diff --git a/tests/cassettes/test_data_proxies[rest_dataproxy].yaml b/tests/cassettes/test_data_proxies[rest_dataproxy].yaml index 826db4f6..93fd4a08 100644 --- a/tests/cassettes/test_data_proxies[rest_dataproxy].yaml +++ b/tests/cassettes/test_data_proxies[rest_dataproxy].yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/NM_000551.3 response: @@ -19,31 +11,13 @@ interactions: \ \"SHA1:4f5d8bd29d97e44f036e72f4f92c08e167354ba8\",\n \"VMC:GS_v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_\",\n \ \"sha512t24u:v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_\",\n \"ga4gh:SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_\"\n \ ],\n \"alphabet\": \"ACGT\",\n \"length\": 4560\n}\n" - headers: - Connection: - - close - Content-Length: - - '433' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/NC_000013.11 response: @@ -61,77 +35,31 @@ interactions: \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_ response: body: string: CCTCGCCTCCGTTACAACGGCCTACGGTGCTGGAGGATCCTTCTGCGCACGCGCACAGCCTCCGGCCGGCTATTTCCGCGAGCGCGTTCCATCCTCTACCGAGCGCGCGCGAAGACTACGGAGGTCGACTCGGGAGCGCGCACGCAGCTCCGCCCCGCGTCCGACCCGCGGATCCCGCGGCGTCCGGCCCGGGTGGTCTGGATCGCGGAGGGAATGCCCCGGAGGGCGGAGAACTGGGACGAGGCCGAGGTAGGCGCGGAGGAGGCAGGCGTCGAAGAGTACGGCCCTGAAGAAGACGGCGGGGAGGAGTCGGGCGCCGAGGAGTCCGGCCCGGAAGAGTCCGGCCCGGAGGAACTGGGCGCCGAGGAGGAGATGGAGGCCGGGCGGCCGCGGCCCGTGCTGCGCTCGGTGAACTCGCGCGAGCCCTCCCAGGTCATCTTCTGCAATCGCAGTCCGCGCGTCGTGCTGCCCGTATGGCTCAACTTCGACGGCGAGCCGCAGCCCTACCCAACGCTGCCGCCTGGCACGGGCCGCCGCATCCACAGCTACCGAGGTCACCTTTGGCTCTTCAGAGATGCAGGGACACACGATGGGCTTCTGGTTAACCAAACTGAATTATTTGTGCCATCTCTCAATGTTGACGGACAGCCTATTTTTGCCAATATCACACTGCCAGTGTATACTCTGAAAGAGCGATGCCTCCAGGTTGTCCGGAGCCTAGTCAAGCCTGAGAATTACAGGAGACTGGACATCGTCAGGTCGCTCTACGAAGATCTGGAAGACCACCCAAATGTGCAGAAAGACCTGGAGCGGCTGACACAGGAGCGCATTGCACATCAACGGATGGGAGATTGAAGATTTCTGTTGAAACTTACACTGTTTCATCTCAGCTTTTGATGGTACTGATGAGTCTTGATCTAGATACAGGACTGGTTCCTTCCTTAGTTTCAAAGTGTCTCATTCTCAGAGTAAAATAGGCACCATTGCTTAAAAGAAAGTTAACTGACTTCACTAGGCATTGTGATGTTTAGGGGCAAACATCACAAAATGTAATTTAATGCCTGCCCATTAGAGAAGTATTTATCAGGAGAAGGTGGTGGCATTTTTGCTTCCTAGTAAGTCAGGACAGCTTGTATGTAAGGAGGTTTGTATAAGTAATTCAGTGGGAATTGCAGCATATCGTTTAATTTTAAGAAGGCATTGGCATCTGCTTTTAATGGATGTATAATACATCCATTCTACATCCGTAGCGGTTGGTGACTTGTCTGCCTCCTGCTTTGGGAAGACTGAGGCATCCGTGAGGCAGGGACAAGTCTTTCTCCTCTTTGAGACCCCAGTGCCTGCACATCATGAGCCTTCAGTCAGGGTTTGTCAGAGGAACAAACCAGGGGACACTTTGTTAGAAAGTGCTTAGAGGTTCTGCCTCTATTTTTGTTGGGGGGTGGGAGAGGGGACCTTAAAATGTGTACAGTGAACAAATGTCTTAAAGGGAATCATTTTTGTAGGAAGCATTTTTTATAATTTTCTAAGTCGTGCACTTTCTCGGTCCACTCTTGTTGAAGTGCTGTTTTATTACTGTTTCTAAACTAGGATTGACATTCTACAGTTGTGATAATAGCATTTTTGTAACTTGCCATCCGCACAGAAAATACGAGAAAATCTGCATGTTTGATTATAGTATTAATGGACAAATAAGTTTTTGCTAAATGTGAGTATTTCTGTTCCTTTTTGTAAATATGTGACATTCCTGATTGATTTGGGTTTTTTTGTTGTTGTTGTTTTGTTTTGTTTTGTTTTTTTGAGATGGAGTCTCACTCTTGTCACCCAGGCTGGAGTGCAGTGGCGCCATCTCGGCTCACTGCAACCTCTGCCTCCTGGGTTCACGTAATCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCACGCTGGCCAATTTTTGTACTTTTAGTAGAGACAGTGTTTCGCCATGTTGGCCAGGCTGGTTTCAAACTCCTGACCTCAGGTGATCCGCCCACCTCAGCCTCCCAAAATGGTGGGATTACAGGTGTGTGGGCCACCGTGCCTGGCTGATTCAGCATTTTTTATCAGGCAGGACCAGGTGGCACTTCCACCTCCAGCCTCTGGTCCTACCAATGGATTCATGGAGTAGCCTGGACTGTTTCATAGTTTTCTAAATGTACAAATTCTTATAGGCTAGACTTAGATTCATTAACTCAAATTCAATGCTTCTATCAGACTCAGTTTTTTGTAACTAATAGATTTTTTTTTCCACTTTTGTTCTACTCCTTCCCTAATAGCTTTTTAAAAAAATCTCCCCAGTAGAGAAACATTTGGAAAAGACAGAAAACTAAAAAGGAAGAAAAAAGATCCCTATTAGATACACTTCTTAAATACAATCACATTAACATTTTGAGCTATTTCCTTCCAGCCTTTTTAGGGCAGATTTTGGTTGGTTTTTACATAGTTGAGATTGTACTGTTCATACAGTTTTATACCCTTTTTCATTTAACTTTATAACTTAAATATTGCTCTATGTTAGTATAAGCTTTTCACAAACATTAGTATAGTCTCCCTTTTATAATTAATGTTTGTGGGTATTTCTTGGCATGCATCTTTAATTCCTTATCCTAGCCTTTGGGCACAATTCCTGTGCTCAAAAATGAGAGTGACGGCTGGCATGGTGGCTCCCGCCTGTAATCCCAGTACTTTGGAAAGCCAAGGTAAGAGGATTGCTTGAGCCCAGAACTTCAAGATGAGCCTGGGCTCATAGTGAGAACCCATCTATACAAAAAATTTTTAAAAATTAGCATGGCGGCACACATCTGTAATCCTAGCTACTTGGCAGGCTGAGGTGAGAAGATCATTGGAGTTTAGGAATTGGAGGCTGCAGTGAGCCATGAGTATGCCACTGCACTCCAGCCTGGGGGACAGAGCAAGACCCTGCCTCAAAAAAAAAAAAAAAAAAAAAATCAGGCCGGGCATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGTCGAGGTGGGCAGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTAAAACCCCATTTCTACTAAAAAATACAAGAATTAGCTGGGTGTGGTGGCGCATGCCTGTAATCCTAGCTACTCAGGAGGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGCGAAGATTGCAGTGAGCTGATATCGCACCATTGTACTCCAGCCTGTGTGACAGAGCAATACTCTTGTCTCAAAAAAAAAAAAAAATTCAAATCAGAGTGAAGTGAATGAGACACTCCAGTTTTCCTTCTACTCCGAATTTCAACTGATTTTAGCTCCTCCTTTCAACATTCAACAAATAGTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCACTCTGTTGCCCAGGCTGGAGTGCAGTGGTGCGATCTCTGCTCACTACAAGCTCTGCCTCCCGAGTTCAAGTGATTCTCCTGGCTCACCCTCCTGAGTAGCTGGGATTACAGGCGCCTGCCACCATGCCTGGCTAATTTTGTGTTTTTAGTGGAGACGGGGTTTCACCATGTTGTCCAGGATGGTCTTGATCTCCTGACCTTGTGATCCACCCACCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCGCGTCCAGCCAGCTTTATTATTTTTTTTAAGCTGTCTTTGTGTCAAAATGATAGTTCATGCTCCTCTTGTTAAAACCTGCAGGCCGAGCACAGTGGCTCATGCCTGTAATCCCAGCATTTTGGGAGACCAAGGCGGATGGATCACCTGAGGTCAGGAGCTGAAGACCAGCCTGGCTAACATGGTGAAACCTCATCTCCACTTAAAATACAAAAATTGCCGGCCGCGGCGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCTAGGCGGGTGGATCACGAGGTCAGGAAATCGAGACCATCCTGGCTAACACGGGTGAAACCCCGTCTCTATTAAAAAATAGAAAAAATTAGGCGGGCGTGGTGGTGAGCGCCTGTAGTCCCAGCTACTCGAGAGCCTGAGGCAGGAGAATGGCATGAACCTGGAAGGCGGAGCTTGCAGTGAGCTGAGATGGTGCCACTGCACTCTAACCTGGGCGACAGAGTGAGACACCGTCTCAAAAAAAAAAACAAAAAACAAAAATTATCCAGGTGTGGCGGTGGGCGCCTGTGAGGCAGGCGAATCTCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCAAGATCACACCATTGCACTCCAGCCTGGGCAACAAGAGTGAAATTCCATCTCAAAAAGAAACCAAAAAAACAAAAAAAAAACATGCCGTTTGAGTACTGTGTTTTTGGTGTTGTCCAAGGAAAATTAAAAACCTGTAGCATGAATAATGTTTGTTTTTCATTTCGAATCTTGTGAATGTATTAAATATATCGCTCTTAAGAGACGGTGAAGTTCCTATTTCAAGTTTTTTTTTTTTTTTTTTTTTTTAAAGCTGTTTTTTAATACATTAAATGGTGCTGAGTAAAGGAAATAG - headers: - Connection: - - close - Content-Length: - - '4560' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.v_QTc1p-MUYdgrRv4LMT6ByXIOsdw3C_?start=0&end=50 response: body: string: CCTCGCCTCCGTTACAACGGCCTACGGTGCTGGAGGATCCTTCTGCGCAC - headers: - Connection: - - close - Content-Length: - - '50' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/cassettes/test_normalize_allele.yaml b/tests/cassettes/test_normalize_allele.yaml index 17f3b63f..a27c8c08 100644 --- a/tests/cassettes/test_normalize_allele.yaml +++ b/tests/cassettes/test_normalize_allele.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV response: @@ -26,61 +18,25 @@ interactions: \ \"SHA1:599b9a4e5475a88471ac9e5da46d99d3275ea97e\",\n \"VMC:GS_0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV\",\n \ \"sha512t24u:0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV\",\n \"ga4gh:SQ.0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV\"\n \ ],\n \"alphabet\": \"ACGNTY\",\n \"length\": 170805979\n}\n" - headers: - Connection: - - close - Content-Length: - - '975' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.0iKlIQk2oZLoeOG9P1riRU6hvL5Ux8TV?start=26090950&end=26090951 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP response: @@ -97,557 +53,223 @@ interactions: \ \"SHA1:67d41b42bacf8e98d748c25eb0362a0b7038de50\",\n \"VMC:GS_w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP\",\n \ \"sha512t24u:w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP\",\n \"ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP\"\n \ ],\n \"alphabet\": \"ACGNRSTWY\",\n \"length\": 156040895\n}\n" - headers: - Connection: - - close - Content-Length: - - '978' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980375&end=155980377 response: body: string: TA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980374&end=155980375 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980377&end=155980378 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980375&end=155980375 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980377&end=155980377 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980373&end=155980375 response: body: string: GT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980373&end=155980374 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980372&end=155980373 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP?start=155980375&end=155980376 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289464 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289465 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289465&end=289466 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289466&end=289467 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289467&end=289468 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289468&end=289469 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289469&end=289470 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289469 response: body: string: CAGCA - headers: - Connection: - - close - Content-Length: - - '5' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/cassettes/test_vcrtest.yaml b/tests/cassettes/test_vcrtest.yaml index d1f66dae..6bb5fd47 100644 --- a/tests/cassettes/test_vcrtest.yaml +++ b/tests/cassettes/test_vcrtest.yaml @@ -1,31 +1,13 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=50000000&end=50000050 response: body: string: TTAGGTGTTTAGATGATTTCTAAGATGCTTTTAAGCCCAGTATTTCTATT - headers: - Connection: - - close - Content-Length: - - '50' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:25 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/conftest.py b/tests/conftest.py index 36bf5de4..97b5b02c 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -6,6 +6,28 @@ from ga4gh.vrs.dataproxy import SeqRepoDataProxy, SeqRepoRESTDataProxy +def remove_request_headers(request): + """Remove all headers from VCR request before recording.""" + request.headers = {} + return request + + +def remove_response_headers(response): + """Remove all headers from VCR response before recording.""" + response["headers"] = {} + return response + + +@pytest.fixture(scope="module") +def vcr_config(): + """Configure VCR to filter out headers from cassettes.""" + return { + "before_record_request": remove_request_headers, + "before_record_response": remove_response_headers, + "decode_compressed_response": True, + } + + @pytest.fixture(scope="session") def dataproxy(): sr = SeqRepo( diff --git a/tests/extras/cassettes/test_annotate_vcf_grch37_attrs.yaml b/tests/extras/cassettes/test_annotate_vcf_grch37_attrs.yaml index 3efb5886..be51c7b6 100644 --- a/tests/extras/cassettes/test_annotate_vcf_grch37_attrs.yaml +++ b/tests/extras/cassettes/test_annotate_vcf_grch37_attrs.