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jsstevensonjsstevenson
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ok tests passing again
1 parent 32aba22 commit ad7fb3a

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-488
lines changed

‎src/anyvlm/anyvar/python_client.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@ def put_allele_expressions(
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)
4444
except TranslationError:
4545
_logger.exception("Failed to translate expression: %s", expression)
46-
self.av.put_objects([translated_variation]) # type: ignore
46+
self.av.put_objects([translated_variation]) # type: ignore
4747
results.append(translated_variation.id) # type: ignore
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return results
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‎tests/unit/anyvar/cassettes/test_http_client/test_put_allele_expressions.yaml‎

Lines changed: 86 additions & 49 deletions
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‎tests/unit/anyvar/cassettes/test_http_client/test_put_allele_expressions_invalid_assembly.yaml‎

Lines changed: 44 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,49 @@ interactions:
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- request:
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body: '{"definition": "Y", "assembly_name": "GRCh30000", "input_type": "Allele"}'
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headers: {}
5-
method: POST
5+
method: PUT
6+
uri: http://localhost:8000/variation
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response:
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body:
9+
string: '{"detail":[{"type":"enum","loc":["body","assembly_name"],"msg":"Input
10+
should be ''GRCh37'' or ''GRCh38''","input":"GRCh30000","ctx":{"expected":"''GRCh37''
11+
or ''GRCh38''"}}]}'
12+
headers: {}
13+
status:
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code: 422
15+
message: Unprocessable Entity
16+
- request:
17+
body: '{"definition": "Y", "assembly_name": "GRCh30000", "input_type": "Allele"}'
18+
headers: {}
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method: PUT
20+
uri: http://localhost:8000/variation
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response:
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body:
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string: '{"detail":[{"type":"enum","loc":["body","assembly_name"],"msg":"Input
24+
should be ''GRCh37'' or ''GRCh38''","input":"GRCh30000","ctx":{"expected":"''GRCh37''
25+
or ''GRCh38''"}}]}'
26+
headers: {}
27+
status:
28+
code: 422
29+
message: Unprocessable Entity
30+
- request:
31+
body: '{"definition": "Y", "assembly_name": "GRCh30000", "input_type": "Allele"}'
32+
headers: {}
33+
method: PUT
34+
uri: http://localhost:8000/variation
35+
response:
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body:
37+
string: '{"detail":[{"type":"enum","loc":["body","assembly_name"],"msg":"Input
38+
should be ''GRCh37'' or ''GRCh38''","input":"GRCh30000","ctx":{"expected":"''GRCh37''
39+
or ''GRCh38''"}}]}'
40+
headers: {}
41+
status:
42+
code: 422
43+
message: Unprocessable Entity
44+
- request:
45+
body: '{"definition": "Y", "assembly_name": "GRCh30000", "input_type": "Allele"}'
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headers: {}
47+
method: PUT
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uri: http://localhost:8000/variation
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response:
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body:
@@ -16,7 +58,7 @@ interactions:
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- request:
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body: '{"definition": "Y", "assembly_name": "GRCh30000", "input_type": "Allele"}'
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headers: {}
19-
method: POST
61+
method: PUT
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uri: http://localhost:8000/variation
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response:
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body:

‎tests/unit/anyvar/cassettes/test_http_client/test_put_objects.yaml‎

Lines changed: 0 additions & 343 deletions
This file was deleted.

‎tests/unit/anyvar/cassettes/test_http_client/test_search_by_interval.yaml‎

Lines changed: 136 additions & 4 deletions
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‎tests/unit/anyvar/cassettes/test_http_client/test_search_by_interval_not_found.yaml‎

