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korikuzmakorikuzma
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Merge pull request #238 from cancervariants/staging
Staging
2 parents e8a99e9 + a4a3400 commit 73fc73c

19 files changed

+94
-583
lines changed

‎tests/fixtures/translators.yml‎

Lines changed: 1 addition & 482 deletions
Large diffs are not rendered by default.

‎tests/validators/validator_base.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -69,7 +69,7 @@ def test_matches(self):
6969
tokens = self.tokenizer.perform(x['query'], [])
7070
classification = self.classifier.match(tokens)
7171
validation_results = self.validator.validate(
72-
classification, normalize_endpoint=True,
72+
classification, normalize_endpoint=False,
7373
hgvs_dup_del_mode="default"
7474
)
7575
is_valid = False

‎variation/schemas/to_vrs_response_schema.py‎

Lines changed: 0 additions & 24 deletions
Original file line numberDiff line numberDiff line change
@@ -125,30 +125,6 @@ def schema_extra(schema: Dict[str, Any],
125125
"type": "LiteralSequenceExpression",
126126
"sequence": "E"
127127
}
128-
},
129-
{
130-
"_id": "ga4gh:VA.8JkgnqIgYqufNl-OV_hpRG_aWF9UFQCE",
131-
"type": "Allele",
132-
"location": {
133-
"_id": "ga4gh:VSL.AqrQ-EkAvTrXOFn70_8i3dXF5shBBZ5i", # noqa: E501
134-
"type": "SequenceLocation",
135-
"sequence_id": "ga4gh:SQ.WaAJ_cXXn9YpMNfhcq9lnzIvaB9ALawo", # noqa: E501
136-
"interval": {
137-
"type": "SequenceInterval",
138-
"start": {
139-
"type": "Number",
140-
"value": 639
141-
},
142-
"end": {
143-
"type": "Number",
144-
"value": 640
145-
}
146-
}
147-
},
148-
"state": {
149-
"type": "LiteralSequenceExpression",
150-
"sequence": "E"
151-
}
152128
}
153129
],
154130
"service_meta_": {

‎variation/validators/amino_acid_deletion.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -107,7 +107,7 @@ def get_valid_invalid_results(self, classification_tokens, transcripts,
107107
t, s.end_aa_del, s.end_pos_del, errors
108108
)
109109

110-
if not errors:
110+
if not errors and normalize_endpoint:
111111
mane = self.mane_transcript.get_mane_transcript(
112112
t, s.start_pos_del, s.end_pos_del,
113113
s.reference_sequence,
@@ -125,10 +125,11 @@ def get_valid_invalid_results(self, classification_tokens, transcripts,
125125
if is_identifier:
126126
break
127127

128-
self.add_mane_to_validation_results(
129-
mane_data_found, valid_alleles, results,
130-
classification, gene_tokens
131-
)
128+
if normalize_endpoint:
129+
self.add_mane_to_validation_results(
130+
mane_data_found, valid_alleles, results,
131+
classification, gene_tokens
132+
)
132133

133134
def get_gene_tokens(self, classification) -> List[GeneMatchToken]:
134135
"""Return gene tokens for a classification.

‎variation/validators/amino_acid_delins.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -110,7 +110,7 @@ def get_valid_invalid_results(
110110
t, s.end_aa_del, s.end_pos_del, errors
111111
)
112112

113-
if not errors:
113+
if not errors and normalize_endpoint:
114114
mane = self.mane_transcript.get_mane_transcript(
115115
t, s.start_pos_del, s.end_pos_del,
116116
s.reference_sequence,
@@ -128,10 +128,11 @@ def get_valid_invalid_results(
128128
if is_identifier:
129129
break
130130

131-
self.add_mane_to_validation_results(
132-
mane_data_found, valid_alleles, results,
133-
classification, gene_tokens
134-
)
131+
if normalize_endpoint:
132+
self.add_mane_to_validation_results(
133+
mane_data_found, valid_alleles, results,
134+
classification, gene_tokens
135+
)
135136

136137
def get_gene_tokens(self, classification) -> List[GeneMatchToken]:
137138
"""Return gene tokens for a classification.

