def __init__(self, *args, **kwargs):
self.fields = [
Column("id", primitives.StringField),
# xml:id (or equivalent in JSON).
Column("extension", CompositeArray(ElementExtension()))
# Additional Content defined by implementations.
]
def include_object(object, name, type_, reflected, compare_to):
if (
type_ == "column"
and not reflected
and object.info.get("skip_autogenerate", False)
):
return False
else:
if compare_to is None:
# copy object to compare_to when the value of compare_to is
# None. Without this there is no way to assign a column
# type when generating the migrations
compare_to = object
if type_ == "column" and isinstance(compare_to.type, NullType):
type_name = "fhir_"
module = Fields
if isinstance(object.type, PgComposite):
type_name = object.type.name[5:]
compare_to.type = module.get(type_name)()
elif isinstance(object.type, CompositeArray):
type_name = object.type.item_type.name[5:]
compare_to.type = CompositeArray(module.get(type_name)())
else:
return False
return True
def generate_element_definition(self):
properties = self.element_properties()
if len(properties) > 0:
for prop in properties:
name = prop.name
nullable = True if (prop.cardinality["mini"] == 0) else False
field_type = (CompositeArray(prop.type) if
(prop.cardinality["maxi"] == -1) else prop.type)
new_column = Column(name, field_type, nullable=nullable)
field_names = [col.name for col in self.fields]
if name not in field_names:
self.fields.append(new_column)
data_type = "fhir_%s" % self.__class__.__name__.lower()
return PgComposite(data_type, self.fields)
def apply_constraints(self):
for resource in all_resources:
self.resource_instance[resource.__tablename__.lower()] = resource
if self.resource_name in self.resource_instance:
res = self.resource_instance.get(self.resource_name)
for field in self.fields:
name = field.get("name")
cardinality = field.get("cardinality")
# get the column from schema definition
col = res.__table__.columns.get(name)
if col is not None:
default_type = col.type
if cardinality["mini"] == "1" and col.nullable:
col.nullable = False
if cardinality["maxi"] == "*" and not (isinstance(
col.type, CompositeArray)):
col.type = CompositeArray(default_type)
self.profiled_columns.append(col)
# replace the schema definition with our profile definition
for column in self.profiled_columns:
res.__table__.columns.replace(column)
return res
else:
raise Exception(
"Missing Resource",
"The resource is not available in this server or it has "
"not been registered",
)
class Account(self.Base):
__tablename__ = 'account'
id = sa.Column(sa.Integer, primary_key=True)
balances = sa.Column(CompositeArray(self.type))
class Account(Base):
__tablename__ = 'account'
id = sa.Column(sa.Integer, primary_key=True)
categories = sa.Column(CompositeArray(type_))
def upgrade():
### commands auto generated by Alembic - please adjust! ###
op.create_table(
"organization",
sa.Column("id",
fhir_server.elements.primitives.IdField(),
nullable=False),
sa.Column("implicitRules",
fhir_server.elements.primitives.URIField(),
nullable=True),
sa.Column("language",
fhir_server.elements.primitives.CodeField(),
nullable=True),
sa.Column("active",
fhir_server.elements.primitives.BooleanField(),
nullable=True),
sa.Column("name",
fhir_server.elements.primitives.StringField(),
nullable=True),
sa.Column(
"identifier",
sqlalchemy_utils.types.pg_composite.CompositeArray(
PgComposite(
"fhir_identifier",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("system", URIField()),
Column("use", CodeField()),
Column("value", StringField()),
Column(
"assigner",
PgComposite(
"fhir_reference",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("display", StringField()),
Column("reference", StringField()),
],
),
),
Column(
"period",
PgComposite(
"fhir_period",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("end_time",
DateTimeField(timezone=True)),
Column("start_time",
DateTimeField(timezone=True)),
],
),
),
Column(
"type",
PgComposite(
"fhir_codeableconcept",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("text", StringField()),
Column(
"coding",
CompositeArray(
PgComposite(
"fhir_coding",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url",
StringField(
),
nullable=
False,
),
Column(
"value",
OpenType()
),
],
),
),
Column(
"id", StringField()),
Column(
"code", CodeField()),
Column(
"display",
StringField()),
Column(
"system", URIField()),
Column(
"user_selected",
BooleanField()),
Column(
"version",
StringField()),
],
)),
),
],
),
),
],
)),
nullable=True,
),
sa.Column(
"type",
fhir_server.elements.base.complex_mixin.PgComposite(
"fhir_codeableconcept",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("text", StringField()),
Column(
"coding",
CompositeArray(
PgComposite(
"fhir_coding",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("code", CodeField()),
Column("display", StringField()),
Column("system", URIField()),
Column("user_selected", BooleanField()),
Column("version", StringField()),
],
)),
),
],
),
nullable=True,
),
sa.Column(
"telecom",
sqlalchemy_utils.types.pg_composite.CompositeArray(
PgComposite(
"fhir_contactpoint",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("rank", PositiveIntField()),
Column("system", CodeField()),
Column("use", CodeField()),
Column("value", StringField()),
Column(
"period",
PgComposite(
"fhir_period",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("end_time",
DateTimeField(timezone=True)),
Column("start_time",
DateTimeField(timezone=True)),
],
),
),
],
)),
nullable=True,
),
sa.Column(
"address",
sqlalchemy_utils.types.pg_composite.CompositeArray(
PgComposite(
"fhir_address",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("city", StringField()),
