diff --git a/src/ga4gh/vrs/extras/translator.py b/src/ga4gh/vrs/extras/translator.py index 941666eb..c37cc346 100644 --- a/src/ga4gh/vrs/extras/translator.py +++ b/src/ga4gh/vrs/extras/translator.py @@ -451,6 +451,7 @@ def _post_process_imported_allele(self, allele): if self.identify: allele.id = ga4gh_identify(allele) + allele.location.id = ga4gh_identify(allele.location) return allele 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 dcf59ba6..fcaf9952 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 @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -34,7 +34,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:38 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -50,7 +50,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181220 response: @@ -64,7 +64,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:38 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -80,7 +80,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181218&end=55181219 response: @@ -94,7 +94,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:38 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -110,7 +110,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181220&end=55181221 response: @@ -124,7 +124,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:38 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -140,7 +140,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181219 response: @@ -154,7 +154,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:38 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -170,7 +170,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181220&end=55181220 response: @@ -184,7 +184,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:39 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -200,7 +200,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181220 response: @@ -214,7 +214,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:39 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -230,7 +230,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -254,20 +254,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:39 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322C565FBBD0434500004A8944D27A9C.1.1.m_5 + - D0BD7A022C7C6FC500006196F8D78473.1.1.m_5 NCBI-SID: - - 2EC1575CB80AC993_35F8SID + - 91F987A90C4FE16A_3574SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=2EC1575CB80AC993_35F8SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:39 GMT + - ncbi_sid=91F987A90C4FE16A_3574SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:34 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -275,9 +275,7 @@ interactions: X-RateLimit-Limit: - '3' X-RateLimit-Remaining: - - '2' - X-Test-Test: - - test42 + - '1' X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -297,7 +295,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -322,20 +320,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:40 GMT + - Sat, 17 Jun 2023 01:04:34 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322C565FBBD0434500006189494D7737.1.1.m_5 + - D0BD7A022C7C6FC500003D96FBDCD3A4.1.1.m_5 NCBI-SID: - - 7A77E41933C60584_3EA6SID + - 06B6CAAF520F975A_7A87SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=7A77E41933C60584_3EA6SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:40 GMT + - ncbi_sid=06B6CAAF520F975A_7A87SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:34 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -343,9 +341,7 @@ interactions: X-RateLimit-Limit: - '3' X-RateLimit-Remaining: - - '2' - X-Test-Test: - - test42 + - '1' X-UA-Compatible: - IE=Edge X-XSS-Protection: 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 e5a8b15c..b727a5de 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 @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -34,7 +34,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:40 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -50,7 +50,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181230 response: @@ -64,7 +64,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -80,7 +80,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181229&end=55181230 response: @@ -94,7 +94,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -110,7 +110,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181231 response: @@ -124,7 +124,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -140,7 +140,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181230 response: @@ -154,7 +154,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -170,7 +170,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181230 response: @@ -184,7 +184,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -200,7 +200,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -224,20 +224,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:35 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322C565FBBD04345000063894CCEC8B1.1.1.m_5 + - 322C88C3B864A66500005B882C71FAF6.1.1.m_5 NCBI-SID: - - 0A1500EC54F12D18_9F90SID + - 9D0BE2B460CC0B21_E5FFSID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=0A1500EC54F12D18_9F90SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:41 GMT + - ncbi_sid=9D0BE2B460CC0B21_E5FFSID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:35 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -246,8 +246,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -267,7 +265,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -292,20 +290,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:41 GMT + - Sat, 17 Jun 2023 01:04:36 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5131D558E5C500004E9D1F064DD1.1.1.m_5 + - 322C88C3B864A66500004E882E0A4658.1.1.m_5 NCBI-SID: - - F3B91B8A0E37B02B_FB41SID + - C594BF4A99D6CFF8_948ASID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=F3B91B8A0E37B02B_FB41SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:42 GMT + - ncbi_sid=C594BF4A99D6CFF8_948ASID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:36 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -314,8 +312,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -335,7 +331,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -359,20 +355,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:42 GMT + - Sat, 17 Jun 2023 01:04:36 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5131D558E5C50000339D2037274E.1.1.m_5 + - 939B236CFCF1AA15000058A14C241824.1.1.m_5 NCBI-SID: - - 190C71F5745DB337_5126SID + - B00CB2AA37D87866_4816SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=190C71F5745DB337_5126SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:42 GMT + - ncbi_sid=B00CB2AA37D87866_4816SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:37 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -381,8 +377,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: 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 f569d17a..94c259de 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 @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NC_000007.14 response: @@ -34,7 +34,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -50,7 +50,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -75,7 +75,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -91,7 +91,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181319&end=55181320 response: @@ -105,7 +105,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -121,7 +121,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181318&end=55181319 response: @@ -135,7 +135,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -151,7 +151,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181320&end=55181321 response: @@ -165,7 +165,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -181,7 +181,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181320&end=55181321 response: @@ -195,7 +195,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -211,7 +211,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181319&end=55181319 response: @@ -225,7 +225,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -241,7 +241,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181320&end=55181320 response: @@ -255,7 +255,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -271,7 +271,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul response: @@ -296,7 +296,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -312,7 +312,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181319&end=55181320 response: @@ -326,7 +326,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:36 GMT + - Sat, 17 Jun 2023 01:04:33 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -342,7 +342,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -366,20 +366,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:37 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322C565FBBD04345000040893C94F822.1.1.m_5 + - D0BD7A022C7C6FC500004D96F27FB4D6.1.1.m_5 NCBI-SID: - - 420C5BCCD1C6E9B2_5C0FSID + - 2DACA0C3DC694FC7_FC49SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=420C5BCCD1C6E9B2_5C0FSID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:37 GMT + - ncbi_sid=2DACA0C3DC694FC7_FC49SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:32 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -387,9 +387,7 @@ interactions: X-RateLimit-Limit: - '3' X-RateLimit-Remaining: - - '2' - X-Test-Test: - - test42 + - '1' X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -409,7 +407,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -434,20 +432,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:38 GMT + - Sat, 17 Jun 2023 01:04:32 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000060A99C5B806E.1.1.m_5 + - 939B236CFCF1AA15000053A143205DFE.1.1.m_5 NCBI-SID: - - 9F459694A41DE3F9_CA92SID + - DDC9B27ECA7F1CC1_1C9ESID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=9F459694A41DE3F9_CA92SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:38 GMT + - ncbi_sid=DDC9B27ECA7F1CC1_1C9ESID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:33 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -456,8 +454,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: 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 07eacd7b..c438cbb0 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 @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=32316466&end=32316467 response: @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT response: @@ -65,7 +65,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -81,7 +81,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316466&end=32316467 response: @@ -95,7 +95,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -111,7 +111,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316466&end=32316467 response: @@ -125,7 +125,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -141,7 +141,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316465&end=32316466 response: @@ -155,7 +155,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -171,7 +171,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316467&end=32316468 response: @@ -185,7 +185,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -201,7 +201,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316466&end=32316467 response: @@ -215,7 +215,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -231,7 +231,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316467&end=32316467 response: @@ -245,7 +245,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -261,7 +261,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316466&end=32316467 response: @@ -275,7 +275,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -291,7 +291,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -315,20 +315,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:46 GMT + - Sat, 17 Jun 2023 01:04:40 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B0799500004DA9BB579367.1.1.m_5 + - 322C88C3B864A665000024883973E939.1.1.m_5 NCBI-SID: - - A99BC07B6CCB24A8_D60CSID + - 21345483F31464C3_317ESID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=A99BC07B6CCB24A8_D60CSID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:46 GMT + - ncbi_sid=21345483F31464C3_317ESID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:41 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -337,8 +337,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -358,7 +356,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -383,20 +381,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:46 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322C565FBBD04345000057895FDB1C8F.1.1.m_5 + - 939B236CFCF1AA15000027A15AE8E37B.1.1.m_5 NCBI-SID: - - 8E14879EC2176674_ED23SID + - 22EACE5C291E1D28_BD4CSID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=8E14879EC2176674_ED23SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:46 