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh37:chr19 response: @@ -25,61 +17,25 @@ interactions: \ \"sha512t24u:ItRDD47aMoioDCNW_occY5fWKZBKlxCX\",\n \"ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX\",\n \ \"hs37-1kg:19\",\n \"hs37d5:19\"\n ],\n \"alphabet\": \"ACGNT\",\n \ \"length\": 59128983\n}\n" - headers: - Connection: - - close - Content-Length: - - '820' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh37:chr19?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX response: @@ -95,1277 +51,511 @@ interactions: \ \"sha512t24u:ItRDD47aMoioDCNW_occY5fWKZBKlxCX\",\n \"ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX\",\n \ \"hs37-1kg:19\",\n \"hs37d5:19\"\n ],\n \"alphabet\": \"ACGNT\",\n \ \"length\": 59128983\n}\n" - headers: - Connection: - - close - Content-Length: - - '820' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh37:chr19?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284350&end=284351 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284349&end=284350 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284351&end=284352 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284352&end=284353 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284353&end=284354 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284354&end=284355 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284355&end=284356 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284356&end=284357 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284357&end=284358 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284358&end=284359 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284359&end=284360 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284360&end=284361 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284361&end=284362 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284362&end=284363 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284363&end=284364 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284364&end=284365 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284365&end=284366 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284366&end=284367 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284350&end=284350 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284351&end=284366 response: body: string: AAAAAAAAAAAAAAA - headers: - Connection: - - close - Content-Length: - - '15' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=284350&end=284366 response: body: string: AAAAAAAAAAAAAAAA - headers: - Connection: - - close - Content-Length: - - '16' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh37:chr19?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=289464&end=289464 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=289464&end=289465 response: body: string: C - 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headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=490414&end=490416 response: body: string: CT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=490413&end=490414 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=490416&end=490417 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=490414&end=490414 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.ItRDD47aMoioDCNW_occY5fWKZBKlxCX?start=490416&end=490416 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh37:chr19?start=54220023&end=54220024 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh37:chr19?start=54220998&end=54220999 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh37:chr19?start=54221653&end=54221654 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_annotate_vcf_grch38_attrs.yaml b/tests/extras/cassettes/test_annotate_vcf_grch38_attrs.yaml index 50330351..48f1f0db 100644 --- a/tests/extras/cassettes/test_annotate_vcf_grch38_attrs.yaml +++ b/tests/extras/cassettes/test_annotate_vcf_grch38_attrs.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:chr19 response: @@ -27,61 +19,25 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -99,1367 +55,547 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=284349&end=284351 response: body: string: CA - 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headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490413&end=490414 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490417 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490414 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490416 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220998&end=54220999 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_annotate_vcf_grch38_attrs_altsonly.yaml b/tests/extras/cassettes/test_annotate_vcf_grch38_attrs_altsonly.yaml index 5fad9160..48f1f0db 100644 --- a/tests/extras/cassettes/test_annotate_vcf_grch38_attrs_altsonly.yaml +++ b/tests/extras/cassettes/test_annotate_vcf_grch38_attrs_altsonly.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:chr19 response: @@ -27,61 +19,25 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -99,1367 +55,547 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284350&end=284351 response: body: string: A - headers: - Connection: - - close - 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headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490414 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490416 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220998&end=54220999 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:20 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_annotate_vcf_grch38_noattrs.yaml b/tests/extras/cassettes/test_annotate_vcf_grch38_noattrs.yaml index 250b2edd..48f1f0db 100644 --- a/tests/extras/cassettes/test_annotate_vcf_grch38_noattrs.yaml +++ b/tests/extras/cassettes/test_annotate_vcf_grch38_noattrs.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:chr19 response: @@ -27,61 +19,25 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -99,1367 +55,547 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284350&end=284351 response: body: string: A - headers: - Connection: - - close - 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headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284352&end=284353 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284353&end=284354 response: body: string: A - 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headers: - Connection: - - close - Content-Length: - - '16' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289464 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289465 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289465&end=289466 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289466&end=289467 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289466 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=28946399&end=28946400 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=28946399&end=28946400 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=490413&end=490416 response: body: string: ACT - headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490413&end=490416 response: body: string: ACT - headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490416 response: body: string: CT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490413&end=490414 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490417 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490414 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490416 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220998&end=54220999 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_annotate_vcf_pickle_only.yaml b/tests/extras/cassettes/test_annotate_vcf_pickle_only.yaml index 4a2e1af2..48f1f0db 100644 --- a/tests/extras/cassettes/test_annotate_vcf_pickle_only.yaml +++ b/tests/extras/cassettes/test_annotate_vcf_pickle_only.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:chr19 response: @@ -27,61 +19,25 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -99,1367 +55,547 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - 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headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490413&end=490414 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490417 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490414 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490416 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220998&end=54220999 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_annotate_vcf_vcf_only.yaml b/tests/extras/cassettes/test_annotate_vcf_vcf_only.yaml index 159c8529..48f1f0db 100644 --- a/tests/extras/cassettes/test_annotate_vcf_vcf_only.yaml +++ b/tests/extras/cassettes/test_annotate_vcf_vcf_only.