doc/tutorials/dataimport/schema.py
author Sylvain Thénault <sylvain.thenault@logilab.fr>
Tue, 07 Jan 2014 16:19:18 +0100
changeset 9366 bcbc92223b35
parent 8930 6a02be304486
child 9702 c2108dbfb508
permissions -rw-r--r--
set proper PACKAGE information for yams 0.39 Yams 0.39 adds an unobstrusive API to get the package, or cube, defining a part of the schema (entity type, relation type/def). As CubicWeb overrides part of the schema reading process, we have to handle this information on our side so it will be properly set.
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# -*- coding: utf-8 -*-
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# copyright 2012 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
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# contact http://www.logilab.fr -- mailto:contact@logilab.fr
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#
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# This program is free software: you can redistribute it and/or modify it under
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# the terms of the GNU Lesser General Public License as published by the Free
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# Software Foundation, either version 2.1 of the License, or (at your option)
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# any later version.
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#
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# This program is distributed in the hope that it will be useful, but WITHOUT
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# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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# details.
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#
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# You should have received a copy of the GNU Lesser General Public License along
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# with this program. If not, see <http://www.gnu.org/licenses/>.
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"""cubicweb-diseasome schema"""
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from yams.buildobjs import EntityType, SubjectRelation, String, Int
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class Disease(EntityType):
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    """Disease entity definition.
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    A Disease entity is characterized by several attributes which are 
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    defined by URIs:
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    - a name, which we define as a CubicWeb / Yams String object
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    - a label, also defined as a Yams String
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    - a class degree, defined as a Yams Int (that is, an integer)
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    - a degree, also defined as a Yams Int
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    - size, also defined as an Int
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    - classes, defined as a set containing zero, one or several objects 
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      identified by their URIs, that is, objects of type ``ExternalUri``
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    - subtype_of, defined as a set containing zero, one or several
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      objects of type ``Disease``
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    - associated_genes, defined as a set containing zero, one or several
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      objects of type ``Gene``, that is, of genes associated to the
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      disease
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    - possible_drugs, defined as a set containing zero, one or several
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      objects, identified by their URIs, that is, of type ``ExternalUri``
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    - omim and omim_page are identifiers in the OMIM (Online Mendelian
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      Inheritance in Man) database, which contains an inventory of "human
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      genes and genetic phenotypes" 
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      (see http://http://www.ncbi.nlm.nih.gov/omim). Given that a disease
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      only has unique omim and omim_page identifiers, when it has them,
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      these attributes have been defined through relations such that
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      for each disease there is at most one omim and one omim_page. 
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      Each such identifier is defined through an URI, that is, through
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      an ``ExternalUri`` entity.
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      That is, these relations are of cardinality "?*". For optimization
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      purposes, one might be tempted to defined them as inlined, by setting
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      the ``inlined`` keyword argument to ``True``.
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    - chromosomal_location is also defined through a relation of 
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      cardinality "?*", since any disease has at most one chromosomal
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      location associated to it.
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    - same_as is also defined through an URI, and hence through a
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      relation having ``ExternalUri`` entities as objects.
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    For more information on this data set and the data set itself, 
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    please consult http://datahub.io/dataset/fu-berlin-diseasome.
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    """
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/name
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    name = String(maxsize=256, fulltextindexed=True)
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    # Corresponds to http://www.w3.org/2000/01/rdf-schema#label
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    label = String(maxsize=512, fulltextindexed=True)
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/classDegree
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    class_degree = Int()
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/degree
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    degree = Int()
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/size
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    size = Int()
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    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/class
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    classes = SubjectRelation('ExternalUri', cardinality='**')
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/diseaseSubtypeOf
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    subtype_of = SubjectRelation('Disease', cardinality='**')
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/associatedGene
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    associated_genes = SubjectRelation('Gene', cardinality='**')
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    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/possibleDrug
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    possible_drugs = SubjectRelation('ExternalUri', cardinality='**')
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    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/omim
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    omim = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)
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    #Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/omimPage
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    omim_page = SubjectRelation('ExternalUri', cardinality='?*', inlined=True)
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    #Corresponds to 'http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/chromosomalLocation'
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    chromosomal_location = SubjectRelation('ExternalUri', cardinality='?*',
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                                           inlined=True)
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    #Corresponds to http://www.w3.org/2002/07/owl#sameAs
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    same_as = SubjectRelation('ExternalUri', cardinality='**')
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class Gene(EntityType):
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    """Gene entity defintion.
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    A gene is characterized by the following attributes:
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    - label, defined through a Yams String.
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    - bio2rdf_symbol, also defined as a Yams String, since it is 
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      just an identifier.
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    - gene_id is an URI identifying a gene, hence it is defined
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      as a relation with an ``ExternalUri`` object.
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    - a pair of unique identifiers in the HUGO Gene Nomenclature
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      Committee (http://http://www.genenames.org/). They are defined
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      as ``ExternalUri`` entities as well.
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    - same_as is also defined through an URI, and hence through a
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      relation having ``ExternalUri`` entities as objects.
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    """
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    # Corresponds to http://www.w3.org/2000/01/rdf-schema#label
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    label = String(maxsize=512, fulltextindexed=True)
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/geneId
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    gene_id = SubjectRelation('ExternalUri', cardinality='**')
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/hgncId
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    hgnc_id = SubjectRelation('ExternalUri', cardinality='**')
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/hgncIdPage
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    hgnc_page = SubjectRelation('ExternalUri', cardinality='**')
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    # Corresponds to http://www4.wiwiss.fu-berlin.de/diseasome/resource/
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    # diseasome/bio2rdfSymbol
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    bio2rdf_symbol = String(maxsize=64, fulltextindexed=True)
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    #Corresponds to http://www.w3.org/2002/07/owl#sameAs
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    same_as = SubjectRelation('ExternalUri', cardinality='**')