GMT + - ncbi_sid=22EACE5C291E1D28_BD4CSID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:41 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -405,8 +403,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: 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 fe47f96f..05906d33 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 @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=32331092&end=32331094 response: @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT response: @@ -65,7 +65,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -81,7 +81,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331092&end=32331094 response: @@ -95,7 +95,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -111,7 +111,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331093&end=32331094 response: @@ -125,7 +125,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -141,7 +141,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331092&end=32331093 response: @@ -155,7 +155,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -171,7 +171,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331091&end=32331092 response: @@ -185,7 +185,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -201,7 +201,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331090&end=32331091 response: @@ -215,7 +215,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -231,7 +231,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331089&end=32331090 response: @@ -245,7 +245,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -261,7 +261,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331088&end=32331089 response: @@ -275,7 +275,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -291,7 +291,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331087&end=32331088 response: @@ -305,7 +305,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -321,7 +321,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331086&end=32331087 response: @@ -335,7 +335,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -351,7 +351,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331085&end=32331086 response: @@ -365,7 +365,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -381,7 +381,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331084&end=32331085 response: @@ -395,7 +395,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -411,7 +411,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331083&end=32331084 response: @@ -425,7 +425,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -441,7 +441,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331083 response: @@ -455,7 +455,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -471,7 +471,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331081&end=32331082 response: @@ -485,7 +485,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -501,7 +501,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331094&end=32331095 response: @@ -515,7 +515,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -531,7 +531,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331094 response: @@ -545,7 +545,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -561,7 +561,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331094&end=32331094 response: @@ -575,7 +575,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -591,7 +591,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331094 response: @@ -605,7 +605,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:38 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -621,7 +621,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -645,20 +645,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:43 GMT + - Sat, 17 Jun 2023 01:04:37 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5131D558E5C50000499D227007CD.1.1.m_5 + - 322C88C3B864A665000053883184093D.1.1.m_5 NCBI-SID: - - B873AC4E657ED7C0_C753SID + - 7460204ECE221625_1751SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=B873AC4E657ED7C0_C753SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:43 GMT + - ncbi_sid=7460204ECE221625_1751SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:38 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -667,8 +667,6 @@ interactions: - '3' X-RateLimit-Remaining: - '2' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -688,7 +686,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -712,20 +710,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:44 GMT + - Sat, 17 Jun 2023 01:04:39 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000024A9B17E91FA.1.1.m_5 + - 322C88C3B864A66500004C8835631755.1.1.m_5 NCBI-SID: - - 37371425DAD8A934_3859SID + - 0787634CFDA8561D_47C9SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=37371425DAD8A934_3859SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:44 GMT + - ncbi_sid=0787634CFDA8561D_47C9SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:39 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -733,9 +731,7 @@ interactions: X-RateLimit-Limit: - '3' X-RateLimit-Remaining: - - '1' - X-Test-Test: - - test42 + - '2' X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -755,7 +751,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -780,20 +776,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:44 GMT + - Sat, 17 Jun 2023 01:04:40 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000036A9B45A1C06.1.1.m_5 + - 939B236CFCF1AA15000044A156FDAE8F.1.1.m_5 NCBI-SID: - - 1AE5AEB3828CB7CF_1141SID + - 69CA492CCCF1D9ED_30ACSID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=1AE5AEB3828CB7CF_1141SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:44 GMT + - ncbi_sid=69CA492CCCF1D9ED_30ACSID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:40 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -802,8 +798,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -823,7 +817,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -847,20 +841,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:45 GMT + - Sat, 17 Jun 2023 01:04:40 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000031A9B7476820.1.1.m_5 + - 939B236CFCF1AA15000050A158560489.1.1.m_5 NCBI-SID: - - 738A236220A308B6_1223SID + - 6DE6FC530437B9A4_6D0FSID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=738A236220A308B6_1223SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:45 GMT + - ncbi_sid=6DE6FC530437B9A4_6D0FSID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:40 