# 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 file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause 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
The handle returned by these functions can be either in text mode or
in binary mode, depending on the data requested and the results
returned by NCBI Entrez. Typically, XML data will be in binary mode
while other data will be in text mode, as required by the downstream
parser to parse the data.

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.

All the functions that send requests to the NCBI Entrez API will
automatically respect the NCBI rate limit (of 3 requests per second
without an API key, or 10 requests per second with an API key) and
will automatically retry when encountering transient failures
(i.e. connection failures or HTTP 5XX codes). By default, Biopython
does a maximum of three tries before giving up, and sleeps for 15
seconds between tries. You can tweak these parameters by setting
``Bio.Entrez.max_tries`` and ``Bio.Entrez.sleep_between_tries``.

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``).
    - api_key      Personal API key from NCBI. If not set, only 3 queries per
      second are allowed. 10 queries per seconds otherwise with a
      valid API key.
    - max_tries    Configures how many times failed requests will be
      automatically retried on error (default is 3).
    - sleep_between_tries   The delay, in seconds, before retrying a request on
      error (default is 15).

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.
      Alternatively, the XML data can be read from a file opened in binary mode.
      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.esummary(db="pubmed", id="19304878,14630660", retmode="xml")
          >>> records = Entrez.parse(handle)
          >>> for record in records:
          ...     # each record is a Python dictionary or list.
          ...     print(record['Title'])
          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.

"""

import time
import warnings
import io
from urllib.error import URLError, HTTPError
from urllib.parse import urlencode
from urllib.request import urlopen


email = None
max_tries = 3
sleep_between_tries = 15
tool = "biopython"
api_key = None


# 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):
    """Fetch Entrez results which are returned as a handle.

    EFetch retrieves records in the requested format from a list or set 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="AY851612", 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:
        try:
            # ids is a single integer or a string representing a single integer
            ids = str(int(ids))
        except TypeError:
            # ids was not a string; try an iterable:
            ids = ",".join(map(str, ids))
        except ValueError:
            # string with commas or string not representing an integer
            ids = ",".join(map(str, (id.strip() for id in ids.split(","))))

        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):
    """Run an Entrez search and return 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", idtype="acc")
    >>> record = Entrez.read(handle)
    >>> handle.close()
    >>> int(record["Count"]) >= 2
    True
    >>> "EF590893.1" in record["IdList"]
    True
    >>> "EF590892.1" 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):
    """Check for linked external articles and return 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):
    """Return a summary of the Entrez 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):
    """Retrieve 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 19923 in the structure
    database:

    >>> from Bio import Entrez
    >>> Entrez.email = "Your.Name.Here@example.org"
    >>> handle = Entrez.esummary(db="structure", id="19923")
    >>> record = Entrez.read(handle)
    >>> handle.close()
    >>> print(record[0]["Id"])
    19923
    >>> print(record[0]["PdbDescr"])
    Crystal Structure Of E. Coli Aconitase B

    """
    cgi = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
    variables = {}
    variables.update(keywds)
    return _open(cgi, variables)


def egquery(**keywds):
    """Provide 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(int(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):
    """Retrieve spelling suggestions as 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):
    """Retrieve PMIDs for input citation strings, returned as a handle.

    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"}
    >>> handle = Entrez.ecitmatch(db="pubmed", bdata=[citation_1])
    >>> print(handle.read().strip().split("|"))
    ['proc natl acad sci u s a', '1991', '88', '3248', 'mann bj', 'citation_1', '2014248']
    >>> handle.close()

    """
    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, escape=False):
    """Parse 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.

    The handle must be in binary mode. This allows the parser to detect the
    encoding from the XML file, and to use it to convert all text in the XML
    to the correct Unicode string. The functions in Bio.Entrez to access NCBI
    Entrez will automatically return XML data in binary mode. For files,
    please use mode "rb" when opening the file, as in

        >>> from Bio import Entrez
        >>> handle = open("Entrez/esearch1.xml", "rb")  # opened in binary mode
        >>> record = Entrez.read(handle)
        >>> print(record['QueryTranslation'])
        biopython[All Fields]
        >>> handle.close()

    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.

    If escape is True, all characters that are not valid HTML are replaced
    by HTML escape characters to guarantee that the returned strings are
    valid HTML fragments. For example, a less-than sign (<) is replaced by
    &lt;. If escape is False (default), the string is returned as is.

    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, escape)
    record = handler.read(handle)
    return record


def parse(handle, validate=True, escape=False):
    """Parse 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.

    The handle must be in binary mode. This allows the parser to detect the
    encoding from the XML file, and to use it to convert all text in the XML
    to the correct Unicode string. The functions in Bio.Entrez to access NCBI
    Entrez will automatically return XML data in binary mode. For files,
    please use mode "rb" when opening the file, as in

        >>> from Bio import Entrez
        >>> handle = open("Entrez/pubmed1.xml", "rb")  # opened in binary mode
        >>> records = Entrez.parse(handle)
        >>> for record in records:
        ...     print(record['MedlineCitation']['Article']['Journal']['Title'])
        ...
        Social justice (San Francisco, Calif.)
        Biochimica et biophysica acta
        >>> handle.close()

    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.

    If escape is True, all characters that are not valid HTML are replaced
    by HTML escape characters to guarantee that the returned strings are
    valid HTML fragments. For example, a less-than sign (<) is replaced by
    &lt;. If escape is False (default), the string is returned as is.

    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, escape)
    records = handler.parse(handle)
    return records


def _open(cgi, params=None, post=None, ecitmatch=False):
    """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 argument 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 parameters 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 if no API key is provided.
    # Equivalently, at least a third of second between queries
    params = _construct_params(params)
    options = _encode_options(ecitmatch, params)
    # Using just 0.333333334 seconds sometimes hit the NCBI rate limit,
    # the slightly longer pause of 0.37 seconds has been more reliable.
    delay = 0.1 if api_key else 0.37
    current = time.time()
    wait = _open.previous + delay - current
    if wait > 0:
        time.sleep(wait)
        _open.previous = current + wait
    else:
        _open.previous = current

    # 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)

    for i in range(max_tries):
        try:
            if post:
                handle = urlopen(cgi, data=options.encode("utf8"))
            else:
                handle = urlopen(cgi)
        except HTTPError as exception:
            # Reraise if the final try fails
            if i >= max_tries - 1:
                raise
            # Reraise if the exception is triggered by a HTTP 4XX error
            # indicating some kind of bad request, UNLESS it's specifically a
            # 429 "Too Many Requests" response. NCBI seems to sometimes
            # erroneously return 429s even when their rate limit is
            # honored (and indeed even with the rate-limit-related fudging
            # higher up in this function in place), so the best we can do is
            # treat them as a serverside error and try again after sleeping
            # for a bit.
            if exception.code // 100 == 4 and exception.code != 429:
                raise
        except URLError:
            # Reraise if the final try fails
            if i >= max_tries - 1:
                raise
            # Treat as a transient error and try again after a brief delay:
            time.sleep(sleep_between_tries)
        else:
            break

    subtype = handle.headers.get_content_subtype()
    if subtype == "plain":
        url = handle.url
        handle = io.TextIOWrapper(handle, encoding="UTF-8")
        handle.url = url
    return 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,
            )
    if api_key and "api_key" not in params:
        params["api_key"] = api_key
    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


if __name__ == "__main__":
    from Bio._utils import run_doctest

    run_doctest()
