Validate input + reference sequence in `translate_from`

[korikuzma]

Use this method:

vrs-python/src/ga4gh/vrs/extras/translator.py

Lines 473 to 492 in d2fdd9d

	def _is_valid_ref_seq(self, sequence_id: str, start_pos: int, end_pos: int,
	ref: str) -> Tuple[bool, str]:
	"""Return wether or not the expected reference sequence matches the actual reference sequence
	:param str sequence_id: Sequence ID to use
	:param int start_pos: Start pos (inter-residue) on the sequence_id
	:param int end_pos: End pos (inter-residue) on the sequence_id
	:param str ref: The expected reference sequence on the sequence_id given the
	start_pos and end_pos
	:return: Tuple containing whether or not actual reference sequence matches
	the expected reference sequence and error message if mismatch
	"""
	actual_ref = self.data_proxy.get_sequence(sequence_id, start_pos, end_pos)
	is_valid = actual_ref == ref
	err_msg = ""
	if not is_valid:
	err_msg = f"Expected reference sequence {ref} on {sequence_id} at positions "\
	f"({start_pos}, {end_pos}) but found {actual_ref}"
	_logger.warning(err_msg)
	return is_valid, err_msg

and update regex

for these from_translators (where applicable):

vrs-python/src/ga4gh/vrs/extras/translator.py

Lines 532 to 537 in d2fdd9d

	from_translators = {
	"beacon": _from_beacon,
	"gnomad": _from_gnomad,
	"hgvs": _from_hgvs,
	"spdi": _from_spdi,
	"vrs": _from_vrs,

Similar to what was done in #147

[github-actions]

This issue was marked stale due to inactivity.

[larrybabb]

changing this to a "bug" because it is a bug IMO. We should NOT be accepting invalid input and producing valid responses. I think it's fair to say that as we go through the effort to transform data we have a minimal responsibility for validating the input we receive. We can be somewhat forgiving with the looseness of hgvs but when reference alleles are included in the del delins and snv formats we should be validating that they match.