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -868,9 +862,7 @@ interactions: X-RateLimit-Limit: - '3' X-RateLimit-Remaining: - - '1' - X-Test-Test: - - test42 + - '0' X-UA-Compatible: - IE=Edge X-XSS-Protection: 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 9b338926..36213f2f 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 @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/NC_000013.11?start=32936731&end=32936732 response: @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:32 GMT + - Sat, 17 Jun 2023 01:04:29 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT response: @@ -65,7 +65,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:32 GMT + - Sat, 17 Jun 2023 01:04:29 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -81,7 +81,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32936731&end=32936732 response: @@ -95,7 +95,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:32 GMT + - Sat, 17 Jun 2023 01:04:29 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -111,7 +111,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32936731&end=32936732 response: @@ -125,7 +125,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:32 GMT + - Sat, 17 Jun 2023 01:04:29 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -141,7 +141,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -165,20 +165,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:35 GMT + - Sat, 17 Jun 2023 01:04:31 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000033A99595C676.1.1.m_5 + - D0BD7A022C7C6FC500002E96EE3E6D62.1.1.m_5 NCBI-SID: - - EF12D6B754467448_5D6DSID + - 29CB87EB7B7DD577_9797SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=EF12D6B754467448_5D6DSID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:36 GMT + - ncbi_sid=29CB87EB7B7DD577_9797SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:32 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -187,8 +187,6 @@ interactions: - '3' X-RateLimit-Remaining: - '2' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: diff --git a/tests/extras/cassettes/test_hgvs[NM_001331029.1:n.872A>G-expected6].yaml b/tests/extras/cassettes/test_hgvs[NM_001331029.1:n.872A>G-expected6].yaml index fce6694d..98366397 100644 --- a/tests/extras/cassettes/test_hgvs[NM_001331029.1:n.872A>G-expected6].yaml +++ b/tests/extras/cassettes/test_hgvs[NM_001331029.1:n.872A>G-expected6].yaml @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NM_001331029.1 response: @@ -28,7 +28,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -44,7 +44,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK response: @@ -63,7 +63,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -79,7 +79,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=871&end=872 response: @@ -93,7 +93,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -109,7 +109,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=870&end=871 response: @@ -123,7 +123,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -139,7 +139,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=872&end=873 response: @@ -153,7 +153,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -169,7 +169,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=871&end=871 response: @@ -183,7 +183,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -199,7 +199,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=872&end=872 response: @@ -213,7 +213,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -229,7 +229,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK response: @@ -248,7 +248,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -264,7 +264,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK?start=871&end=872 response: @@ -278,7 +278,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -294,7 +294,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -319,20 +319,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:47 GMT + - Sat, 17 Jun 2023 01:04:41 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000056A9C362B8D5.1.1.m_5 + - 322C88C3B864A665000029883CE8D086.1.1.m_5 NCBI-SID: - - 88E44ABEB372520E_1268SID + - 80E9370C369020AD_8FD5SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=88E44ABEB372520E_1268SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:47 GMT + - ncbi_sid=80E9370C369020AD_8FD5SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:42 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -341,8 +341,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -362,7 +360,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -387,20 +385,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:48 GMT + - Sat, 17 Jun 2023 01:04:42 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322C565FBBD04345000044896663FA92.1.1.m_5 + - 322C88C3B864A665000028883F0093E3.1.1.m_5 NCBI-SID: - - FD3F2684EEAF25BB_F979SID + - FBC24E5DE2F0B43E_EC52SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=FD3F2684EEAF25BB_F979SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:48 GMT + - ncbi_sid=FBC24E5DE2F0B43E_EC52SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:43 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -409,8 +407,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: diff --git a/tests/extras/cassettes/test_hgvs[NM_181798.1:n.1263G>T-expected7].yaml b/tests/extras/cassettes/test_hgvs[NM_181798.1:n.1263G>T-expected7].yaml index 2438cf23..37d4f6f3 100644 --- a/tests/extras/cassettes/test_hgvs[NM_181798.1:n.1263G>T-expected7].yaml +++ b/tests/extras/cassettes/test_hgvs[NM_181798.1:n.1263G>T-expected7].yaml @@ -9,7 +9,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/refseq:NM_181798.1 response: @@ -28,7 +28,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:48 GMT + - Sat, 17 Jun 2023 01:04:43 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -44,7 +44,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg response: @@ -63,7 +63,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:48 GMT + - Sat, 17 Jun 2023 01:04:43 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -79,7 +79,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1262&end=1263 response: @@ -93,7 +93,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:48 GMT + - Sat, 17 Jun 2023 01:04:43 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -109,7 +109,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1261&end=1262 