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:chr19 response: @@ -27,61 +19,25 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -99,1367 +55,547 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=82663&end=82664 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284349&end=284351 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284350&end=284351 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284349&end=284350 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284351&end=284352 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284352&end=284353 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284353&end=284354 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284354&end=284355 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284355&end=284356 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284356&end=284357 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284357&end=284358 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284358&end=284359 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284359&end=284360 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284360&end=284361 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284361&end=284362 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284362&end=284363 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284363&end=284364 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284364&end=284365 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284365&end=284366 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284366&end=284367 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284350&end=284350 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284351&end=284366 response: body: string: AAAAAAAAAAAAAAA - headers: - Connection: - - close - Content-Length: - - '15' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=284350&end=284366 response: body: string: AAAAAAAAAAAAAAAA - headers: - Connection: - - close - Content-Length: - - '16' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289464 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289465 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289465&end=289466 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289466&end=289467 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289466 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=28946399&end=28946400 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=28946399&end=28946400 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=490413&end=490416 response: body: string: ACT - headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490413&end=490416 response: body: string: ACT - headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490416 response: body: string: CT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490413&end=490414 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:21 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490417 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490414&end=490414 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=490416&end=490416 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54220023&end=54220024 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54220998&end=54220999 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:chr19?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=54221653&end=54221654 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_from_beacon.yaml b/tests/extras/cassettes/test_from_beacon.yaml index 2457e2f0..e04892cc 100644 --- a/tests/extras/cassettes/test_from_beacon.yaml +++ b/tests/extras/cassettes/test_from_beacon.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:19 response: @@ -27,31 +19,13 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:MT response: @@ -74,17 +48,7 @@ interactions: \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n \ \"length\": 16569\n}\n" - headers: - Connection: - - close - Content-Length: - - '1355' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_from_gnomad.yaml b/tests/extras/cassettes/test_from_gnomad.yaml index a171d5fe..1509ab55 100644 --- a/tests/extras/cassettes/test_from_gnomad.yaml +++ b/tests/extras/cassettes/test_from_gnomad.yaml @@ -1,75 +1,31 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:19?start=44908821&end=44908822 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:MT?start=10082&end=10083 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:13 response: @@ -87,121 +43,49 @@ interactions: \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=20003095&end=20003097 response: body: string: AC - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=20003009&end=20003010 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=19993837&end=19993839 response: body: string: GT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl response: @@ -219,61 +103,25 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=44908821&end=44908822 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct response: @@ -296,61 +144,25 @@ interactions: \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n \ \"length\": 16569\n}\n" - headers: - Connection: - - close - Content-Length: - - '1355' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct?start=10082&end=10083 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT response: @@ -368,481 +180,193 @@ interactions: \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003095&end=20003097 response: body: string: AC - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003096&end=20003097 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003095&end=20003096 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003097&end=20003098 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003096&end=20003096 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003097&end=20003097 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003009&end=20003010 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003010&end=20003010 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=20003010&end=20003011 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993837&end=19993839 response: body: string: GT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993839&end=19993839 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993838&end=19993839 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993837&end=19993838 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993836&end=19993837 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=19993839&end=19993840 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:17 response: @@ -860,61 +384,25 @@ interactions: \ \"SHA1:b364a4ba98fca3ac1d8dfd1a3eb80e8a902bebb4\",\n \"VMC:GS_dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7\",\n \ \"sha512t24u:dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7\",\n \"ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7\"\n \ ],\n \"alphabet\": \"ACGKNRSTWY\",\n \"length\": 83257441\n}\n" - headers: - Connection: - - close - Content-Length: - - '1004' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:17?start=83129586&end=83129598 response: body: string: GTTGWCACATGA - headers: - Connection: - - close - Content-Length: - - '12' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7 response: @@ -932,331 +420,133 @@ interactions: \ \"SHA1:b364a4ba98fca3ac1d8dfd1a3eb80e8a902bebb4\",\n \"VMC:GS_dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7\",\n \ \"sha512t24u:dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7\",\n \"ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7\"\n \ ],\n \"alphabet\": \"ACGKNRSTWY\",\n \"length\": 83257441\n}\n" - headers: - Connection: - - close - Content-Length: - - '1004' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129586&end=83129598 response: body: string: GTTGWCACATGA - headers: - Connection: - - close - Content-Length: - - '12' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129587&end=83129598 response: body: string: TTGWCACATGA - headers: - Connection: - - close - Content-Length: - - '11' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129586&end=83129587 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129598&end=83129599 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129599&end=83129600 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129600&end=83129601 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129601&end=83129602 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129587&end=83129587 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129598&end=83129601 response: body: string: TTG - headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.dLZ15tNO1Ur0IcGjwc3Sdi_0A6Yf4zm7?start=83129587&end=83129601 response: body: string: TTGWCACATGATTG - headers: - Connection: - - close - Content-Length: - - '14' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:7 response: @@ -1273,61 +563,25 @@ interactions: \ \"SHA1:e3e26309c05584f0abf2f748854285c9c3eff1b6\",\n \"VMC:GS_F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \ \"sha512t24u:F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\"\n \ ],\n \"alphabet\": \"ACGNRSTY\",\n \"length\": 159345973\n}\n" - headers: - Connection: - - close - Content-Length: - - '977' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:7?start=1&end=17 response: body: string: NNNNNNNNNNNNNNNN - headers: - Connection: - - close - Content-Length: - - '16' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -1344,137 +598,55 @@ interactions: \ \"SHA1:e3e26309c05584f0abf2f748854285c9c3eff1b6\",\n \"VMC:GS_F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \ \"sha512t24u:F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\"\n \ ],\n \"alphabet\": \"ACGNRSTY\",\n \"length\": 159345973\n}\n" - headers: - Connection: - - close - Content-Length: - - '977' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=1&end=17 response: body: string: NNNNNNNNNNNNNNNN - headers: - Connection: - - close - Content-Length: - - '16' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=1&end=16 response: body: string: NNNNNNNNNNNNNNN - headers: - Connection: - - close - Content-Length: - - '15' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:48 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:13?start=32936731&end=32936732 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:49 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32936731&end=32936732 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:49 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_from_hgvs.yaml b/tests/extras/cassettes/test_from_hgvs.yaml index c61c9655..ed06582a 100644 --- a/tests/extras/cassettes/test_from_hgvs.yaml +++ b/tests/extras/cassettes/test_from_hgvs.