Column("country", StringField()),
Column("district", StringField()),
Column("line", CompositeArray(StringField())),
Column("postal_code", StringField()),
Column("state", StringField()),
Column("type", CodeField()),
Column("text", StringField()),
Column("use", CodeField()),
Column(
"period",
PgComposite(
"fhir_period",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("end_time",
DateTimeField(timezone=True)),
Column("start_time",
DateTimeField(timezone=True)),
],
),
),
],
)),
nullable=True,
),
sa.Column(
"part_of",
fhir_server.elements.base.complex_mixin.PgComposite(
"fhir_reference",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("display", StringField()),
Column("reference", StringField()),
],
),
nullable=True,
),
sa.Column(
"contact",
sqlalchemy_utils.types.pg_composite.CompositeArray(
PgComposite(
"fhir_organizationcontact",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column(
"purpose",
PgComposite(
"fhir_codeableconcept",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("text", StringField()),
Column(
"coding",
CompositeArray(
PgComposite(
"fhir_coding",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url",
StringField(
),
nullable=
False,
),
Column(
"value",
OpenType()
),
],
),
),
Column(
"id", StringField()),
Column(
"code", CodeField()),
Column(
"display",
StringField()),
Column(
"system", URIField()),
Column(
"user_selected",
BooleanField()),
Column(
"version",
StringField()),
],
)),
),
],
),
),
Column(
"name",
PgComposite(
"fhir_humanname",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("family",
CompositeArray(StringField())),
Column("given",
CompositeArray(StringField())),
Column("prefix",
CompositeArray(StringField())),
Column("suffix",
CompositeArray(StringField())),
Column("text", StringField()),
Column("use", CodeField()),
Column(
"period",
PgComposite(
"fhir_period",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url",
StringField(),
nullable=False,
),
Column(
"value",
OpenType()),
],
),
),
Column("id", StringField()),
Column(
"end_time",
DateTimeField(
timezone=True),
),
Column(
"start_time",
DateTimeField(
timezone=True),
),
],
),
),
],
),
),
Column(
"address",
PgComposite(
"fhir_address",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("city", StringField()),
Column("country", StringField()),
Column("district", StringField()),
Column("line", CompositeArray(
StringField())),
Column("postal_code", StringField()),
Column("state", StringField()),
Column("type", CodeField()),
Column("text", StringField()),
Column("use", CodeField()),
Column(
"period",
PgComposite(
"fhir_period",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url",
StringField(),
nullable=False,
),
Column(
"value",
OpenType()),
],
),
),
Column("id", StringField()),
Column(
"end_time",
DateTimeField(
timezone=True),
),
Column(
"start_time",
DateTimeField(
timezone=True),
),
],
),
),
],
),
),
Column(
"telecom",
CompositeArray(
PgComposite(
"fhir_contactpoint",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url",
StringField(),
nullable=False,
),
Column(
"value", OpenType()),
],
),
),
Column("id", StringField()),
Column("rank", PositiveIntField()),
Column("system", CodeField()),
Column("use", CodeField()),
Column("value", StringField()),
Column(
"period",
PgComposite(
"fhir_period",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column(
"url",
StringField(
),
nullable=
False,
),
Column(
"value",
OpenType()
),
],
),
),
Column(
"id", StringField()),
Column(
"end_time",
DateTimeField(
timezone=True),
),
Column(
"start_time",
DateTimeField(
timezone=True),
),
],
),
),
],
)),
),
],
)),
nullable=True,
),
sa.Column(
"meta",
fhir_server.elements.base.complex_mixin.PgComposite(
"fhir_meta",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url", StringField(), nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("version_id", IdField()),
Column("last_updated", InstantField(timezone=True)),
Column("profile", CompositeArray(URIField())),
Column(
"security",
CompositeArray(
PgComposite(
"fhir_coding",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("code", CodeField()),
Column("display", StringField()),
Column("system", URIField()),
Column("user_selected", BooleanField()),
Column("version", StringField()),
],
)),
),
Column(
"tag",
CompositeArray(
PgComposite(
"fhir_coding",
[
Column(
"extension",
PgComposite(
"fhir_extension",
[
Column("url",
StringField(),
nullable=False),
Column("value", OpenType()),
],
),
),
Column("id", StringField()),
Column("code", CodeField()),
Column("display", StringField()),
Column("system", URIField()),
Column("user_selected", BooleanField()),
Column("version", StringField()),
],
)),
),
],
),
nullable=True,
),
sa.PrimaryKeyConstraint("id"),
)
### end Alembic commands ###
conn = op.get_bind()
for resource in all_resources:
conn.execute(
sa.sql.text("""
DROP INDEX IF EXISTS {0}_meta_version_id;
CREATE UNIQUE INDEX {0}_meta_version_id ON {0} (
((meta).version_id));
DROP TRIGGER IF EXISTS meta_version_id_concurrency ON {0};
CREATE TRIGGER meta_version_id_concurrency BEFORE INSERT OR UPDATE ON {0}
FOR EACH ROW EXECUTE PROCEDURE meta_version_id_concurrency();
""".format(resource.__tablename__)))
profiled_resources = {
con.get("resource"): con.get("fields")
for con in constraints
}
for resource, const in profiled_resources.items():
for c in const:
field = c.get("name")
mini = str(c.get("cardinality").get("mini"))
maxi = str(c.get("cardinality").get("maxi"))
conn.execute(
sa.sql.text("""
DROP TRIGGER IF EXISTS validate_meta_fields_{1} ON {0};
CREATE TRIGGER validate_meta_fields_{1} BEFORE INSERT OR UPDATE ON {0}
FOR EACH ROW EXECUTE PROCEDURE validate_meta_fields({1}, '{2}', '{3}');
""".format(resource.lower(), field, mini, maxi)))