# -*- coding: utf-8 -*-

# copyright 2012 LOGILAB S.A. (Paris, FRANCE), all rights reserved.

# contact http://www.logilab.fr -- mailto:contact@logilab.fr

#

# This program is free software: you can redistribute it and/or modify it under

# the terms of the GNU Lesser General Public License as published by the Free

# Software Foundation, either version 2.1 of the License, or (at your option)

# any later version.

#

# This program is distributed in the hope that it will be useful, but WITHOUT

# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS

# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more

# details.

#

# You should have received a copy of the GNU Lesser General Public License along

# with this program. If not, see <http://www.gnu.org/licenses/>.

"""cubicweb-diseasome schema"""

from yams.buildobjs import EntityType, SubjectRelation, String, Int

from cubicweb.schemas.base import ExternalUri

class Disease(EntityType):

    """Disease entity definition.

    A Disease entity is characterized by several attributes which are 

    defined by URIs:

    - a name, which we define as a CubicWeb / Yams String object

    - a label, also defined as a Yams String

    - a class degree, defined as a Yams Int (that is, an integer)

    - a degree, also defined as a Yams Int

    - size, also defined as an Int

    - classes, defined as a set containing zero, one or several objects 

      identified by their URIs, that is, objects of type ``ExternalUri``

    - subtype_of, defined as a set containing zero, one or several

      objects of type ``Disease``

    - associated_genes, defined as a set containing zero, one or several

      objects of type ``Gene``, that is, of genes associated to the

      disease

    - possible_drugs, defined as a set containing zero, one or several

      objects, identified by their URIs, that is, of type ``ExternalUri``

    - omim and omim_page are identifiers in the OMIM (Online Mendelian

      Inheritance in Man) database, which contains an inventory of "human

      genes and genetic phenotypes" 

      (see http://http://www.ncbi.nlm.nih.gov/omim). Given that a disease

      only has unique omim and omim_page identifiers, when it has them,

      these attributes have been defined through relations such that

      for each disease there is at most one omim and one omim_page. 

      Each such identifier is defined through an URI, that is, through

      an ``ExternalUri`` entity.

      That is, these relations are of cardinality "?*". For optimization

      purposes, one might be tempted to defined them as inlined, by setting

      the ``inlined`` keyword argument to ``True``.

    - chromosomal_location is also defined through a relation of 

      cardinality "?*", since any disease has at most one chromosomal

      location associated to it.

    - same_as is also defined through an URI, and hence through a

      relation having ``ExternalUri`` entities as objects.

    For more information on this data set and the data set itself, 

    please consult http://datahub.io/dataset/fu-berlin-diseasome.

    """

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/name

    name = String(maxsize=256, fulltextindexed=True)

    # Corresponds to http://www.w3.org/2000/01/rdf-schema#label

    label = String(maxsize=512, fulltextindexed=True)

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/classDegree

    class_degree = Int()

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/degree

    degree = Int()

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/size

    size = Int()

    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/class

    classes = SubjectRelation('ExternalUri', cardinality='**')

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/diseaseSubtypeOf

    subtype_of = SubjectRelation('Disease', cardinality='**')

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/associatedGene

    associated_genes = SubjectRelation('Gene', cardinality='**')

    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/possibleDrug

    possible_drugs = SubjectRelation('ExternalUri', cardinality='**')

    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/omim

    omim = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)

    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/omimPage

    omim_page = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)

    #Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/chromosomalLocation'

    chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*',

                                           inlined=True)

    #Corresponds to http://www.w3.org/2002/07/owl#sameAs

    same_as = SubjectRelation('ExternalUri', cardinality='**')

class Gene(EntityType):

    """Gene entity defintion.

    A gene is characterized by the following attributes:

    - label, defined through a Yams String.

    - bio2rdf_symbol, also defined as a Yams String, since it is 

      just an identifier.

    - gene_id is an URI identifying a gene, hence it is defined

      as a relation with an ``ExternalUri`` object.

    - a pair of unique identifiers in the HUGO Gene Nomenclature

      Committee (http://http://www.genenames.org/). They are defined

      as ``ExternalUri`` entities as well.

    - same_as is also defined through an URI, and hence through a

      relation having ``ExternalUri`` entities as objects.

    """

    # Corresponds to http://www.w3.org/2000/01/rdf-schema#label

    label = String(maxsize=512, fulltextindexed=True)

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/geneId

    gene_id = SubjectRelation('ExternalUri', cardinality='**')

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/hgncId

    hgnc_id = SubjectRelation('ExternalUri', cardinality='**')

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/hgncIdPage

    hgnc_page = SubjectRelation('ExternalUri', cardinality='**')

    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/

    # diseasome/bio2rdfSymbol

    bio2rdf_symbol = String(maxsize=64, fulltextindexed=True)

    #Corresponds to http://www.w3.org/2002/07/owl#sameAs

    same_as = SubjectRelation('ExternalUri', cardinality='**')