How to use the bioservices.services.REST function in bioservices

from bioservices.services import REST
from bioservices import logger
logger.name = __name__


__all__ = ["PRIDE"]


@wrapt.decorator
def params_to_update(wrapped, instance, args, kwargs):
    vars(wrapped)['actual_kwargs'] = kwargs
    return wrapped(*args, **kwargs)



class PRIDE(REST):
    """Interface to the `PRIDE `_ service



    """
    _url = "https://www.ebi.ac.uk/pride/ws/archive"

    def __init__(self, verbose=False, cache=False):
        """**Constructor**

        :param verbose: set to False to prevent informative messages
        """
        super(PRIDE, self).__init__(name="PRIDE", url=PRIDE._url,
                verbose=verbose, cache=cache)

    def get_project(self, identifier):

from functools import reduce # python3 compat
except:
    pass
from bioservices.services import REST, BioServicesError
import webbrowser
import copy
from bioservices import logger
logger.name = __name__


from easydev.logging_tools import Logging

__all__ = ["KEGG",  "KEGGParser"]


class KEGG(REST):
    """Interface to the `KEGG `_ service

    This class provides an interface to the KEGG REST API. The weblink tools
    are partially accesible. All dbentries can be parsed into dictionaries using
    the :class:`KEGGParser`

    Here are some examples. In order to retrieve the entry of the 
    gene identifier 7535 of the **hsa** organism, type::

        from bioservices import KEGG
        s = KEGG()
        print(s.get("hsa:7535"))

    The output is the raw ouput sent by KEGG API. See :class:`KEGGParser` to
    parse this output.

"OMA": "OMA_ID",
           "OrthoDB": "ORTHODB_ID",
           "ProtClustDB": "PROTCLUSTDB_ID",
           "BioCyc": "BIOCYC_ID",
           "Reactome": "REACTOME_ID",
           "UniPathWay": "UNIPATHWAY_ID",
           "CleanEx": "CLEANEX_ID",
           "GermOnline": "GERMONLINE_ID",
           "ChEMBL": "CHEMBL_ID",
           "ChiTaRS": "CHITARS_ID",
           "DrugBank": "DRUGBANK_ID",
           "GenomeRNAi": "GENOMERNAI_ID",
           "NextBio": "NEXTBIO_ID"}


class UniProt(REST):
    """Interface to the `UniProt `_ service

    .. rubric:: Identifiers mapping between databases:

    ::

        >>> from bioservices import UniProt
        >>> u = UniProt(verbose=False)
        >>> u.mapping("ACC", "KEGG_ID", query='P43403')
        defaultdict(, {'P43403': ['hsa:7535']})
        >>> res = u.search("P43403")

        # Returns sequence on the ZAP70_HUMAN accession Id
        >>> sequence = u.search("ZAP70_HUMAN", columns="sequence")

    """

##############################################################################

# About Clinvitae (http://clinvitae.invitae.com/)

# "CLINVITAE is a database of clinically-observed genetic variants aggregated
# from public sources, operated and made freely available by INVITAE." - CLINVITAE website

from bioservices.services import REST
from bioservices import logger
logger.name = __name__


__all__ = ["Clinvitae"]


class Clinvitae(REST):
    """
    class for interfacing with the Clinvitae web service

    Requests will return a list of json dicts. each dict has the following fields::

        accessionId
        gene
        nucleotideChanges
        description
        classification
        reportedClassification
        url
        region
        proteinChange
        lastUpdated
        alias

using the interactive interface. "

        -- From the PICR home page, Dec 2012


"""
from bioservices.services import REST


__all__ = ["PICR"]
#//the NEWT taxonomy ID to limit the mappings to
#//can be null or a number. Do not specify 0 for null.
#String taxonID = "9606";     //H. Sapiens


class PICR(REST):
    """Interface to the `PICR (Protein Identifier Cross reference) `_ service

    .. doctest::

        >>> from bioservices import PICR
        >>> p = PICR()
        >>> res = p.getMappedDatabaseNames() # get list of valid database
        >>> results = p.getUPIForSequence(p._sequence_example, \
                ["IPI", "ENSEMBL", "SWISSPROT"])