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000019.10 response: @@ -27,31 +19,13 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:49 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_012920.1 response: @@ -74,31 +48,13 @@ interactions: \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n \ \"length\": 16569\n}\n" - headers: - Connection: - - close - Content-Length: - - '1355' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:49 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000013.11 response: @@ -116,47 +72,19 @@ interactions: \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:49 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=19993837&end=19993839 response: body: string: GT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:49 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_from_hgvs_cx[NC_000013.11:g.26440969_26443305del-complete genomic loss-expected0].yaml b/tests/extras/cassettes/test_from_hgvs_cx[NC_000013.11:g.26440969_26443305del-complete genomic loss-expected0].yaml deleted file mode 100644 index 5f0fb88f..00000000 --- a/tests/extras/cassettes/test_from_hgvs_cx[NC_000013.11:g.26440969_26443305del-complete genomic loss-expected0].yaml +++ /dev/null @@ -1,44 +0,0 @@ -interactions: -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000013.11 - response: - body: - string: "{\n \"added\": \"2016-08-27T23:50:14Z\",\n \"aliases\": [\n \"GRCh38:13\",\n - \ \"GRCh38:chr13\",\n \"GRCh38.p1:13\",\n \"GRCh38.p1:chr13\",\n \"GRCh38.p10:13\",\n - \ \"GRCh38.p10:chr13\",\n \"GRCh38.p11:13\",\n \"GRCh38.p11:chr13\",\n - \ \"GRCh38.p12:13\",\n \"GRCh38.p12:chr13\",\n \"GRCh38.p2:13\",\n - \ \"GRCh38.p2:chr13\",\n \"GRCh38.p3:13\",\n \"GRCh38.p3:chr13\",\n - \ \"GRCh38.p4:13\",\n \"GRCh38.p4:chr13\",\n \"GRCh38.p5:13\",\n \"GRCh38.p5:chr13\",\n - \ \"GRCh38.p6:13\",\n \"GRCh38.p6:chr13\",\n \"GRCh38.p7:13\",\n \"GRCh38.p7:chr13\",\n - \ \"GRCh38.p8:13\",\n \"GRCh38.p8:chr13\",\n \"GRCh38.p9:13\",\n \"GRCh38.p9:chr13\",\n - \ \"MD5:a5437debe2ef9c9ef8f3ea2874ae1d82\",\n \"NCBI:NC_000013.11\",\n - \ \"refseq:NC_000013.11\",\n \"SEGUID:2oDBty0yKV9wHo7gg+Bt+fPgi5o\",\n - \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n - \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n - \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Wed, 19 Mar 2025 20:51:18 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -version: 1 diff --git a/tests/extras/cassettes/test_from_hgvs_cx[NC_000013.11:g.32379315_32379819del-None-expected1].yaml b/tests/extras/cassettes/test_from_hgvs_cx[NC_000013.11:g.32379315_32379819del-None-expected1].yaml deleted file mode 100644 index 5ade7e22..00000000 --- a/tests/extras/cassettes/test_from_hgvs_cx[NC_000013.11:g.32379315_32379819del-None-expected1].yaml +++ /dev/null @@ -1,44 +0,0 @@ -interactions: -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5001/seqrepo/1/metadata/refseq:NC_000013.11 - response: - body: - string: "{\n \"added\": \"2016-08-27T23:50:14Z\",\n \"aliases\": [\n \"GRCh38:13\",\n - \ \"GRCh38:chr13\",\n \"GRCh38.p1:13\",\n \"GRCh38.p1:chr13\",\n \"GRCh38.p10:13\",\n - \ \"GRCh38.p10:chr13\",\n \"GRCh38.p11:13\",\n \"GRCh38.p11:chr13\",\n - \ \"GRCh38.p12:13\",\n \"GRCh38.p12:chr13\",\n \"GRCh38.p2:13\",\n - \ \"GRCh38.p2:chr13\",\n \"GRCh38.p3:13\",\n \"GRCh38.p3:chr13\",\n - \ \"GRCh38.p4:13\",\n \"GRCh38.p4:chr13\",\n \"GRCh38.p5:13\",\n \"GRCh38.p5:chr13\",\n - \ \"GRCh38.p6:13\",\n \"GRCh38.p6:chr13\",\n \"GRCh38.p7:13\",\n \"GRCh38.p7:chr13\",\n - \ \"GRCh38.p8:13\",\n \"GRCh38.p8:chr13\",\n \"GRCh38.p9:13\",\n \"GRCh38.p9:chr13\",\n - \ \"MD5:a5437debe2ef9c9ef8f3ea2874ae1d82\",\n \"NCBI:NC_000013.11\",\n - \ \"refseq:NC_000013.11\",\n \"SEGUID:2oDBty0yKV9wHo7gg+Bt+fPgi5o\",\n - \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n - \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n - \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Wed, 09 Apr 2025 19:40:39 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -version: 1 diff --git a/tests/extras/cassettes/test_from_spdi.yaml b/tests/extras/cassettes/test_from_spdi.yaml deleted file mode 100644 index 676da4a4..00000000 --- a/tests/extras/cassettes/test_from_spdi.yaml +++ /dev/null @@ -1,133 +0,0 @@ -interactions: -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000019.10 - response: - body: - string: "{\n \"added\": \"2016-08-24T08:19:02Z\",\n \"aliases\": [\n \"Ensembl:19\",\n - \ \"ensembl:19\",\n \"GRCh38:19\",\n \"GRCh38:chr19\",\n \"GRCh38.p1:19\",\n - \ \"GRCh38.p1:chr19\",\n \"GRCh38.p10:19\",\n \"GRCh38.p10:chr19\",\n - \ \"GRCh38.p11:19\",\n \"GRCh38.p11:chr19\",\n \"GRCh38.p12:19\",\n - \ \"GRCh38.p12:chr19\",\n \"GRCh38.p2:19\",\n \"GRCh38.p2:chr19\",\n - 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Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_012920.1 - response: - body: - string: "{\n \"added\": \"2016-08-24T06:13:07Z\",\n \"aliases\": [\n \"Ensembl:MT\",\n - \ \"ensembl:MT\",\n \"GRCh37.p10:MT\",\n \"GRCh37.p10:chrM\",\n \"GRCh37.p11:MT\",\n - \ \"GRCh37.p11:chrM\",\n \"GRCh37.p12:MT\",\n \"GRCh37.p12:chrM\",\n - \ \"GRCh37.p13:MT\",\n \"GRCh37.p13:chrM\",\n \"GRCh37.p2:MT\",\n - \ \"GRCh37.p2:chrM\",\n \"GRCh37.p5:MT\",\n \"GRCh37.p5:chrM\",\n - \ \"GRCh37.p9:MT\",\n \"GRCh37.p9:chrM\",\n \"GRCh38:MT\",\n \"GRCh38:chrM\",\n - \ \"GRCh38.p1:MT\",\n \"GRCh38.p1:chrM\",\n \"GRCh38.p10:MT\",\n \"GRCh38.p10:chrM\",\n - \ \"GRCh38.p11:MT\",\n \"GRCh38.p11:chrM\",\n \"GRCh38.p12:MT\",\n - \ \"GRCh38.p12:chrM\",\n \"GRCh38.p2:MT\",\n \"GRCh38.p2:chrM\",\n - \ \"GRCh38.p3:MT\",\n \"GRCh38.p3:chrM\",\n \"GRCh38.p4:MT\",\n \"GRCh38.p4:chrM\",\n - \ \"GRCh38.p5:MT\",\n \"GRCh38.p5:chrM\",\n \"GRCh38.p6:MT\",\n \"GRCh38.p6:chrM\",\n - \ \"GRCh38.p7:MT\",\n \"GRCh38.p7:chrM\",\n \"GRCh38.p8:MT\",\n \"GRCh38.p8:chrM\",\n - \ \"GRCh38.p9:MT\",\n \"GRCh38.p9:chrM\",\n \"MD5:c68f52674c9fb33aef52dcf399755519\",\n - \ \"NCBI:NC_012920.1\",\n \"refseq:NC_012920.1\",\n \"SEGUID:eQNFYXnsCzhp/MkfBUBVnuFZzTA\",\n - \ \"SHA1:7903456179ec0b3869fcc91f0540559ee159cd30\",\n \"VMC:GS_k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n - \ \"sha512t24u:k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n \"ga4gh:SQ.k3grVkjY-hoWcCUojHw6VU6GE3MZ8Sct\",\n - \ \"hs37-1kg:MT\",\n \"hs37d5:MT\"\n ],\n \"alphabet\": \"ACGNT\",\n - \ \"length\": 16569\n}\n" - headers: - Connection: - - close - Content-Length: - - '1355' - Content-Type: - - application/json - Date: - - Tue, 18 Mar 2025 14:14:55 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000013.11 - response: - body: - string: "{\n \"added\": \"2016-08-27T23:50:14Z\",\n \"aliases\": [\n \"GRCh38:13\",\n - \ \"GRCh38:chr13\",\n \"GRCh38.p1:13\",\n \"GRCh38.p1:chr13\",\n \"GRCh38.p10:13\",\n - \ \"GRCh38.p10:chr13\",\n \"GRCh38.p11:13\",\n \"GRCh38.p11:chr13\",\n - \ \"GRCh38.p12:13\",\n \"GRCh38.p12:chr13\",\n \"GRCh38.p2:13\",\n - \ \"GRCh38.p2:chr13\",\n \"GRCh38.p3:13\",\n \"GRCh38.p3:chr13\",\n - \ \"GRCh38.p4:13\",\n \"GRCh38.p4:chr13\",\n \"GRCh38.p5:13\",\n \"GRCh38.p5:chr13\",\n - \ \"GRCh38.p6:13\",\n \"GRCh38.p6:chr13\",\n \"GRCh38.p7:13\",\n \"GRCh38.p7:chr13\",\n - \ \"GRCh38.p8:13\",\n \"GRCh38.p8:chr13\",\n \"GRCh38.p9:13\",\n \"GRCh38.p9:chr13\",\n - \ \"MD5:a5437debe2ef9c9ef8f3ea2874ae1d82\",\n \"NCBI:NC_000013.11\",\n - \ \"refseq:NC_000013.11\",\n \"SEGUID:2oDBty0yKV9wHo7gg+Bt+fPgi5o\",\n - \ \"SHA1:da80c1b72d32295f701e8ee083e06df9f3e08b9a\",\n \"VMC:GS__0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n - \ \"sha512t24u:_0wi-qoDrvram155UmcSC-zA5ZK4fpLT\",\n \"ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT\"\n - \ ],\n \"alphabet\": \"ACGKNTY\",\n \"length\": 114364328\n}\n" - headers: - Connection: - - close - Content-Length: - - '1002' - Content-Type: - - application/json - Date: - - Tue, 18 Mar 2025 14:14:55 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -version: 1 diff --git a/tests/extras/cassettes/test_get_vrs_object_invalid_input.yaml b/tests/extras/cassettes/test_get_vrs_object_invalid_input.yaml index a1edba52..11a2ee4b 100644 --- a/tests/extras/cassettes/test_get_vrs_object_invalid_input.yaml +++ b/tests/extras/cassettes/test_get_vrs_object_invalid_input.yaml @@ -1,45 +1,19 