[schema] First version of the cube: schema and entities, closes #3912377

schema.py

@@ -16,3 +16,66 @@
 # with this program. If not, see <http://www.gnu.org/licenses/>.
 
 """cubicweb-clinipath schema"""
+
+from yams.buildobjs import (EntityType, SubjectRelation, String, RichString, Int, Date)
+
+
+class Biopsy(EntityType):
+    """Biopsy attributes"""
+    biopsy_type = String(maxsize=512)
+    extraction_date = Date()
+    size = String(maxsize=128)
+    tumoral_cell_percent = Float(indexed=True)
+    necrosis_percent = Float(indexed=True)
+    has_gene_expression = Boolean()
+    proliferating_cell_percent = Float()
+    has_neoangiogenesis = Boolean()
+    has_necrosis = Boolean()
+    conclusions = String(maxsize=2056, fulltextindexed=True)
+
+
+class BiopsySample(EntityType):
+    size = String(maxsize=128)
+    tumoral_cell_percent = Float(indexed=True)
+    necrosis_percent = Float(indexed=True)
+    has_gene_expression = Boolean()
+    proliferating_cell_percent = Float()
+    has_neoangiogenesis = Boolean()
+    has_necrosis = Boolean()
+    extracted_from = SubjectRelation('Biopsy', cardinality='1*', inlined=True)
+
+
+class CellCulture(EntityType):
+    """ Models cell cultures, with passages for now. Related to a
+    Biopsy."""
+    code = Int()
+    culture_passage = Int()
+    related_biopsy = SubjectRelation('Biopsy', cardinality='?*',
+                                     inlined=True, composite='object')
+
+
+class BloodSample(EntityType):
+    """ Blood sample data """
+    code = Int(required=True)
+    volume_ml = Int()
+    sampling_date = Date()
+
+
+class IHCMeasure(EntityType):
+    """An IHC measure."""
+    measured_on = SubjectRelation(('Biopsy', 'CellCulture'), inlined=True, cardinality='1*')
+
+
+class IHCResult(EntityType):
+    """ An IHC result."""
+    expression_value = Int(indexed=True)
+    related_measure = SubjectRelation('IHCMeasure', inlined=True, cardinality='1*')
+
+
+class AnatomicPathologyReport(EntityType):
+    """ An Anatomic pathology report """
+    code = Int(required=True)
+    description = RichString(fulltextindexed=True)
+    conclusions = RichString(fulltextindexed=True)
+    report_on = SubjectRelation(('Biopsy', 'CellCulture', 'BloodSample'),
+                                inlined=True, cardinality='1*')