Skip to content

Commit

Permalink
issue #33, check that json values can be decoded
Browse files Browse the repository at this point in the history
  • Loading branch information
Manuel Marin committed Apr 8, 2019
1 parent 60b4088 commit 178d747
Showing 1 changed file with 122 additions and 46 deletions.
168 changes: 122 additions & 46 deletions spinedb_api/diff_database_mapping.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@

import time
import logging
import json
from .database_mapping import DatabaseMapping
from sqlalchemy import MetaData, Table, Column, Integer, String, func, or_, and_, event
from sqlalchemy.ext.automap import automap_base
Expand Down Expand Up @@ -967,8 +968,10 @@ def check_object_class(self, kwargs, object_class_names):
except KeyError:
raise SpineIntegrityError("Missing object class name.")
if name in object_class_names:
raise SpineIntegrityError("There can't be more than one object class called '{}'.".format(name),
id=object_class_names[name])
raise SpineIntegrityError(
"There can't be more than one object class called '{}'.".format(name),
id=object_class_names[name]
)

def check_objects_for_insert(self, *kwargs_list, strict=False):
"""Check that objects respect integrity constraints for an insert operation."""
Expand Down Expand Up @@ -1039,8 +1042,10 @@ def check_object(self, kwargs, object_names, object_class_id_list):
except KeyError:
raise SpineIntegrityError("Missing object name.")
if (class_id, name) in object_names:
raise SpineIntegrityError("There's already an object called '{}' in the same class.".format(name),
id=object_names[class_id, name])
raise SpineIntegrityError(
"There's already an object called '{}' in the same class.".format(name),
id=object_names[class_id, name]
)

def check_wide_relationship_classes_for_insert(self, *wide_kwargs_list, strict=False):
"""Check that relationship classes respect integrity constraints for an insert operation."""
Expand Down Expand Up @@ -1118,8 +1123,10 @@ def check_wide_relationship_class(self, wide_kwargs, relationship_class_names, o
except KeyError:
raise SpineIntegrityError("Missing relationship class name.")
if name in relationship_class_names:
raise SpineIntegrityError("There can't be more than one relationship class called '{}'.".format(name),
id=relationship_class_names[name])
raise SpineIntegrityError(
"There can't be more than one relationship class called '{}'.".format(name),
id=relationship_class_names[name]
)

def check_wide_relationships_for_insert(self, *wide_kwargs_list, strict=False):
"""Check that relationships respect integrity constraints for an insert operation."""
Expand Down Expand Up @@ -1228,8 +1235,10 @@ def check_wide_relationship(
except KeyError:
raise SpineIntegrityError("Missing relationship class identifier.")
if (class_id, name) in relationship_names:
raise SpineIntegrityError("There's already a relationship called '{}' in the same class.".format(name),
id=relationship_names[class_id, name])
raise SpineIntegrityError(
"There's already a relationship called '{}' in the same class.".format(name),
id=relationship_names[class_id, name]
)
try:
object_class_id_list = relationship_class_dict[class_id]['object_class_id_list']
except KeyError:
Expand All @@ -1245,15 +1254,21 @@ def check_wide_relationship(
if given_object_class_id_list != object_class_id_list:
object_name_list = [object_dict[id]['name'] for id in object_id_list]
relationship_class_name = relationship_class_dict[class_id]['name']
raise SpineIntegrityError("Incorrect objects '{}' for "
"relationship class '{}'.".format(object_name_list, relationship_class_name))
raise SpineIntegrityError(
"Incorrect objects '{}' for relationship class '{}'.".format(
object_name_list, relationship_class_name
)
)
join_object_id_list = ",".join([str(x) for x in object_id_list])
if (class_id, join_object_id_list) in relationship_objects:
object_name_list = [object_dict[id]['name'] for id in object_id_list]
relationship_class_name = relationship_class_dict[class_id]['name']
raise SpineIntegrityError("There's already a relationship between objects {} "
"in class {}.".format(object_name_list, relationship_class_name),
id=relationship_objects[class_id, join_object_id_list])
raise SpineIntegrityError(
"There's already a relationship between objects {} in class {}.".format(
object_name_list, relationship_class_name
),
id=relationship_objects[class_id, join_object_id_list]
)