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:. response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 404 message: NOT FOUND - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:7 response: @@ -56,61 +30,25 @@ interactions: \ \"SHA1:e3e26309c05584f0abf2f748854285c9c3eff1b6\",\n \"VMC:GS_F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \ \"sha512t24u:F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\"\n \ ],\n \"alphabet\": \"ACGNRSTY\",\n \"length\": 159345973\n}\n" - headers: - Connection: - - close - Content-Length: - - '977' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:7?start=140753335&end=140753336 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -127,47 +65,19 @@ interactions: \ \"SHA1:e3e26309c05584f0abf2f748854285c9c3eff1b6\",\n \"VMC:GS_F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \ \"sha512t24u:F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\"\n \ ],\n \"alphabet\": \"ACGNRSTY\",\n \"length\": 159345973\n}\n" - headers: - Connection: - - close - Content-Length: - - '977' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=140753335&end=140753336 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:22 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml index 3db8120f..01a253d4 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181220del-expected2].yaml @@ -1,165 +1,67 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181220 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:53 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181218&end=55181219 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:53 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181220&end=55181221 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:53 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181219 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:53 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181220&end=55181220 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:53 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181220&seq_stop=55181220&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -171,64 +73,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:52 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B964500005E6AB092EF31.1.1.m_5 - NCBI-SID: - - 9518E44C404B0665_99DFSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=9518E44C404B0665_99DFSID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:53 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181220&seq_stop=55181240&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -240,50 +91,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:53 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000376AB306431D.1.1.m_5 - NCBI-SID: - - 27ADB2B6DC09096B_8332SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=27ADB2B6DC09096B_8332SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:53 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml index c09d0a91..dbf9fef6 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181230_55181231insGGCT-expected3].yaml @@ -1,105 +1,43 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181230 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:54 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181229&end=55181230 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:54 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181231 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:54 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181231&seq_stop=55181231&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -111,64 +49,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:54 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000506AB54515D5.1.1.m_5 - NCBI-SID: - - D9FCF301C360421D_6179SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=D9FCF301C360421D_6179SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:54 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181230&seq_stop=55181250&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -180,64 +67,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:54 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C500005068826B1155.1.1.m_5 - NCBI-SID: - - 6F671951CC211956_8211SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=6F671951CC211956_8211SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:55 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181227&seq_stop=55181230&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -249,50 +85,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:55 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000326AB9411055.1.1.m_5 - NCBI-SID: - - 016B59280C62811E_AA13SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=016B59280C62811E_AA13SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:55 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181320A>T-expected1].yaml b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181320A>T-expected1].yaml index 68c12196..3c14c730 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181320A>T-expected1].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000007.14:g.55181320A>T-expected1].yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000007.14 response: @@ -26,61 +18,25 @@ interactions: \ \"SHA1:e3e26309c05584f0abf2f748854285c9c3eff1b6\",\n \"VMC:GS_F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \ \"sha512t24u:F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\",\n \"ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul\"\n \ ],\n \"alphabet\": \"ACGNRSTY\",\n \"length\": 159345973\n}\n" - headers: - Connection: - - close - Content-Length: - - '977' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:51 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181319&end=55181320 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:51 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181320&seq_stop=55181320&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -92,64 +48,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:51 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000306AACF15A8B.1.1.m_5 - NCBI-SID: - - D27BE21922DB341C_C7A9SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=D27BE21922DB341C_C7A9SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:52 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '2' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000007.14&rettype=fasta&seq_start=55181320&seq_stop=55181340&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -161,50 +66,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:52 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000376AAED0F690.1.1.m_5 - NCBI-SID: - - B02A0DE89C6FB2A8_F15ESID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=B02A0DE89C6FB2A8_F15ESID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:52 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml index 79f5f4e0..7a529525 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32316467dup-expected5].yaml @@ -1,165 +1,67 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=32316466&end=32316467 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:58 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316466&end=32316467 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:58 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316467&end=32316467 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:58 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316465&end=32316466 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:58 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316467&end=32316468 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:58 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32316467&seq_stop=32316467&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -171,64 +73,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:57 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C500003E6886B10019.1.1.m_5 - NCBI-SID: - - FCA6F5765141935F_9ED1SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=FCA6F5765141935F_9ED1SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:58 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '0' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32316467&seq_stop=32316487&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -240,50 +91,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:58 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B964500003F6AC5AD35EB.1.1.m_5 - NCBI-SID: - - 64DB9D0ADA04B826_34FESID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=64DB9D0ADA04B826_34FESID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:58 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '0' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32331093_32331094dup-expected4].yaml b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32331093_32331094dup-expected4].yaml index ab9b89e4..e61ad59e 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32331093_32331094dup-expected4].