response: @@ -123,7 +123,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:43 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -139,7 +139,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1263&end=1264 response: @@ -153,7 +153,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:43 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -169,7 +169,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1262&end=1262 response: @@ -183,7 +183,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:44 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -199,7 +199,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1263&end=1263 response: @@ -213,7 +213,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:44 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -229,7 +229,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/metadata/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg response: @@ -248,7 +248,7 @@ interactions: Content-Type: - application/json Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:44 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -264,7 +264,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg?start=1262&end=1263 response: @@ -278,7 +278,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:44 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -294,7 +294,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -319,20 +319,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:43 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B07995000026A9CC9DD62E.1.1.m_5 + - 322C88C3B864A665000064884142F0CA.1.1.m_5 NCBI-SID: - - C0E5B98D3C5B65AD_1BC3SID + - 276009E1E93550F1_B8F9SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=C0E5B98D3C5B65AD_1BC3SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:49 GMT + - ncbi_sid=276009E1E93550F1_B8F9SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:43 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -341,8 +341,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -362,7 +360,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.1 + - python-requests/2.29.0 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: @@ -387,20 +385,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Sep 2022 15:07:49 GMT + - Sat, 17 Jun 2023 01:04:44 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B60E632B0799500004AA9D1B992DC.1.1.m_5 + - 322C88C3B864A66500005C88433FE3A9.1.1.m_5 NCBI-SID: - - 3C2715F82F942926_3546SID + - FEE1B01EFB3EB9C2_D894SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=3C2715F82F942926_3546SID; domain=.nih.gov; path=/; expires=Tue, 19 - Sep 2023 15:07:50 GMT + - ncbi_sid=FEE1B01EFB3EB9C2_D894SID; domain=.nih.gov; path=/; expires=Mon, 17 + Jun 2024 01:04:44 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -409,8 +407,6 @@ interactions: - '3' X-RateLimit-Remaining: - '1' - X-Test-Test: - - test42 X-UA-Compatible: - IE=Edge X-XSS-Protection: diff --git a/tests/extras/test_translator.py b/tests/extras/test_translator.py index 30c1c254..f44c61c6 100644 --- a/tests/extras/test_translator.py +++ b/tests/extras/test_translator.py @@ -123,7 +123,9 @@ def test_to_spdi(tlr): hgvs_tests = ( ("NC_000013.11:g.32936732=", { + "id": "ga4gh:VA.zkZpkDHX0xaOHUPxa5kFt3TUiWbr53xm", "location": { + "id": "ga4gh:SL.2Q2SMLzdWQbJvYbXwwgegrjJbOxiLIJP", "end": {"value": 32936732, "type": "Number"}, "start": {"value": 32936731, "type": "Number"}, "sequence_id": "ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT", @@ -136,7 +138,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NC_000007.14:g.55181320A>T", { + "id": "ga4gh:VA.RzhTjgnkCmLnaw3IBWnAubZs7eJHhho_", "location": { + "id": "ga4gh:SL.Npx4j5beiNN9GSFTm8Ml6YxrNj_Ghkac", "end": {"value": 55181320, "type": "Number"}, "start": {"value": 55181319, "type": "Number"}, "sequence_id": "ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul", @@ -149,7 +153,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NC_000007.14:g.55181220del", { + "id": "ga4gh:VA.YdX-N1MsXLxVnfCPYBdkdhzaEJVcPVDA", "location": { + "id": "ga4gh:SL.80HjxOYxb6OtmSUToUehMqU78JJFEaC1", "end": {"value": 55181220, "type": "Number"}, "start": {"value": 55181219, "type": "Number"}, "sequence_id": "ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul", @@ -162,7 +168,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NC_000007.14:g.55181230_55181231insGGCT", { + "id": "ga4gh:VA.osbbI5Me3Paj5mFN3wsD1RpuHhd0dJsv", "location": { + "id": "ga4gh:SL.b30aH2-4AX1oG2LYmMqpBRRyjcpARlgP", "end": {"value": 55181230, "type": "Number"}, "start": {"value": 55181230, "type": "Number"}, "sequence_id": "ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul", @@ -175,7 +183,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NC_000013.11:g.32331093_32331094dup", { + "id": "ga4gh:VA.0wERl6sqiSnHXe44bfbd4c6zvqAZVjqp", "location": { + "id": "ga4gh:SL.OKUia3LZI-04cFnY1uSO0gEicgTz3suN", "end": {"value": 32331094, "type": "Number"}, "start": {"value": 32331082, "type": "Number"}, "sequence_id": "ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT", @@ -188,7 +198,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NC_000013.11:g.32316467dup", { + "id": "ga4gh:VA.iuDk-UaV63YXoYUJHehin3vFfzfYnz0j", "location": { + "id": "ga4gh:SL.yy5lb3KqJGmLbo5kJ7aGf4aW5Ih5-dI3", "end": {"value": 32316467, "type": "Number"}, "start": {"value": 32316466, "type": "Number"}, "sequence_id": "ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT", @@ -201,7 +213,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NM_001331029.1:n.872A>G", { + "id": "ga4gh:VA.j-Lnf0txP05DFsLJNhH6Fau4lIBok-DI", "location": { + "id": "ga4gh:SL.VFlsGPHaAJB_LsYzQd8t6vTWSGKWiEeB", "end": {"value": 872, "type": "Number"}, "start": {"value": 871, "type": "Number"}, "sequence_id": "ga4gh:SQ.MBIgVnoHFw34aFqNUVGM0zgjC3d-v8dK", @@ -214,7 +228,9 @@ def test_to_spdi(tlr): "type": "Allele" }), ("NM_181798.1:n.1263G>T", { + "id": "ga4gh:VA.iLlJQVkxftWXweu4Ad-2NMShYdxUR1DH", "location": { + "id": "ga4gh:SL.rxnYlIIPfVZCxSGhxdvs_nAWlxQd3nen", "end": {"value": 1263, "type": "Number"}, "start": {"value": 1262, "type": "Number"}, "sequence_id": "ga4gh:SQ.KN07u-RFqd1dTyOWOG98HnOq87Nq-ZIg", @@ -233,6 +249,7 @@ def test_to_spdi(tlr): @pytest.mark.vcr def test_hgvs(tlr, hgvsexpr, expected): tlr.normalize = True + tlr.identify = True allele = tlr.translate_from(hgvsexpr, "hgvs") assert expected == allele.as_dict()