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NetCatch.py

# Copyright 2002 by Katharine Lindner.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Code for dealing with lists of URLs (OBSOLETE).

NetCatch enables the user to scan a list of labelled urls and select 
a subset to read into a file.

Functions:
get_urls_by_label
get_urls_by_index
get_urls_by_range
select_output_file

This module is now considered to be obsolete, and is likely to be deprecated
in a future release of Biopython, and later removed.
"""
import os
import urllib
import sgmllib
from Bio import File


def is_absolute_url( candidate ):
    ( url_type, url ) = urllib.splittype( candidate )
    if( url_type == None ):
        return 0
    ( url_host, url ) = urllib.splithost( url )
    if( url_host == None ):
        return 0
    return 1

"""
ExtractUrls.py


Scans a file in http format and builds a dictionary of urls
"""

class ExtractUrls(  sgmllib.SGMLParser ):

    def __init__( self ):
        sgmllib.SGMLParser.__init__( self )
        self.reset()

    def reset( self ):
        sgmllib.SGMLParser.reset( self )
        self.urls = {}
        self._inlink = 0
        self._pending_url = ''
        self.text = ''

    def __str__( self ):
        output = ''
        for key in self.urls.keys():
            val = self.urls[ key ]
            output = output + '%s : %s\n' % ( key, val )
        return output

    def extract_urls(self, handle):
        self.feed(handle)
        return self.urls

    def feed(self, handle):
        """feed(self, handle )

        Feed in data for scanning.  handle is a file-like object
        containing html.

        """
        if isinstance(handle, File.UndoHandle):
            uhandle = handle
        else:
            uhandle = File.UndoHandle(handle)
        text = uhandle.read()
        sgmllib.SGMLParser.feed( self, text )

    def handle_data(self, data):
        if( self._inlink ):
            self.text = self.text + data

    def start_a( self, attrs ):
        self._inlink = 1
        for key, val in attrs:
            if key.lower() == 'href':
                self._pending_url = val

    def end_a( self ):
        self._inlink = 0
        key = self.text
        self.text = ''
        if not key == '':
            key = key.replace( ' ', '_' )
            self.urls[ key ] = self._pending_url

class Url:

    def __init__( self, label, url ):
        assert is_absolute_url( url )
        assert type( label ) == type( '' )
        self.label = label
        self.url = url

00106 class NetCatch:
    """
    Decorator for a dictionary of links. Each link is  indexed by its label.
    Allows the user to select links of interest and read each selection into
    its own file. The filename is contructed by appending the label with an
    extension of html.

    Files can be selected by index, range or label. The destination directory
    defaults to the current directory.  The user can specify another
    dictionary by passing a list of path segments to the constructor.

    net_catch = NetCatch()
    net_catch = NetCatch( [ 'amylase', 'species' ] )
    net_catch.get_all_urls()
    net_catch.get_urls_by_label( [ 'pig', 'dog', 'cow' ] )
    net_catch.get_urls_by_index( [ 1, 4, 6, 9 ] )
    net_catch.get_urls_by_range( 2, 5 )
    """

    def __init__( self, path_segments = [] ):
        self._urls = {}
        self._labels = []
        assert type( path_segments ) == type( [] )
        self.path_segments = path_segments
        self._build_path()

    def _build_path( self ):
        base_path = os.path.join( '' )
        for segment in self.path_segments:
            base_path = os.path.join( base_path, segment )
        self.base_path = base_path

    def __str__( self ):
        i = 0
        output = ''
        for label in self._labels:
            output = output + '%d %s: %s\n' % ( i, label, self._urls[ label ] )
            i = i + 1
        return output

    def import_dict( self, href_dict ):
        for ( key, val ) in href_dict.items():
            self.add_url( key, val )

    def add_url( self, label, url ):
        assert is_absolute_url( url )
        assert type( label ) == type( '' )
        self._labels.append( label )
        self._urls[ label ] = url

    def get_all_urls( self ):
        url_opener = urllib.URLopener()
        i = 0
        for label in self._labels:
            base_path =  self.base_path
            name = '%s%d.htm' % ( label, i )
            full_path = os.path.join( base_path, name )
            out_handle = open( full_path , "wb" )
            i = i + 1
            url = self._urls[ label ]
            url_handle = url_opener.open( url )
            contents = url_handle.read()
            out_handle.write( contents )
            url_opener.close( )
            out_handle.close()

    def get_urls_by_label( self, labels ):
        url_opener = urllib.URLopener()
        for label in labels:
            base_path =  self.base_path
            name = '%s.htm' % ( label )
            full_path = os.path.join( base_path, name )
            out_handle = open( full_path , "wb" )
            url = self._urls[ label ]
            url_handle = url_opener.open( url )
            contents = url_handle.read()
            out_handle.write( contents )
            url_opener.close( )
            out_handle.close( )

    def get_urls_by_index( self, indices ):
        url_opener = urllib.URLopener()
        for index in indices:
            base_path =  self.base_path
            name = '%s.htm' % self._labels[ index ]
            full_path = os.path.join( base_path, name )
            out_handle = open( full_path , "wb" )
            label = self._labels[ index ]
            url = self._urls[ label ]
            url_handle = url_opener.open( url )
            contents = url_handle.read()
            out_handle.write( contents )
            url_opener.close( )
            out_handle.close( )

    def get_urls_by_range( self, low, hi ):
        url_opener = urllib.URLopener(  )
        for index in range( low, hi ):
            base_path =  self.base_path
            name = '%s.htm' % self._labels[ index ]
            full_path = os.path.join( base_path, name )
            out_handle = open( full_path , "wb" )
            label = self._labels[ index ]
            url = self._urls[ label ]
            url_handle = url_opener.open( url )
            contents = url_handle.read()
            out_handle.write( contents )
            url_opener.close( )
            out_handle.close( )



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