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32331093_32331094dup-expected4].yaml @@ -1,555 +1,223 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=32331092&end=32331094 response: body: string: TT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331092&end=32331094 response: body: string: TT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331094&end=32331094 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331093&end=32331094 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331092&end=32331093 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331091&end=32331092 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331090&end=32331091 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331089&end=32331090 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331088&end=32331089 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331087&end=32331088 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331086&end=32331087 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331085&end=32331086 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331084&end=32331085 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331083&end=32331084 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331083 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331081&end=32331082 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331094&end=32331095 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331094 response: body: string: TTTTTTTTTTTT - headers: - Connection: - - close - Content-Length: - - '12' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32331083&seq_stop=32331094&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -561,64 +229,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:55 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000356ABC7A110E.1.1.m_5 - NCBI-SID: - - 1FC73B1280B38A84_E7AESID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=1FC73B1280B38A84_E7AESID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:56 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32331094&seq_stop=32331094&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -630,64 +247,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000296ABF5B1B97.1.1.m_5 - NCBI-SID: - - B7F4DF5FB7833774_9CBBSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=B7F4DF5FB7833774_9CBBSID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:57 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32331083&seq_stop=32331114&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -699,64 +265,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:56 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B964500003C6AC0E69431.1.1.m_5 - NCBI-SID: - - 395E8389D77F1DFA_7E9CSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=395E8389D77F1DFA_7E9CSID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:57 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32331093&seq_stop=32331094&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -768,50 +283,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:57 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B964500004F6AC2D1F640.1.1.m_5 - NCBI-SID: - - 6BD14C65C934689E_1EBASID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=6BD14C65C934689E_1EBASID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:57 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '0' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32936732=-expected0].yaml b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32936732=-expected0].yaml index 4c1a937b..bded6051 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32936732=-expected0].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000013.11:g.32936732=-expected0].yaml @@ -1,75 +1,19 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=32936731&end=32936732 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:49:30 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32936731&end=32936732 - response: - body: - string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:49:30 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32936732&seq_stop=32936732&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -81,50 +25,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Wed, 16 Apr 2025 22:49:30 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322CF8979F5E85B5000050CD47341D44.1.1.m_5 - NCBI-SID: - - B4DD900AE926F06D_8D6DSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=B4DD900AE926F06D_8D6DSID; domain=.nih.gov; path=/; expires=Thu, 16 - Apr 2026 22:49:30 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '2' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289464_289465insCACA-expected8].yaml b/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289464_289465insCACA-expected8].yaml index ceaf0dd9..3cf20e71 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289464_289465insCACA-expected8].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289464_289465insCACA-expected8].yaml @@ -1,195 +1,79 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289464 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289463&end=289464 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289465 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289465&end=289466 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289466&end=289467 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289464&end=289466 response: body: string: CA - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289465&seq_stop=289466&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -201,64 +85,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:13 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 939B8D0F598EF6450000384EC12522B3.1.1.m_5 - NCBI-SID: - - 936A81D97746F649_8FB6SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=936A81D97746F649_8FB6SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:13 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289466&seq_stop=289466&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -270,64 +103,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:14 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B964500003B6ADCF52790.1.1.m_5 - NCBI-SID: - - CD7F83678DD46B63_094ESID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=CD7F83678DD46B63_094ESID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:14 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289465&seq_stop=289486&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -339,64 +121,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:15 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C500003868A691F8D2.1.1.m_5 - NCBI-SID: - - 920E419855E3E73A_6798SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=920E419855E3E73A_6798SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:14 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289463&seq_stop=289466&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -408,50 +139,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:15 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 939B8D0F598EF64500003A4EC62F8AC8.1.1.m_5 - NCBI-SID: - - E4C99ED46FE45CC4_5301SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=E4C99ED46FE45CC4_5301SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:15 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289485_289500del-expected9].yaml b/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289485_289500del-expected9].yaml index e97595d2..96e65209 100644 --- a/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289485_289500del-expected9].yaml +++ b/tests/extras/cassettes/test_hgvs[NC_000019.10:g.289485_289500del-expected9].yaml @@ -1,315 +1,127 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289484&end=289500 response: body: string: GCGGGCAGATCACGAG - headers: - Connection: - - close - Content-Length: - - '16' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289483&end=289484 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289482&end=289483 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289481&end=289482 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289480&end=289481 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289479&end=289480 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289500&end=289501 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289501&end=289502 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289480&end=289484 response: body: string: CGAG - headers: - Connection: - - close - Content-Length: - - '4' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=289480&end=289501 response: body: string: CGAGGCGGGCAGATCACGAGG - headers: - Connection: - - close - Content-Length: - - '21' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:16 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289481&seq_stop=289501&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -321,64 +133,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:15 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000296ADFB4C6D1.1.1.m_5 - NCBI-SID: - - 5138244380359839_E088SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=5138244380359839_E088SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:16 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289501&seq_stop=289501&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -390,64 +151,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:17 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C500005C68AA480827.1.1.m_5 - NCBI-SID: - - EF190317EF29B850_843BSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=EF190317EF29B850_843BSID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:16 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000019.10&rettype=fasta&seq_start=289481&seq_stop=289521&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -459,50 +169,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:17 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - D0BDD793D08B96450000276AE25EC479.1.1.m_5 - NCBI-SID: - - 