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.. _validation:
Validation
----------
Different validation levels are available. They represent different
compromises between speed and warrant of validity. The validation level
can be specified when the :class:`~gfapy.gfa.Gfa` object is created, using the
``vlevel`` parameter of the constructor and of the
`from_file` method. Four levels of validation are defined
(0 = no validation, 1 = validation by reading, 2 = validation by reading
and writing, 3 = continuous validation). The default validation level
value is 1.
Manual validation
~~~~~~~~~~~~~~~~~
Independently from the validation level chosen, the user can always check the
value of a field calling
:meth:`~gfapy.line.common.validate.Validate.validate_field` on the line
instance. If no exception is raised, the field content is valid.
To check if the entire content of the line is valid, the user can call
:meth:`~gfapy.line.common.validate.Validate.validate` on the line instance.
This will check all fields and perform cross-field validations, such as
comparing the length of the sequence of a GFA1 segment, to the value of the LN
tag (if present).
It is also possible to validate the structure of the GFA, for example to
check if there are unresolved references to lines. To do this, use the
:meth:`~gfapy.gfa.Gfa.validate` of the :class:`~gfapy.gfa.Gfa` instance.
No validations
~~~~~~~~~~~~~~
If the validation is set to 0, Gfapy will try to accept any input and
never raise an exception. This is not always possible, and in some
cases, an exception will still be raised, if the data is invalid.
Validation when reading
~~~~~~~~~~~~~~~~~~~~~~~
If the validation level is set to 1 or higher, basic validations will be
performed, such as checking the number of positional fields, the
presence of duplicated tags, the tag datatype of predefined tags.
Additionally, all tags will be validated, either during parsing or on
first access. Record-type cross-field validations will also be
performed.
In other words, a validation of 1 means that Gfapy guarantees (as good
as it can) that the GFA content read from a file is valid, and will
raise an exception on accessing the data if not.
The user is supposed to call `validate_field` after changing
a field content to something which can be potentially invalid, or
:meth:`~gfapy.line.common.validate.Validate.validate` if potentially
cross-field validations could fail.
Validation when writing
~~~~~~~~~~~~~~~~~~~~~~~
Setting the level to 2 will perform all validations described above,
plus validate the fields content when their value is written to string.
In other words, a validation of 2 means that Gfapy guarantee (as good as
it can) that the GFA content read from a file and written to a file is
valid and will raise an exception on accessing the data or writing to
file if not.
Continuous validation
~~~~~~~~~~~~~~~~~~~~~
If the validation level is set to 3, all validations for lower levels
described above are run, plus a validation of fields contents each time
a setter method is used.
A validation of 3 means that Gfapy guarantees (as good as it can) that
the GFA content is always valid.
|
