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# Copyright 1999-2000 by Jeffrey Chang. 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.
"""Provides code to access NCBI over the WWW.
The main Entrez web page is available at:
http://www.ncbi.nlm.nih.gov/Entrez/
A list of the Entrez utilities (will go away Dec 2002) is available
at:
http://www.ncbi.nlm.nih.gov/entrez/utils/utils_index.html
Documentation for the e-utilies are available at:
http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
The main Blast web page is available at:
http://www.ncbi.nlm.nih.gov/BLAST/
Functions:
query Query Entrez.
pmfetch Retrieve results using a unique identifier.
pmqty Search PubMed.
pmneighbor Return a list of related articles for a PubMed entry.
efetch Access the efetch script.
_open
"""
import string
import urllib
from Bio import File
def query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi',
**keywds):
"""query(cmd, db, cgi='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi',
**keywds) -> handle
Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html
Raises an IOError exception if there's a network error.
"""
variables = {'cmd' : cmd, 'db' : db}
variables.update(keywds)
return _open(cgi, variables)
def pmfetch(db, id, report=None, mode=None,
cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi"):
"""pmfetch(db, id, report=None, mode=None,
cgi="http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi")
Query PmFetch and return a handle to the results. See the
online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch_help.html
Raises an IOError exception if there's a network error.
"""
variables = {'db' : db, 'id' : id}
if report is not None:
variables['report'] = report
if mode is not None:
variables['mode'] = mode
return _open(cgi, variables)
def pmqty(db, term, dopt=None,
cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi',
**keywds):
"""pmqty(db, term, dopt=None,
cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi') -> handle
Query PmQty and return a handle to the results. See the
online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty_help.html
Raises an IOError exception if there's a network error.
"""
variables = {'db' : db, 'term' : term}
if dopt is not None:
variables['dopt'] = dopt
variables.update(keywds)
return _open(cgi, variables)
def pmneighbor(pmid, display,
cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi'):
"""pmneighbor(pmid, display,
cgi='http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor.fcgi') -> handle
Query PMNeighbor and return a handle to the results. See the
online documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/utils/pmneighbor_help.html
Raises an IOError exception if there's a network error.
"""
# Warning: HUGE HACK HERE! pmneighbor expects the display
# parameter to be passed as just a tag, with no value.
# Unfortunately, _open doesn't support these types of parameters,
# so I'm building my own cgi string. This is really due to the
# limitations of urllib.urlencode. We'll have to figure out a
# good workaround.
fullcgi = "%s?pmid=%s&%s" % (cgi, pmid, display)
return _open(fullcgi)
# XXX retmode?
def epost(db, id, cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi',
**keywds):
"""epost(db, id[, cgi]) -> handle
Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/epost_help.html
Raises an IOError exception if there's a network error.
"""
variables = {'db' : db, 'id' : id}
variables.update(keywds)
return _open(cgi, variables)
def efetch(db, cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi',
**keywds):
"""efetch(db[, cgi][...]) -> handle
Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
Raises an IOError exception if there's a network error.
"""
variables = {'db' : db}
variables.update(keywds)
return _open(cgi, variables)
def esearch(db, term,
cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi',
**keywds):
"""esearch(db, term[, cgi][...]) -> handle
Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html
Raises an IOError exception if there's a network error.
"""
variables = {'db' : db,
'term' : term}
variables.update(keywds)
return _open(cgi, variables)
def elink(cgi='http://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi',
**keywds):
"""elink([, cgi][...]) -> handle
Query Entrez and return a handle to the results. See the online
documentation for an explanation of the parameters:
http://www.ncbi.nlm.nih.gov/entrez/query/static/elink_help.html
Raises an IOError exception if there's a network error.
"""
variables = {}
variables.update(keywds)
return _open(cgi, variables)
def _open(cgi, params={}, get=1):
"""_open(cgi, params={}, get=1) -> UndoHandle
Open a handle to Entrez. cgi is the URL for the cgi script to access.
params is a dictionary with the options to pass to it. get is a boolean
that describes whether a GET should be used. Does some
simple error checking, and will raise an IOError if it encounters one.
"""
# Open a handle to Entrez.
options = urllib.urlencode(params)
if get: # do a GET
fullcgi = cgi
if options:
fullcgi = "%s?%s" % (cgi, options)
# print fullcgi
handle = urllib.urlopen(fullcgi)
else: # do a POST
handle = urllib.urlopen(cgi, options)
# Wrap the handle inside an UndoHandle.
uhandle = File.UndoHandle(handle)
# Check for errors in the first 5 lines.
# This is kind of ugly.
lines = []
for i in range(5):
lines.append(uhandle.readline())
for i in range(4, -1, -1):
uhandle.saveline(lines[i])
data = string.join(lines, '')
if string.find(data, "500 Proxy Error") >= 0:
# Sometimes Entrez returns a Proxy Error instead of results
raise IOError, "500 Proxy Error (NCBI busy?)"
elif string.find(data, "502 Proxy Error") >= 0:
raise IOError, "502 Proxy Error (NCBI busy?)"
elif string.find(data, "WWW Error 500 Diagnostic") >= 0:
raise IOError, "WWW Error 500 Diagnostic (NCBI busy?)"
elif data[:5] == "ERROR":
# XXX Possible bug here, because I don't know whether this really
# occurs on the first line. I need to check this!
raise IOError, "ERROR, possibly because id not available?"
# Should I check for 404? timeout? etc?
return uhandle
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