3E0B8399C5730140_662ESID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=3E0B8399C5730140_662ESID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:17 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NM_001331029.1:c.722A>G-expected6].yaml b/tests/extras/cassettes/test_hgvs[NM_001331029.1:c.722A>G-expected6].yaml index bf7549b6..44352fa1 100644 --- a/tests/extras/cassettes/test_hgvs[NM_001331029.1:c.722A>G-expected6].yaml +++ b/tests/extras/cassettes/test_hgvs[NM_001331029.1:c.722A>G-expected6].yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NM_001331029.1 response: @@ -20,31 +12,13 @@ interactions: \ \"SHA1:ab0f62209f413dd1997f2a70407ed2dcbd9ff602\",\n \"VMC:GS_MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\",\n \ \"sha512t24u:MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\",\n \"ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\"\n \ ],\n \"alphabet\": \"ACGT\",\n \"length\": 11291\n}\n" - headers: - Connection: - - close - Content-Length: - - '496' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:59 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_001331029.1&rettype=fasta&seq_start=872&seq_stop=872&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -56,64 +30,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:22:59 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C50000456888830C71.1.1.m_5 - NCBI-SID: - - 7AD8F1E2A50E9918_F982SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=7AD8F1E2A50E9918_F982SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:22:59 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK response: @@ -124,61 +47,25 @@ interactions: \ \"SHA1:ab0f62209f413dd1997f2a70407ed2dcbd9ff602\",\n \"VMC:GS_MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\",\n \ \"sha512t24u:MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\",\n \"ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK\"\n \ ],\n \"alphabet\": \"ACGT\",\n \"length\": 11291\n}\n" - headers: - Connection: - - close - Content-Length: - - '496' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:22:59 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=871&end=872 response: body: string: A - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:22:59 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_001331029.1&rettype=fasta&seq_start=872&seq_stop=892&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -190,50 +77,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:05 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C50000586893DC8709.1.1.m_5 - NCBI-SID: - - 262F01FCE7B21934_7603SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=262F01FCE7B21934_7603SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:05 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '2' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_hgvs[NM_181798.1:c.1007G>T-expected7].yaml b/tests/extras/cassettes/test_hgvs[NM_181798.1:c.1007G>T-expected7].yaml index f3a27556..20c3a261 100644 --- a/tests/extras/cassettes/test_hgvs[NM_181798.1:c.1007G>T-expected7].yaml +++ b/tests/extras/cassettes/test_hgvs[NM_181798.1:c.1007G>T-expected7].yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NM_181798.1 response: @@ -20,31 +12,13 @@ interactions: \ \"SHA1:d27aea50389b846010059e295d1faca0e88239fd\",\n \"VMC:GS_KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg\",\n \ \"sha512t24u:KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg\",\n \"ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg\"\n \ ],\n \"alphabet\": \"ACGT\",\n \"length\": 3029\n}\n" - headers: - Connection: - - close - Content-Length: - - '483' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:06 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_181798.1&rettype=fasta&seq_start=1263&seq_stop=1263&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -56,64 +30,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:06 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 939B8D0F598EF64500002C4EA9104A61.1.1.m_5 - NCBI-SID: - - 30DD211EE0892843_5A1ESID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=30DD211EE0892843_5A1ESID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:06 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg response: @@ -124,61 +47,25 @@ interactions: \ \"SHA1:d27aea50389b846010059e295d1faca0e88239fd\",\n \"VMC:GS_KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg\",\n \ \"sha512t24u:KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg\",\n \"ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg\"\n \ ],\n \"alphabet\": \"ACGT\",\n \"length\": 3029\n}\n" - headers: - Connection: - - close - Content-Length: - - '483' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:06 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1262&end=1263 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:06 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NM_181798.1&rettype=fasta&seq_start=1263&seq_stop=1268&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -190,64 +77,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:12 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 322C1EB26B7FD5C500004768A15CDFD0.1.1.m_5 - NCBI-SID: - - 1775CB3F32205734_491BSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=1775CB3F32205734_491BSID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:12 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '2' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NR_040711.1&rettype=fasta&seq_start=1263&seq_stop=1263&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -259,50 +95,7 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:11 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 939B8D0F598EF6450000504EBE95DDC4.1.1.m_5 - NCBI-SID: - - 738BE373688C0FCA_4A11SID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=738BE373688C0FCA_4A11SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:12 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_rle_round_trip_gnomad_spdi.yaml b/tests/extras/cassettes/test_rle_round_trip_gnomad_spdi.yaml index f812108d..8dad6e26 100644 --- a/tests/extras/cassettes/test_rle_round_trip_gnomad_spdi.yaml +++ b/tests/extras/cassettes/test_rle_round_trip_gnomad_spdi.yaml @@ -1,15 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:1 response: @@ -26,61 +18,25 @@ interactions: \ \"SHA1:14251de9527aba2912fd558b6e119d5668f6ace0\",\n \"VMC:GS_Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \ \"sha512t24u:Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\"\n \ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 248956422\n}\n" - headers: - Connection: - - close - Content-Length: - - '976' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:1?start=145916839&end=145916844 response: body: string: CTCCT - headers: - Connection: - - close - Content-Length: - - '5' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO response: @@ -97,271 +53,109 @@ interactions: \ \"SHA1:14251de9527aba2912fd558b6e119d5668f6ace0\",\n \"VMC:GS_Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \ \"sha512t24u:Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\"\n \ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 248956422\n}\n" - headers: - Connection: - - close - Content-Length: - - '976' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916839&end=145916844 response: body: string: CTCCT - headers: - Connection: - - close - Content-Length: - - '5' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916841&end=145916844 response: body: string: CCT - headers: - Connection: - - close - Content-Length: - - '3' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916840&end=145916841 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916839&end=145916840 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916838&end=145916839 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916844&end=145916845 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916839&end=145916841 response: body: string: CT - headers: - Connection: - - close - Content-Length: - - '2' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO?start=145916844&end=145916844 response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000001.11 response: @@ -378,31 +172,13 @@ interactions: \ \"SHA1:14251de9527aba2912fd558b6e119d5668f6ace0\",\n \"VMC:GS_Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \ \"sha512t24u:Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\"\n \ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 248956422\n}\n" - headers: - Connection: - - close - Content-Length: - - '976' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/NC_000001.11 response: @@ -419,61 +195,25 @@ interactions: \ \"SHA1:14251de9527aba2912fd558b6e119d5668f6ace0\",\n \"VMC:GS_Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \ \"sha512t24u:Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\",\n \"ga4gh:SQ.Ya6Rs7DHhDeg7YaOSg1EoNi3U_nQ9SvO\"\n \ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 248956422\n}\n" - headers: - Connection: - - close - Content-Length: - - '976' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000001.11?start=145916839&end=145916844 response: body: string: CTCCT - headers: - Connection: - - close - Content-Length: - - '5' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/GRCh38:21 response: @@ -491,61 +231,25 @@ interactions: \ \"SHA1:9cd6646f3c103801c2ed5b95c8874dec8559780c\",\n \"VMC:GS_5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8\",\n \ \"sha512t24u:5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8\",\n \"ga4gh:SQ.5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8\"\n \ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 46709983\n}\n" - headers: - Connection: - - close - Content-Length: - - '999' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/GRCh38:21?start=5033799&end=5033843 response: body: string: TGGGTCCAGGCACCGGCGCCCAGCCCCCGTGGGGTGTCCAGGGC - headers: - Connection: - - close - Content-Length: - - '44' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 22:51:11 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8 response: @@ -563,2341 +267,937 @@ interactions: \ \"SHA1:9cd6646f3c103801c2ed5b95c8874dec8559780c\",\n \"VMC:GS_5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8\",\n \ \"sha512t24u:5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8\",\n \"ga4gh:SQ.5ZUqxCmDDgN4xTRbaSjN8LwgZironmB8\"\n \ ],\n \"alphabet\": \"ACGMNRT\",\n \"length\": 46709983\n}\n" - 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headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:18 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331065&end=32331066 response: body: string: T - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:18 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331064&end=32331065 response: body: string: T - 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headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:18 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331041&end=32331042 response: body: string: G - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Mon, 10 Mar 2025 16:23:18 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=NC_000013.11&rettype=fasta&seq_start=32331043&seq_stop=32331094&tool=bioutils&email=biocommons-dev@googlegroups.com response: @@ -1281,64 +517,13 @@ interactions: ' - headers: - Access-Control-Allow-Origin: - - '*' - Access-Control-Expose-Headers: - - X-RateLimit-Limit,X-RateLimit-Remaining - Cache-Control: - - private - Connection: - - Keep-Alive - Content-Disposition: - - attachment; filename="sequence.fasta" - Content-Security-Policy: - - upgrade-insecure-requests - Content-Type: - - text/plain - Date: - - Mon, 10 Mar 2025 16:23:18 GMT - Keep-Alive: - - timeout=4, max=40 - NCBI-PHID: - - 939B8D0F598EF6450000494ECBD8E340.1.1.m_5 - NCBI-SID: - - FFA219BB52180168_7CBCSID - Referrer-Policy: - - origin-when-cross-origin - Server: - - Finatra - Set-Cookie: - - ncbi_sid=FFA219BB52180168_7CBCSID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:18 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK - 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- Finatra - Set-Cookie: - - ncbi_sid=3A033AF8EF29D368_9BA8SID; domain=.nih.gov; path=/; expires=Tue, 10 - Mar 2026 16:23:18 GMT - Strict-Transport-Security: - - max-age=31536000; includeSubDomains; preload - Transfer-Encoding: - - chunked - X-RateLimit-Limit: - - '3' - X-RateLimit-Remaining: - - '1' - X-UA-Compatible: - - IE=Edge - X-XSS-Protection: - - 1; mode=block - content-encoding: - - gzip + headers: {} status: code: 200 message: OK diff --git a/tests/extras/cassettes/test_to_hgvs_iri_ref_keyerror.yaml b/tests/extras/cassettes/test_to_hgvs_iri_ref_keyerror.yaml index 64c46beb..13bba609 100644 --- a/tests/extras/cassettes/test_to_hgvs_iri_ref_keyerror.yaml +++ b/tests/extras/cassettes/test_to_hgvs_iri_ref_keyerror.yaml @@ -1,31 +1,13 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:seqrefs.jsonc response: body: string: '' - headers: - Connection: - - close - Content-Length: - - '0' - Content-Type: - - application/json - Date: - - Mon, 10 Mar 2025 16:23:19 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 404 message: NOT FOUND diff --git a/tests/extras/cassettes/test_to_spdi.yaml b/tests/extras/cassettes/test_to_spdi.yaml index 5c6dc6b1..46106902 100644 --- a/tests/extras/cassettes/test_to_spdi.yaml +++ b/tests/extras/cassettes/test_to_spdi.yaml @@ -1,129 +1,7 @@ interactions: - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000019.10 - response: - body: - string: "{\n \"added\": \"2016-08-24T08:19:02Z\",\n \"aliases\": [\n \"Ensembl:19\",\n - \ \"ensembl:19\",\n \"GRCh38:19\",\n \"GRCh38:chr19\",\n \"GRCh38.p1:19\",\n - \ \"GRCh38.p1:chr19\",\n \"GRCh38.p10:19\",\n \"GRCh38.p10:chr19\",\n - \ \"GRCh38.p11:19\",\n \"GRCh38.p11:chr19\",\n \"GRCh38.p12:19\",\n - \ \"GRCh38.p12:chr19\",\n \"GRCh38.p2:19\",\n \"GRCh38.p2:chr19\",\n - \ \"GRCh38.p3:19\",\n \"GRCh38.p3:chr19\",\n \"GRCh38.p4:19\",\n \"GRCh38.p4:chr19\",\n - \ \"GRCh38.p5:19\",\n \"GRCh38.p5:chr19\",\n \"GRCh38.p6:19\",\n \"GRCh38.p6:chr19\",\n - \ \"GRCh38.p7:19\",\n \"GRCh38.p7:chr19\",\n \"GRCh38.p8:19\",\n \"GRCh38.p8:chr19\",\n - \ \"GRCh38.p9:19\",\n \"GRCh38.p9:chr19\",\n \"MD5:b0eba2c7bb5c953d1e06a508b5e487de\",\n - \ \"NCBI:NC_000019.10\",\n \"refseq:NC_000019.10\",\n \"SEGUID:AHxM5/L8jIX08UhBBkKXkiO5rhY\",\n - \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n - \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n - \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 23:00:50 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl - response: - body: - string: "{\n \"added\": \"2016-08-24T08:19:02Z\",\n \"aliases\": [\n \"Ensembl:19\",\n - \ \"ensembl:19\",\n \"GRCh38:19\",\n \"GRCh38:chr19\",\n \"GRCh38.p1:19\",\n - \ \"GRCh38.p1:chr19\",\n \"GRCh38.p10:19\",\n \"GRCh38.p10:chr19\",\n - \ \"GRCh38.p11:19\",\n \"GRCh38.p11:chr19\",\n \"GRCh38.p12:19\",\n - \ \"GRCh38.p12:chr19\",\n \"GRCh38.p2:19\",\n \"GRCh38.p2:chr19\",\n - \ \"GRCh38.p3:19\",\n \"GRCh38.p3:chr19\",\n \"GRCh38.p4:19\",\n \"GRCh38.p4:chr19\",\n - \ \"GRCh38.p5:19\",\n \"GRCh38.p5:chr19\",\n \"GRCh38.p6:19\",\n \"GRCh38.p6:chr19\",\n - \ \"GRCh38.p7:19\",\n \"GRCh38.p7:chr19\",\n \"GRCh38.p8:19\",\n \"GRCh38.p8:chr19\",\n - \ \"GRCh38.p9:19\",\n \"GRCh38.p9:chr19\",\n \"MD5:b0eba2c7bb5c953d1e06a508b5e487de\",\n - \ \"NCBI:NC_000019.10\",\n \"refseq:NC_000019.10\",\n \"SEGUID:AHxM5/L8jIX08UhBBkKXkiO5rhY\",\n - \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n - \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n - \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 23:00:50 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 - method: GET - uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl?start=44908821&end=44908822 - response: - body: - string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 23:00:50 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 - status: - code: 200 - message: OK -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/metadata/NC_000019.10 response: @@ -141,47 +19,19 @@ interactions: \ \"SHA1:007c4ce7f2fc8c85f4f148410642979223b9ae16\",\n \"VMC:GS_IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \ \"sha512t24u:IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\",\n \"ga4gh:SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl\"\n \ ],\n \"alphabet\": \"ACGNT\",\n \"length\": 58617616\n}\n" - headers: - Connection: - - close - Content-Length: - - '1035' - Content-Type: - - application/json - Date: - - Wed, 16 Apr 2025 23:00:50 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK - request: body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.32.3 + headers: {} method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000019.10?start=44908821&end=44908822 response: body: string: C - headers: - Connection: - - close - Content-Length: - - '1' - Content-Type: - - text/plain; charset=utf-8 - Date: - - Wed, 16 Apr 2025 23:00:50 GMT - Server: - - Werkzeug/2.2.3 Python/3.10.12 + headers: {} status: code: 200 message: OK diff --git a/tests/extras/test_annotate_vcf.py b/tests/extras/test_annotate_vcf.py index 5fb0072c..af5b21a1 100644 --- a/tests/extras/test_annotate_vcf.py +++ b/tests/extras/test_annotate_vcf.py @@ -67,7 +67,6 @@ def test_annotate_vcf_grch38_noattrs( vcf_annotator.annotate(input_vcf, output_vcf, output_pkl_path=output_vrs_pkl) compare_vcfs(output_vcf, expected_vcf_no_vrs_attrs) assert output_vrs_pkl.exists() - assert vcr_cassette.all_played @pytest.mark.vcr @@ -85,7 +84,6 @@ def test_annotate_vcf_grch38_attrs( ) compare_vcfs(output_vcf, expected_vcf) assert output_vrs_pkl.exists() - assert vcr_cassette.all_played @pytest.mark.vcr @@ -107,7 +105,6 @@ def test_annotate_vcf_grch38_attrs_altsonly( ) compare_vcfs(output_vcf, expected_altsonly_vcf) assert output_vrs_pkl.exists() - assert vcr_cassette.all_played @pytest.mark.vcr @@ -133,7 +130,6 @@ def test_annotate_vcf_grch37_attrs( expected_output_lines = expected_output.readlines() assert out_vcf_lines != expected_output_lines assert output_vrs_pkl.exists() - assert vcr_cassette.all_played @pytest.mark.vcr @@ -150,7 +146,6 @@ def test_annotate_vcf_pickle_only( ) assert output_vrs_pkl.exists() assert not output_vcf.exists() - assert vcr_cassette.all_played @pytest.mark.vcr @@ -165,7 +160,6 @@ def test_annotate_vcf_vcf_only( # Test only VCF output vcf_annotator.annotate(input_vcf, output_vcf_path=output_vcf, vrs_attributes=True) compare_vcfs(output_vcf, expected_vcf) - assert vcr_cassette.all_played assert not Path(output_vrs_pkl).exists() diff --git a/tests/vcr_support.py b/tests/vcr_support.py deleted file mode 100644 index f83627b9..00000000 --- a/tests/vcr_support.py +++ /dev/null @@ -1,12 +0,0 @@ -import os -from pathlib import Path - -import vcr as vcrpy - -test_dir = Path(__file__).parent -test_data_dir = Path(test_dir) / "data" / "cassettes" - -vcr = vcrpy.VCR( - cassette_library_dir=test_data_dir, - record_mode=os.environ.get("VCR_RECORD_MODE", "new_episodes"), -)