def check_parameter_definitions_for_insert(self, *kwargs_list, strict=False):
"""Check that parameters respect integrity constraints for an insert operation."""
Expand All @@ -1268,11 +1283,13 @@ def check_parameter_definitions_for_insert(self, *kwargs_list, strict=False):
rel_parameter_definition_names[x.relationship_class_id, x.name] = x.id
object_class_dict = {x.id: x.name for x in self.object_class_list()}
relationship_class_dict = {x.id: x.name for x in self.wide_relationship_class_list()}
parameter_value_list_dict = {
x.id: x.value_list for x in self.wide_parameter_value_list_list()}
for kwargs in kwargs_list:
try:
self.check_parameter_definition(
kwargs, obj_parameter_definition_names, rel_parameter_definition_names,
object_class_dict, relationship_class_dict)
object_class_dict, relationship_class_dict, parameter_value_list_dict)
checked_kwargs_list.append(kwargs)
object_class_id = kwargs.get("object_class_id", None)
relationship_class_id = kwargs.get("relationship_class_id", None)
Expand All @@ -1293,7 +1310,7 @@ def check_parameter_definitions_for_update(self, *kwargs_list, strict=False):
parameter_list = self.parameter_list() # Query db only once
obj_parameter_definition_names = {}
rel_parameter_definition_names = {}
for x in self.parameter_list():
for x in parameter_list:
if x.object_class_id:
obj_parameter_definition_names[x.object_class_id, x.name] = x.id
elif x.relationship_class_id:
Expand All @@ -1302,11 +1319,15 @@ def check_parameter_definitions_for_update(self, *kwargs_list, strict=False):
x.id: {
"name": x.name,
"object_class_id": x.object_class_id,
"relationship_class_id": x.relationship_class_id
"relationship_class_id": x.relationship_class_id,
"parameter_value_list_id": x.parameter_value_list_id,
"default_value": x.default_value
} for x in parameter_list
}
object_class_dict = {x.id: x.name for x in self.object_class_list()}
relationship_class_dict = {x.id: x.name for x in self.wide_relationship_class_list()}
parameter_value_list_dict = {
x.id: x.value_list for x in self.wide_parameter_value_list_list()}
for kwargs in kwargs_list:
try:
id = kwargs["id"]
Expand Down Expand Up @@ -1340,7 +1361,7 @@ def check_parameter_definitions_for_update(self, *kwargs_list, strict=False):
updated_kwargs.update(kwargs)
self.check_parameter_definition(
updated_kwargs, obj_parameter_definition_names, rel_parameter_definition_names,
object_class_dict, relationship_class_dict)
object_class_dict, relationship_class_dict, parameter_value_list_dict)
checked_kwargs_list.append(kwargs)
object_class_id = kwargs.get("object_class_id", None)
relationship_class_id = kwargs.get("relationship_class_id", None)
Expand All @@ -1357,7 +1378,7 @@ def check_parameter_definitions_for_update(self, *kwargs_list, strict=False):

