doc/tutorials/dataimport/schema.py
author Rémi Cardona <remi.cardona@logilab.fr>
Wed, 28 Jan 2015 11:53:20 +0100
changeset 10165 7f1f7f710b16
parent 9702 c2108dbfb508
permissions -rw-r--r--
[web/data] Never hide JS errors in our Deferred implementation Modern browsers have good debugging tools, let exceptions go all the way up. This only affects exceptions raised in the js code, if there's an issue on the server/python side, they'll keep going through our error callbacks. Closes #4881300

# -*- 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.
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# 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


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 a 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 a 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 a 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 a 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='**')