‎variation/validators/amino_acid_insertion.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -112,7 +112,7 @@ def get_valid_invalid_results(
112112
t, s.end_aa_flank, s.end_pos_flank, errors
113113
)
114114

115-
if not errors:
115+
if not errors and normalize_endpoint:
116116
mane = self.mane_transcript.get_mane_transcript(
117117
t, s.start_pos_flank, s.end_pos_flank,
118118
s.reference_sequence,
@@ -129,10 +129,11 @@ def get_valid_invalid_results(
129129
if is_identifier:
130130
break
131131

132-
self.add_mane_to_validation_results(
133-
mane_data_found, valid_alleles, results,
134-
classification, gene_tokens
135-
)
132+
if normalize_endpoint:
133+
self.add_mane_to_validation_results(
134+
mane_data_found, valid_alleles, results,
135+
classification, gene_tokens
136+
)
136137

137138
def get_gene_tokens(self, classification) -> List[GeneMatchToken]:
138139
"""Return gene tokens for a classification.

‎variation/validators/coding_dna_deletion.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -79,7 +79,7 @@ def get_valid_invalid_results(
7979
self.check_reference_sequence(t, s, errors,
8080
cds_start=cds_start)
8181

82-
if not errors:
82+
if not errors and normalize_endpoint:
8383
mane = self.mane_transcript.get_mane_transcript(
8484
t, s.start_pos_del, s.end_pos_del,
8585
s.reference_sequence,
@@ -100,10 +100,11 @@ def get_valid_invalid_results(
100100
if is_identifier:
101101
break
102102

103-
self.add_mane_to_validation_results(
104-
mane_data_found, valid_alleles, results,
105-
classification, gene_tokens
106-
)
103+
if normalize_endpoint:
104+
self.add_mane_to_validation_results(
105+
mane_data_found, valid_alleles, results,
106+
classification, gene_tokens
107+
)
107108

108109
def get_gene_tokens(self, classification) -> List[GeneMatchToken]:
109110
"""Return gene tokens for a classification.

‎variation/validators/coding_dna_delins.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -74,7 +74,7 @@ def get_valid_invalid_results(
7474
if not errors:
7575
self.check_pos_index(t, s, errors)
7676

77-
if not errors:
77+
if not errors and normalize_endpoint:
7878
mane = self.mane_transcript.get_mane_transcript(
7979
t, s.start_pos_del, s.end_pos_del,
8080
s.reference_sequence,
@@ -94,10 +94,11 @@ def get_valid_invalid_results(
9494
if is_identifier:
9595
break
9696

97-
self.add_mane_to_validation_results(
98-
mane_data_found, valid_alleles, results,
99-
classification, gene_tokens
100-
)
97+
if normalize_endpoint:
98+
self.add_mane_to_validation_results(
99+
mane_data_found, valid_alleles, results,
100+
classification, gene_tokens
101+
)
101102

102103
def get_gene_tokens(self, classification) -> List[GeneMatchToken]:
103104
"""Return gene tokens for a classification.

‎variation/validators/coding_dna_substitution.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -82,7 +82,7 @@ def get_valid_invalid_results(
8282
self.check_ref_nucleotide(ref_nuc, s.ref_nucleotide,
8383
s.position, t, errors)
8484

85-
if not errors:
85+
if not errors and normalize_endpoint:
8686
mane = self.mane_transcript.get_mane_transcript(
8787
t, s.position, s.position, s.reference_sequence,
8888
ref=s.ref_nucleotide,
@@ -102,10 +102,11 @@ def get_valid_invalid_results(
102102
if is_identifier:
103103
break
104104

105-
self.add_mane_to_validation_results(
106-
mane_data_found, valid_alleles, results,
107-
classification, gene_tokens
108-
)
105+
if normalize_endpoint:
106+
self.add_mane_to_validation_results(
107+
mane_data_found, valid_alleles, results,
108+
classification, gene_tokens
109+
)
109110

110111
def get_gene_tokens(self, classification) -> List[GeneMatchToken]:
111112
"""Return gene tokens for a classification.

‎variation/validators/genomic_deletion.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -86,7 +86,7 @@ def get_valid_invalid_results(
8686
else:
8787
variation = None
8888

89-
if not errors:
89+
if not errors and normalize_endpoint:
9090
self._get_normalize_variation(
9191
gene_tokens, s, t, errors, hgvs_dup_del_mode,
9292
mane_data_found, start, end)
@@ -99,10 +99,11 @@ def get_valid_invalid_results(
9999
if is_identifier:
100100
break
101101

102-
self.add_mane_to_validation_results(
103-
mane_data_found, valid_alleles, results,
104-
classification, gene_tokens
105-
)
102+
if normalize_endpoint:
103+
self.add_mane_to_validation_results(
104+
mane_data_found, valid_alleles, results,
105+
classification, gene_tokens
106+
)
106107

107108
def _get_normalize_variation(
108109
self, gene_tokens: List, s: Token, t: str, errors: List,

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