Lines changed: 60 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,64 @@
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interactions:
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- request:
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body: null
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headers: {}
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method: GET
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uri: http://localhost:8000/search?accession=ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=1&end=100
7+
response:
8+
body:
9+
string: '{"variations":[]}'
10+
headers: {}
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status:
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code: 200
13+
message: OK
14+
- request:
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body: null
16+
headers: {}
17+
method: GET
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uri: http://localhost:8000/search?accession=ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=1&end=100
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response:
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body:
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string: '{"variations":[]}'
22+
headers: {}
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status:
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code: 200
25+
message: OK
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- request:
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body: null
28+
headers: {}
29+
method: GET
30+
uri: http://localhost:8000/search?accession=ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=1&end=100
31+
response:
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body:
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string: '{"variations":[]}'
34+
headers: {}
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status:
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code: 200
37+
message: OK
38+
- request:
39+
body: null
40+
headers: {}
41+
method: GET
42+
uri: http://localhost:8000/search?accession=ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=1&end=100
43+
response:
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body:
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string: '{"variations":[]}'
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headers: {}
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status:
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code: 200
49+
message: OK
50+
- request:
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body: null
52+
headers: {}
53+
method: GET
54+
uri: http://localhost:8000/search?accession=ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=1&end=100
55+
response:
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body:
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string: '{"variations":[]}'
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headers: {}
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status:
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code: 200
61+
message: OK
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- request:
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body: null
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headers: {}

‎tests/unit/anyvar/cassettes/test_http_client/test_search_by_interval_unknown_accession.yaml‎

Lines changed: 60 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,64 @@
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interactions:
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- request:
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body: null
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headers: {}
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method: GET
6+
uri: http://localhost:8000/search?accession=ga4gh:SQ.ZZZZZu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=2781760&end=2781768
7+
response:
8+
body:
9+
string: '{"variations":[]}'
10+
headers: {}
11+
status:
12+
code: 200
13+
message: OK
14+
- request:
15+
body: null
16+
headers: {}
17+
method: GET
18+
uri: http://localhost:8000/search?accession=ga4gh:SQ.ZZZZZu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=2781760&end=2781768
19+
response:
20+
body:
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string: '{"variations":[]}'
22+
headers: {}
23+
status:
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code: 200
25+
message: OK
26+
- request:
27+
body: null
28+
headers: {}
29+
method: GET
30+
uri: http://localhost:8000/search?accession=ga4gh:SQ.ZZZZZu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=2781760&end=2781768
31+
response:
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body:
33+
string: '{"variations":[]}'
34+
headers: {}
35+
status:
36+
code: 200
37+
message: OK
38+
- request:
39+
body: null
40+
headers: {}
41+
method: GET
42+
uri: http://localhost:8000/search?accession=ga4gh:SQ.ZZZZZu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=2781760&end=2781768
43+
response:
44+
body:
45+
string: '{"variations":[]}'
46+
headers: {}
47+
status:
48+
code: 200
49+
message: OK
50+
- request:
51+
body: null
52+
headers: {}
53+
method: GET
54+
uri: http://localhost:8000/search?accession=ga4gh:SQ.ZZZZZu1aycC0tPQPFmUaGXJLDs5SbPZ5&start=2781760&end=2781768
55+
response:
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body:
57+
string: '{"variations":[]}'
58+
headers: {}
59+
status:
60+
code: 200
61+
message: OK
262
- request:
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body: null
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headers: {}

‎tests/unit/anyvar/cassettes/test_http_client/test_search_by_interval_unknown_alias.yaml‎

Lines changed: 60 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,64 @@
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interactions:
2+
- request:
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body: null
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headers: {}
5+
method: GET
6+
uri: http://localhost:8000/search?accession=GRCh45.p1:Y&start=2781760&end=2781760
7+
response:
8+
body:
9+
string: '{"detail":"Unable to dereference provided accession ID"}'
10+
headers: {}
11+
status:
12+
code: 404
13+
message: Not Found
14+
- request:
15+
body: null
16+
headers: {}
17+
method: GET
18+
uri: http://localhost:8000/search?accession=GRCh45.p1:Y&start=2781760&end=2781760
19+
response:
20+
body:
21+
string: '{"detail":"Unable to dereference provided accession ID"}'
22+
headers: {}
23+
status:
24+
code: 404
25+
message: Not Found
26+
- request:
27+
body: null
28+
headers: {}
29+
method: GET
30+
uri: http://localhost:8000/search?accession=GRCh45.p1:Y&start=2781760&end=2781760
31+
response:
32+
body:
33+
string: '{"detail":"Unable to dereference provided accession ID"}'
34+
headers: {}
35+
status:
36+
code: 404
37+
message: Not Found
38+
- request:
39+
body: null
40+
headers: {}
41+
method: GET
42+
uri: http://localhost:8000/search?accession=GRCh45.p1:Y&start=2781760&end=2781760
43+
response:
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body:
45+
string: '{"detail":"Unable to dereference provided accession ID"}'
46+
headers: {}
47+
status:
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code: 404
49+
message: Not Found
50+
- request:
51+
body: null
52+
headers: {}
53+
method: GET
54+
uri: http://localhost:8000/search?accession=GRCh45.p1:Y&start=2781760&end=2781760
55+
response:
56+
body:
57+
string: '{"detail":"Unable to dereference provided accession ID"}'
58+
headers: {}
59+
status:
60+
code: 404
61+
message: Not Found
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- request:
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body: null
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headers: {}