def check_parameter_definition(
self, kwargs, obj_parameter_definition_names, rel_parameter_definition_names,
object_class_dict, relationship_class_dict):
object_class_dict, relationship_class_dict, parameter_value_list_dict):
"""Raise a SpineIntegrityError if the parameter definition given by `kwargs` violates any
integrity constraints."""
object_class_id = kwargs.get("object_class_id", None)
Expand All @@ -1371,8 +1392,11 @@ def check_parameter_definition(
relationship_class_name = relationship_class_dict[relationship_class_id]
except KeyError:
relationship_class_name = 'id ' + relationship_class_id
raise SpineIntegrityError("Can't associate a parameter to both object class '{}' and "
"relationship class '{}'.".format(object_class_name, relationship_class_name))
raise SpineIntegrityError(
"Can't associate a parameter to both object class '{}' and relationship class '{}'.".format(
object_class_name, relationship_class_name
)
)
if object_class_id:
if object_class_id not in object_class_dict:
raise SpineIntegrityError("Object class not found.")
Expand All @@ -1381,8 +1405,10 @@ def check_parameter_definition(
except KeyError:
raise SpineIntegrityError("Missing parameter name.")
if (object_class_id, name) in obj_parameter_definition_names:
raise SpineIntegrityError("There's already a parameter called '{}' in this class.".format(name),
id=obj_parameter_definition_names[object_class_id, name])
raise SpineIntegrityError(
"There's already a parameter called '{}' in this class.".format(name),
id=obj_parameter_definition_names[object_class_id, name]
)
elif relationship_class_id:
if relationship_class_id not in relationship_class_dict:
raise SpineIntegrityError("Relationship class not found.")
Expand All @@ -1391,10 +1417,31 @@ def check_parameter_definition(
except KeyError:
raise SpineIntegrityError("Missing parameter name.")
if (relationship_class_id, name) in rel_parameter_definition_names:
raise SpineIntegrityError("There's already a parameter called '{}' in this class.".format(name),
id=rel_parameter_definition_names[relationship_class_id, name])
raise SpineIntegrityError(
"There's already a parameter called '{}' in this class.".format(name),
id=rel_parameter_definition_names[relationship_class_id, name]
)
else:
raise SpineIntegrityError("Missing object class or relationship class identifier.")
value_list = None
if 'parameter_value_list_id' in kwargs:
parameter_value_list_id = kwargs["parameter_value_list_id"]
if parameter_value_list_id:
if parameter_value_list_id not in parameter_value_list_dict:
raise SpineIntegrityError("Invalid parameter value list.")
value_list = parameter_value_list_dict[parameter_value_list_id].split(",")
if 'default_value' in kwargs:
default_value = kwargs['default_value']
try:
json.loads(default_value)
except json.JSONDecodeError as err:
raise SpineIntegrityError("Couldn't decode default value '{}' as JSON: {}".format(default_value, err))
if default_value is not None and value_list is not None and default_value not in value_list:
raise SpineIntegrityError(
"The value '{}' is not a valid default value for the associated list (valid values are: {})".format(
default_value, name, ", ".join(value_list)
)
)

