schema.py
author Dimitri Papadopoulos <dimitri.papadopoulos@cea.fr>
Fri, 14 Mar 2014 00:08:55 +0100
changeset 757 be6bf760d99c
parent 313 e539166c4e6d
child 372 f8d0427934e1
child 382 5ae60d9e641c
child 610 4cc5dbf87763
child 623 983e8adfeaea
permissions -rw-r--r--
preparing 0.4.6

# -*- coding: utf-8 -*-
# copyright 2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# copyright 2013 CEA (Saclay, 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-brainomics schema"""
from cubicweb.schemas.base import CWUser
from yams.buildobjs import (EntityType, RelationDefinition, SubjectRelation, String, RichString,
                            Int, Float, Boolean)

from cubes.questionnaire.schema import QuestionnaireRun, Questionnaire, Question
from cubes.neuroimaging.schema import Scan, AnatomicalRegion
from cubes.genomics.schema import GenomicMeasure, ColumnRef
from cubes.medicalexp.schema  import Assessment, ProcessingRun, ScoreDefinition, ScoreValue

from cubes.brainomics import COMMENTED_ENTITIES, WIKI_ENTITIES


# ProcessingRun -> Measure
ProcessingRun.add_relation(SubjectRelation('QuestionnaireRun', cardinality='**'), name='inputs')
ProcessingRun.add_relation(SubjectRelation('Scan', cardinality='**'), name='inputs')
ProcessingRun.add_relation(SubjectRelation('GenomicMeasure', cardinality='**'), name='inputs')

ProcessingRun.add_relation(SubjectRelation('QuestionnaireRun', cardinality='**'), name='outputs')
ProcessingRun.add_relation(SubjectRelation('Scan', cardinality='**'), name='outputs')
ProcessingRun.add_relation(SubjectRelation('GenomicMeasure', cardinality='**'), name='outputs')

# Maesure -> Subject
QuestionnaireRun.add_relation(SubjectRelation(('Subject', 'Group'), cardinality='1*', inlined=True), name='concerns')
Scan.add_relation(SubjectRelation(('Subject', 'Group'), cardinality='1*', inlined=True), name='concerns')
GenomicMeasure.add_relation(SubjectRelation(('Subject', 'Group'), cardinality='1*', inlined=True), name='concerns')

# Assessment -> Measure
Assessment.add_relation(SubjectRelation('QuestionnaireRun', cardinality='**'), name='uses')
Assessment.add_relation(SubjectRelation('Scan', cardinality='**'), name='uses')
Assessment.add_relation(SubjectRelation('GenomicMeasure', cardinality='**'), name='uses')

Assessment.add_relation(SubjectRelation('QuestionnaireRun', cardinality='?*'), name='generates')
Assessment.add_relation(SubjectRelation('Scan', cardinality='?*'), name='generates')
Assessment.add_relation(SubjectRelation('GenomicMeasure', cardinality='?*'), name='generates')

# Score -> Measure
ScoreValue.add_relation(SubjectRelation('QuestionnaireRun', cardinality='?*'), name='measure')
ScoreValue.add_relation(SubjectRelation('Scan', cardinality='?*'), name='measure')
ScoreValue.add_relation(SubjectRelation('GenomicMeasure', cardinality='?*'), name='measure')

# Use for filepath computation
QuestionnaireRun.add_relation(SubjectRelation('Study', cardinality='1*', inlined=True), name='related_study')
Scan.add_relation(SubjectRelation('Study', cardinality='1*', inlined=True), name='related_study')
GenomicMeasure.add_relation(SubjectRelation('Study', cardinality='1*', inlined=True), name='related_study')
QuestionnaireRun.add_relation(SubjectRelation('Study', cardinality='**'), name='other_studies')
Scan.add_relation(SubjectRelation('Study', cardinality='**'), name='other_studies')
GenomicMeasure.add_relation(SubjectRelation('Study', cardinality='**'), name='other_studies')

# Device -> Measure
QuestionnaireRun.add_relation(SubjectRelation('Device', cardinality='?*', inlined=True), name='uses_device')
Scan.add_relation(SubjectRelation('Device', cardinality='?*', inlined=True), name='uses_device')
GenomicMeasure.add_relation(SubjectRelation('Device', cardinality='?*', inlined=True), name='uses_device')

# Measure -> ExternalResources
# Questionnaire may have some specifications files
Questionnaire.add_relation(SubjectRelation('ExternalResource', cardinality='*1'), name='external_resources')
# Some questionnaire run could have specific results files (subject dependant)
QuestionnaireRun.add_relation(SubjectRelation('ExternalResource', cardinality='*1'), name='external_resources')
Scan.add_relation(SubjectRelation('ExternalResource', cardinality='*1'), name='external_resources')
GenomicMeasure.add_relation(SubjectRelation('ExternalResource', cardinality='*1'), name='external_resources')

# Various relations
Questionnaire.add_relation(SubjectRelation('ScoreDefinition', cardinality='*?'), name='definitions')
ScoreDefinition.add_relation(SubjectRelation('Question', cardinality='**'), name='used_by')
AnatomicalRegion.add_relation(SubjectRelation('ScoreValue', cardinality='**'), name='concerned_by')
ColumnRef.add_relation(SubjectRelation('Assessment', cardinality='1*', inlined=True), name='assessment')

# Extra fields for CWUser

CWUser.add_relation(String(maxsize=512, fulltextindexed=True), name='affiliation')
CWUser.add_relation(String(maxsize=512, fulltextindexed=True), name='extra_infos')


# Comments for entities
class comments(RelationDefinition):
    subject = 'Comment'
    object = COMMENTED_ENTITIES

# Links to "Wikis" / Cards
class wiki(RelationDefinition):
    subject = WIKI_ENTITIES
    object = 'Card'
    cardinality = '**'