‎tests/unit/anyvar/cassettes/test_http_client/test_search_by_interval_with_alias.yaml‎

Lines changed: 63 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -6,7 +6,31 @@ interactions:
66
uri: http://localhost:8000/search?accession=GRCh38.p1:Y&start=2781760&end=2781760
77
response:
88
body:
9-
string: '{"variations":[{"id":"ga4gh:VA.IM4QyU9D2kTJzeftUBBD4Vcd1peq0dn1","type":"Allele","digest":"IM4QyU9D2kTJzeftUBBD4Vcd1peq0dn1","location":{"id":"ga4gh:SL.sWfeTXwGUkfIuYRAkiFGPjkSk_mIDuXG","type":"SequenceLocation","digest":"sWfeTXwGUkfIuYRAkiFGPjkSk_mIDuXG","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781762},"state":{"type":"LiteralSequenceExpression","sequence":"CA"}},{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}},{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}}]}'
9+
string: '{"variations":[{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}},{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}}]}'
10+
headers: {}
11+
status:
12+
code: 200
13+
message: OK
14+
- request:
15+
body: null
16+
headers: {}
17+
method: GET
18+
uri: http://localhost:8000/search?accession=GRCh38.p1:Y&start=2781760&end=2781760
19+
response:
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body:
21+
string: '{"variations":[{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}},{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}}]}'
22+
headers: {}
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status:
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code: 200
25+
message: OK
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- request:
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body: null
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headers: {}
29+
method: GET
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uri: http://localhost:8000/search?accession=GRCh38.p1:Y&start=2781760&end=2781760
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response:
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body:
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string: '{"variations":[{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}},{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}}]}'
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headers: {}
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status:
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code: 200
@@ -18,7 +42,7 @@ interactions:
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uri: http://localhost:8000/search?accession=GRCh38.p1:Y&start=2781760&end=2781760
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response:
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body:
21-
string: '{"variations":[{"id":"ga4gh:VA.IM4QyU9D2kTJzeftUBBD4Vcd1peq0dn1","type":"Allele","digest":"IM4QyU9D2kTJzeftUBBD4Vcd1peq0dn1","location":{"id":"ga4gh:SL.sWfeTXwGUkfIuYRAkiFGPjkSk_mIDuXG","type":"SequenceLocation","digest":"sWfeTXwGUkfIuYRAkiFGPjkSk_mIDuXG","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781762},"state":{"type":"LiteralSequenceExpression","sequence":"CA"}},{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}},{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}}]}'
45+
string: '{"variations":[{"id":"ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","type":"Allele","digest":"9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"A"}},{"id":"ga4gh:VA.xbX035HgURWIUAjn6x3cS26jafP8Q_bk","type":"Allele","digest":"xbX035HgURWIUAjn6x3cS26jafP8Q_bk","location":{"id":"ga4gh:SL.sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","type":"SequenceLocation","digest":"sYiBcbbgF-1CANNCTfQ6zwZOU0iHhymR","sequenceReference":{"type":"SequenceReference","refgetAccession":"SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5"},"start":2781760,"end":2781761},"state":{"type":"LiteralSequenceExpression","sequence":"C"}}]}'
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headers: {}
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status:
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code: 200
@@ -30,7 +54,43 @@ interactions:
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uri: http://localhost:8000/search?accession=GRCh38.p1:Y&start=2781760&end=2781760
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response:
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body:
33-
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57+
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