" + `len(query)` + "\n\n")

    sock.send(query)

    except socket.error, e:

    print 'Error: %s' % e

    while 1:

    rcvmsg = sock.recv(1024)

    print rcvmsg,

    if rcvmsg == :

    break

    sock.close