# Copyright 1999-2000 by Jeffrey Chang. All rights reserved. # Copyright 2008-2013 by Michiel de Hoon. All rights reserved. # Revisions copyright 2011-2016 by Peter Cock. All rights reserved. # Revisions copyright 2015 by Eric Rasche. All rights reserved. # Revisions copyright 2015 by Carlos Pena. 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/ Entrez Programming Utilities web page is available at: http://www.ncbi.nlm.nih.gov/books/NBK25501/ This module provides a number of functions like ``efetch`` (short for Entrez Fetch) which will return the data as a handle object. This is a standard interface used in Python for reading data from a file, or in this case a remote network connection, and provides methods like ``.read()`` or offers iteration over the contents line by line. See also "What the heck is a handle?" in the Biopython Tutorial and Cookbook: http://biopython.org/DIST/docs/tutorial/Tutorial.html http://biopython.org/DIST/docs/tutorial/Tutorial.pdf Unlike a handle to a file on disk from the ``open(filename)`` function, which has a ``.name`` attribute giving the filename, the handles from ``Bio.Entrez`` all have a ``.url`` attribute instead giving the URL used to connect to the NCBI Entrez API. The Entrez module also provides an XML parser which takes a handle as input. Variables: - email Set the Entrez email parameter (default is not set). - tool Set the Entrez tool parameter (default is ``biopython``). Functions: - efetch Retrieves records in the requested format from a list of one or more primary IDs or from the user's environment - epost Posts a file containing a list of primary IDs for future use in the user's environment to use with subsequent search strategies - esearch Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user's environment. - elink Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs. - einfo Provides field index term counts, last update, and available links for each database. - esummary Retrieves document summaries from a list of primary IDs or from the user's environment. - egquery Provides Entrez database counts in XML for a single search using Global Query. - espell Retrieves spelling suggestions. - ecitmatch Retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings. - read Parses the XML results returned by any of the above functions. Typical usage is: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> handle = Entrez.einfo() # or esearch, efetch, ... >>> record = Entrez.read(handle) >>> handle.close() where record is now a Python dictionary or list. - parse Parses the XML results returned by those of the above functions which can return multiple records - such as efetch, esummary and elink. Typical usage is: >>> handle = Entrez.efetch("pubmed", id="19304878,14630660", retmode="xml") >>> records = Entrez.parse(handle) >>> for record in records: ... # each record is a Python dictionary or list. ... print(record['MedlineCitation']['Article']['ArticleTitle']) Biopython: freely available Python tools for computational molecular biology and bioinformatics. PDB file parser and structure class implemented in Python. >>> handle.close() This function is appropriate only if the XML file contains multiple records, and is particular useful for large files. - _open Internally used function. """ from __future__ import print_function import time import warnings # Importing these functions with leading underscore as not intended for reuse from Bio._py3k import urlopen as _urlopen from Bio._py3k import urlencode as _urlencode from Bio._py3k import HTTPError as _HTTPError from Bio._py3k import _binary_to_string_handle, _as_bytes email = None tool = "biopython" # XXX retmode? def epost(db, **keywds): """Post a file of identifiers for future use. Posts a file containing a list of UIs for future use in the user's environment to use with subsequent search strategies. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EPost Return a handle to the results. Raises an IOError exception if there's a network error. """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/epost.fcgi' variables = {'db': db} variables.update(keywds) return _open(cgi, variables, post=True) def efetch(db, **keywords): """Fetches Entrez results which are returned as a handle. EFetch retrieves records in the requested format from a list of one or more UIs or from user's environment. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch Return a handle to the results. Raises an IOError exception if there's a network error. Short example: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> handle = Entrez.efetch(db="nucleotide", id="57240072", rettype="gb", retmode="text") >>> print(handle.readline().strip()) LOCUS AY851612 892 bp DNA linear PLN 10-APR-2007 >>> handle.close() This will automatically use an HTTP POST rather than HTTP GET if there are over 200 identifiers as recommended by the NCBI. **Warning:** The NCBI changed the default retmode in Feb 2012, so many databases which previously returned text output now give XML. """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi' variables = {'db': db} variables.update(keywords) post = False try: ids = variables["id"] except KeyError: pass else: if isinstance(ids, list): ids = ",".join(ids) variables["id"] = ids elif isinstance(ids, int): ids = str(ids) variables["id"] = ids if ids.count(",") >= 200: # NCBI prefers an HTTP POST instead of an HTTP GET if there are # more than about 200 IDs post = True return _open(cgi, variables, post=post) def esearch(db, term, **keywds): """ESearch runs an Entrez search and returns a handle to the results. ESearch searches and retrieves primary IDs (for use in EFetch, ELink and ESummary) and term translations, and optionally retains results for future use in the user's environment. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch Return a handle to the results which are always in XML format. Raises an IOError exception if there's a network error. Short example: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> handle = Entrez.esearch(db="nucleotide", retmax=10, term="opuntia[ORGN] accD") >>> record = Entrez.read(handle) >>> handle.close() >>> record["Count"] >= 2 True >>> "156535671" in record["IdList"] True >>> "156535673" in record["IdList"] True """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi' variables = {'db': db, 'term': term} variables.update(keywds) return _open(cgi, variables) def elink(**keywds): """ELink checks for linked external articles and returns a handle. ELink checks for the existence of an external or Related Articles link from a list of one or more primary IDs; retrieves IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and attributes for multiple IDs. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ELink Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. This example finds articles related to the Biopython application note's entry in the PubMed database: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> pmid = "19304878" >>> handle = Entrez.elink(dbfrom="pubmed", id=pmid, linkname="pubmed_pubmed") >>> record = Entrez.read(handle) >>> handle.close() >>> print(record[0]["LinkSetDb"][0]["LinkName"]) pubmed_pubmed >>> linked = [link["Id"] for link in record[0]["LinkSetDb"][0]["Link"]] >>> "17121776" in linked True This is explained in much more detail in the Biopython Tutorial. """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi' variables = {} variables.update(keywds) return _open(cgi, variables) def einfo(**keywds): """EInfo returns a summary of the Entez databases as a results handle. EInfo provides field names, index term counts, last update, and available links for each Entrez database. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EInfo Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. Short example: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> record = Entrez.read(Entrez.einfo()) >>> 'pubmed' in record['DbList'] True """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi' variables = {} variables.update(keywds) return _open(cgi, variables) def esummary(**keywds): """ESummary retrieves document summaries as a results handle. ESummary retrieves document summaries from a list of primary IDs or from the user's environment. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESummary Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. This example discovers more about entry 30367 in the journals database: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> handle = Entrez.esummary(db="journals", id="30367") >>> record = Entrez.read(handle) >>> handle.close() >>> print(record[0]["Id"]) 30367 >>> print(record[0]["Title"]) Computational biology and chemistry """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' variables = {} variables.update(keywds) return _open(cgi, variables) def egquery(**keywds): """EGQuery provides Entrez database counts for a global search. EGQuery provides Entrez database counts in XML for a single search using Global Query. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EGQuery Return a handle to the results in XML format. Raises an IOError exception if there's a network error. This quick example based on a longer version from the Biopython Tutorial just checks there are over 60 matches for 'Biopython' in PubMedCentral: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> handle = Entrez.egquery(term="biopython") >>> record = Entrez.read(handle) >>> handle.close() >>> for row in record["eGQueryResult"]: ... if "pmc" in row["DbName"]: ... print(row["Count"] > 60) True """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/egquery.fcgi' variables = {} variables.update(keywds) return _open(cgi, variables) def espell(**keywds): """ESpell retrieves spelling suggestions, returned in a results handle. ESpell retrieves spelling suggestions, if available. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESpell Return a handle to the results, by default in XML format. Raises an IOError exception if there's a network error. Short example: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> record = Entrez.read(Entrez.espell(term="biopythooon")) >>> print(record["Query"]) biopythooon >>> print(record["CorrectedQuery"]) biopython """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/espell.fcgi' variables = {} variables.update(keywds) return _open(cgi, variables) def _update_ecitmatch_variables(keywds): # XML is the only supported value, and it actually returns TXT. variables = {'retmode': 'xml'} citation_keys = ('journal_title', 'year', 'volume', 'first_page', 'author_name', 'key') # Accept pre-formatted strings if isinstance(keywds['bdata'], str): variables.update(keywds) else: # Alternatively accept a nicer interface variables['db'] = keywds['db'] bdata = [] for citation in keywds['bdata']: formatted_citation = '|'.join([citation.get(key, "") for key in citation_keys]) bdata.append(formatted_citation) variables['bdata'] = '\r'.join(bdata) return variables def ecitmatch(**keywds): """ECitMatch retrieves PMIDs-Citation linking ECitMatch retrieves PubMed IDs (PMIDs) that correspond to a set of input citation strings. See the online documentation for an explanation of the parameters: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ECitMatch Return a handle to the results, by default in plain text Raises an IOError exception if there's a network error. Short example: >>> from Bio import Entrez >>> Entrez.email = "Your.Name.Here@example.org" >>> citation_1 = { ... "journal_title": "proc natl acad sci u s a", ... "year": "1991", "volume": "88", "first_page": "3248", ... "author_name": "mann bj", "key": "citation_1"} >>> record = Entrez.ecitmatch(db="pubmed", bdata=[citation_1]) >>> print(record["Query"]) """ cgi = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/ecitmatch.cgi' variables = _update_ecitmatch_variables(keywds) return _open(cgi, variables, ecitmatch=True) def read(handle, validate=True): """Parses an XML file from the NCBI Entrez Utilities into python objects. This function parses an XML file created by NCBI's Entrez Utilities, returning a multilevel data structure of Python lists and dictionaries. Most XML files returned by NCBI's Entrez Utilities can be parsed by this function, provided its DTD is available. Biopython includes the DTDs for most commonly used Entrez Utilities. If validate is True (default), the parser will validate the XML file against the DTD, and raise an error if the XML file contains tags that are not represented in the DTD. If validate is False, the parser will simply skip such tags. Whereas the data structure seems to consist of generic Python lists, dictionaries, strings, and so on, each of these is actually a class derived from the base type. This allows us to store the attributes (if any) of each element in a dictionary my_element.attributes, and the tag name in my_element.tag. """ from .Parser import DataHandler handler = DataHandler(validate) record = handler.read(handle) return record def parse(handle, validate=True): """Parses an XML file from the NCBI Entrez Utilities into python objects. This function parses an XML file created by NCBI's Entrez Utilities, returning a multilevel data structure of Python lists and dictionaries. This function is suitable for XML files that (in Python) can be represented as a list of individual records. Whereas 'read' reads the complete file and returns a single Python list, 'parse' is a generator function that returns the records one by one. This function is therefore particularly useful for parsing large files. Most XML files returned by NCBI's Entrez Utilities can be parsed by this function, provided its DTD is available. Biopython includes the DTDs for most commonly used Entrez Utilities. If validate is True (default), the parser will validate the XML file against the DTD, and raise an error if the XML file contains tags that are not represented in the DTD. If validate is False, the parser will simply skip such tags. Whereas the data structure seems to consist of generic Python lists, dictionaries, strings, and so on, each of these is actually a class derived from the base type. This allows us to store the attributes (if any) of each element in a dictionary my_element.attributes, and the tag name in my_element.tag. """ from .Parser import DataHandler handler = DataHandler(validate) records = handler.parse(handle) return records def _open(cgi, params=None, post=None, ecitmatch=False): """Helper function to build the URL and open a handle to it (PRIVATE). 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. Does some simple error checking, and will raise an IOError if it encounters one. The arugment post should be a boolean to explicitly control if an HTTP POST should be used rather an HTTP GET based on the query length. By default (post=None), POST is used if the URL encoded paramters would be over 1000 characters long. This function also enforces the "up to three queries per second rule" to avoid abusing the NCBI servers. """ # NCBI requirement: At most three queries per second. # Equivalently, at least a third of second between queries delay = 0.333333334 current = time.time() wait = _open.previous + delay - current if wait > 0: time.sleep(wait) _open.previous = current + wait else: _open.previous = current params = _construct_params(params) options = _encode_options(ecitmatch, params) # By default, post is None. Set to a boolean to over-ride length choice: if post is None and len(options) > 1000: post = True cgi = _construct_cgi(cgi, post, options) try: if post: handle = _urlopen(cgi, data=_as_bytes(options)) else: handle = _urlopen(cgi) except _HTTPError as exception: raise exception return _binary_to_string_handle(handle) _open.previous = 0 def _construct_params(params): if params is None: params = {} # Remove None values from the parameters for key, value in list(params.items()): if value is None: del params[key] # Tell Entrez that we are using Biopython (or whatever the user has # specified explicitly in the parameters or by changing the default) if "tool" not in params: params["tool"] = tool # Tell Entrez who we are if "email" not in params: if email is not None: params["email"] = email else: warnings.warn(""" Email address is not specified. To make use of NCBI's E-utilities, NCBI requires you to specify your email address with each request. As an example, if your email address is A.N.Other@example.com, you can specify it as follows: from Bio import Entrez Entrez.email = 'A.N.Other@example.com' In case of excessive usage of the E-utilities, NCBI will attempt to contact a user at the email address provided before blocking access to the E-utilities.""", UserWarning) return params def _encode_options(ecitmatch, params): # Open a handle to Entrez. options = _urlencode(params, doseq=True) # _urlencode encodes pipes, which NCBI expects in ECitMatch if ecitmatch: options = options.replace('%7C', '|') return options def _construct_cgi(cgi, post, options): if not post: # HTTP GET cgi += "?" + options return cgi def _test(): """Run the module's doctests (PRIVATE).""" print("Running doctests...") import doctest doctest.testmod() print("Done") if __name__ == "__main__": _test()