    """
    _sequence_example="MDSTNVRSGMKSRKKKPKTTVIDDDDDCMTCSACQSKLVKISDITKVSLDYINTMRGNTLACAACGSSLKLLNDFAS"
    _blastfrag_example="MSVMYKKILYPTDFSETAEIALKHVKAFKTLKAEEVILLHVIDEREIKKRDIFSLLLGVAGLNKSVEEFENELKNKLTEEAKNKMENIKKELEDVGFKVKDIIVVGIPHEEIVKIAEDEGVDIIIMGSHGKTNLKEILLGSVTENVIKKSNKPVLVVKRKNS"
    _accession_example = "P29375"
    _url = "http://www.ebi.ac.uk/Tools/picr/rest"

-- from Rhea Home page, Dec 2012 (http://www.ebi.ac.uk/rhea/about.xhtml)

"""
from __future__ import print_function
from collections import defaultdict

from bioservices.services import REST
from bioservices import logger
logger.name = __name__


__all__ = ["Rhea"]



class Rhea(REST):
    """Interface to the `Rhea `_ service

    You can search by compound name, ChEBI ID, reaction ID, cross reference
    (e.g., EC number) or citation (author name, title, abstract text, publication ID).
    You can use double quotes - to match an exact phrase - and the following
    wildcards:

        * ? (question mark = one character),
        * `*` (asterisk = several characters).

    Searching for caffe* will find reactions with participants such as caffeine,
    trans-caffeic acid or caffeoyl-CoA::

        from bioservices import Rhea
        r = Rhea()
        response = r.search("caffe*")

-- from NCBIblast web page


"""
import sys
import time

from bioservices.services import REST
from bioservices import logger
logger.name = __name__


__all__ = ["NCBIblast"]


class NCBIblast(REST):
    """Interface to the `NCBIblast `_ service.


    ::

        >>> from bioservices import *
        >>> s = NCBIblast(verbose=False)
        >>> jobid = s.run(program="blastp", sequence=s._sequence_example,
            stype="protein", database="uniprotkb", email="name@provider")
        >>> s.getResult(jobid, "out")

    .. warning:: It is very important to provide a real e-mail address as your
        job otherwise very likely will be killed and your IP, Organisation or
        entire domain black-listed.

    When running a blast request, a program is required. You can obtain the

"""
import io
from bioservices.services import REST
from bioservices import logger
logger.name = __name__

try:
    import pandas as pd
except:
    pass

__all__ = ["BioDBNet"]



class BioDBNet(REST):
    """Interface to the `BioDBNet `_ service

    ::

        >>> from bioservices import *
        >>> s = BioDBNet()

    Most of the BioDBNet WSDL are available. There are functions added to
    the original interface such as :meth:`extra_getReactomeIds`.

    Use :meth:`db2db` to convert from 1 database to some databases.
    Use :meth:`dbReport` to get the convertion from one database to all
    databases.

    """
    _url = 'https://biodbnet-abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.json'

An Information Portal to Biological Macromolecular Structures

        -- PDB home page, Feb 2013

    :Status: in progress not for production

"""
from __future__ import print_function

from bioservices.services import REST

__all__ = ["PDB"]


class PDB(REST):
    """Interface to part of the `PDB `_ service

    :Status: in progress not for production. You can get all ID and retrieve
        uncompressed file in PDB/FASTA formats for now. New features will be
        added on request.

    .. doctest::

        >>> from bioservices import PDB
        >>> s = PDB()
        >>> res = s.get_file("1FBV", "pdb")

    """

    def __init__(self, verbose=False, cache=False):
        """.. rubric:: Constructor

"""
import types
import io

from bioservices.services import REST
from bioservices import logger
logger.name = __name__


__all__ = ["EVA"]



class EVA(REST):
    """Interface to the `EVA `_ service


    * version: indicates the version of the API, this defines the available
      filters and JSON schema to be returned. Currently there is only
      version 'v1'.
    * category: this defines what objects we want to query. Currently there
      are five different categories: variants, segments, genes, files and
      studies.
    * resource: specifies the resource to be returned, therefore the JSON
      data model.
    * filters: each specific endpoint allows different filters. 
    """
    _url = "http://wwwdev.ebi.ac.uk/eva/webservices/rest/"

    def __init__(self, verbose=False, cache=False):