def check_parameter_values_for_insert(self, *kwargs_list, strict=False):
"""Check that parameter values respect integrity constraints for an insert operation."""
Expand Down Expand Up @@ -1545,14 +1592,22 @@ def check_parameter_value(
parameter_definition = parameter_definition_dict[parameter_definition_id]
except KeyError:
raise SpineIntegrityError("Parameter not found.")
parameter_value_list_id = parameter_definition["parameter_value_list_id"]
if parameter_value_list_id in parameter_value_list_dict:
value_list = parameter_value_list_dict[parameter_value_list_id].split(",")
if 'value' in kwargs and kwargs['value'] and kwargs['value'] not in value_list:
valid_values = "', '".join(value_list)
raise SpineIntegrityError("The value '{}' is not a valid value "
"for parameter '{}' (valid values are: "
"'{}')".format(kwargs['value'], parameter_definition['name'], valid_values))
if 'value' in kwargs:
value = kwargs['value']
try:
json.loads(value)
except json.JSONDecodeError as err:
raise SpineIntegrityError("Couldn't decode '{}' as JSON: {}".format(value, err))
parameter_value_list_id = parameter_definition["parameter_value_list_id"]
if parameter_value_list_id in parameter_value_list_dict:
value_list = parameter_value_list_dict[parameter_value_list_id].split(",")
if value and value not in value_list:
valid_values = ", ".join(value_list)
raise SpineIntegrityError(
"The value '{}' is not a valid value for parameter '{}' (valid values are: {})".format(
value, parameter_definition['name'], valid_values
)
)
object_id = kwargs.get("object_id", None)
relationship_id = kwargs.get("relationship_id", None)
if object_id and relationship_id:
Expand All @@ -1564,8 +1619,11 @@ def check_parameter_value(
relationship_name = relationship_dict[relationship_id]['name']
except KeyError:
relationship_name = 'relationship id ' + relationship_id
raise SpineIntegrityError("Can't associate a parameter value to both "
"object '{}' and relationship '{}'.".format(object_name, relationship_name))
raise SpineIntegrityError(
"Can't associate a parameter value to both object '{}' and relationship '{}'.".format(
object_name, relationship_name
)
)
if object_id:
try:
object_class_id = object_dict[object_id]['class_id']
Expand All @@ -1579,9 +1637,12 @@ def check_parameter_value(
if (object_id, parameter_definition_id) in object_parameter_values:
object_name = object_dict[object_id]['name']
parameter_name = parameter_definition['name']
raise SpineIntegrityError("The value of parameter '{}' for object '{}' is "
"already specified.".format(parameter_name, object_name),
id=object_parameter_values[object_id, parameter_definition_id])
raise SpineIntegrityError(
"The value of parameter '{}' for object '{}' is already specified.".format(
parameter_name, object_name
),
id=object_parameter_values[object_id, parameter_definition_id]
)
elif relationship_id:
try:
relationship_class_id = relationship_dict[relationship_id]['class_id']
Expand All @@ -1590,14 +1651,20 @@ def check_parameter_value(
if relationship_class_id != parameter_definition["relationship_class_id"]:
relationship_name = relationship_dict[relationship_id]['name']
parameter_name = parameter_definition['name']
raise SpineIntegrityError("Incorrect relationship '{}' for "
"parameter '{}'.".format(relationship_name, parameter_name))
raise SpineIntegrityError(
"Incorrect relationship '{}' for parameter '{}'.".format(
relationship_name, parameter_name
)
)
if (relationship_id, parameter_definition_id) in relationship_parameter_values:
relationship_name = relationship_dict[relationship_id]['name']
parameter_name = parameter_definition['name']
raise SpineIntegrityError("The value of parameter '{}' for relationship '{}' is "
"already specified.".format(parameter_name, relationship_name),
id=relationship_parameter_values[relationship_id, parameter_definition_id])
raise SpineIntegrityError(
"The value of parameter '{}' for relationship '{}' is already specified.".format(
parameter_name, relationship_name
),
id=relationship_parameter_values[relationship_id, parameter_definition_id]
)
else:
raise SpineIntegrityError("Missing object or relationship identifier.")

Expand Down Expand Up @@ -1712,8 +1779,10 @@ def check_parameter_definition_tag(self, kwargs, parameter_definition_tags,
except KeyError:
raise SpineIntegrityError("Parameter tag not found.")
if (parameter_definition_id, parameter_tag_id) in parameter_definition_tags:
raise SpineIntegrityError("Parameter '{0}' already has the tag '{1}'.".format(parameter_name, tag),
id=parameter_definition_tags[parameter_definition_id, parameter_tag_id])
raise SpineIntegrityError(
"Parameter '{0}' already has the tag '{1}'.".format(parameter_name, tag),
id=parameter_definition_tags[parameter_definition_id, parameter_tag_id]
)

def check_wide_parameter_value_lists_for_insert(self, *wide_kwargs_list, strict=False):
"""Check that parameter value_lists respect integrity constraints for an insert operation."""
Expand Down Expand Up @@ -1786,14 +1855,21 @@ def check_wide_parameter_value_list(self, wide_kwargs, parameter_value_list_name
except KeyError:
raise SpineIntegrityError("Missing parameter value list name.")
if name in parameter_value_list_names:
raise SpineIntegrityError("There can't be more than one parameter value_list called '{}'.".format(name),
id=parameter_value_list_names[name])
raise SpineIntegrityError(
"There can't be more than one parameter value_list called '{}'.".format(name),
id=parameter_value_list_names[name]
)
try:
value_list = wide_kwargs["value_list"]
except KeyError:
raise SpineIntegrityError("Missing list of values.")
if len(value_list) != len(set(value_list)):
raise SpineIntegrityError("Values must be unique.")
for value in value_list:
try:
json.loads(value)
except json.JSONDecodeError as err:
raise SpineIntegrityError("Unable to decode value '{}' as JSON: {}".format(value, err))

def next_id_with_lock(self):
"""A 'next_id' item to use for adding new items."""
Expand Down

0 comments on commit 178d747

Please sign in to comment.