From cef704dd05b9110ab33ee9bc312b5bd760f65bc5 Mon Sep 17 00:00:00 2001 From: Kori Kuzma Date: Wed, 13 Mar 2024 12:17:46 -0400 Subject: [PATCH] feat!: parameterize normalize in translator (#361) * feat!: parameterize normalize in translator * new kwarg (do_normalize) in translate_from methods. Set to determine if normalization should be performed * add test from spdi cassette --- src/ga4gh/vrs/extras/translator.py | 24 ++- tests/extras/cassettes/test_from_spdi.yaml | 86 +++++++++++ ...NC_000007.14:g.55181220del-expected2].yaml | 44 +++--- ...g.55181230_55181231insGGCT-expected3].yaml | 48 +++--- ...NC_000007.14:g.55181320A>T-expected1].yaml | 32 ++-- ...NC_000013.11:g.32316467dup-expected5].yaml | 44 +++--- ....11:g.32331093_32331094dup-expected4].yaml | 122 ++++++++-------- ...s[NC_000013.11:g.32936732=-expected0].yaml | 16 +- ....10:g.289464_289465insCACA-expected8].yaml | 138 ++++-------------- ...0019.10:g.289485_289500del-expected9].yaml | 52 +++---- ...vs[NM_001331029.1:n.872A>G-expected6].yaml | 36 ++--- ...hgvs[NM_181798.1:n.1263G>T-expected7].yaml | 38 ++--- tests/extras/cassettes/test_to_spdi.yaml | 74 ++++++++++ tests/extras/test_allele_translator.py | 90 ++++++------ tests/extras/test_cnv_translator.py | 1 - 15 files changed, 464 insertions(+), 381 deletions(-) create mode 100644 tests/extras/cassettes/test_from_spdi.yaml create mode 100644 tests/extras/cassettes/test_to_spdi.yaml diff --git a/src/ga4gh/vrs/extras/translator.py b/src/ga4gh/vrs/extras/translator.py index dfe0bdc4..f3faa987 100644 --- a/src/ga4gh/vrs/extras/translator.py +++ b/src/ga4gh/vrs/extras/translator.py @@ -54,14 +54,12 @@ def __init__( self, data_proxy, default_assembly_name="GRCh38", - normalize=True, identify=True, rle_seq_limit: Optional[int] = 50 ): self.default_assembly_name = default_assembly_name self.data_proxy = data_proxy self.identify = identify - self.normalize = normalize self.rle_seq_limit = rle_seq_limit self.hgvs_tools = None self.from_translators = {} @@ -127,6 +125,8 @@ def translate_from(self, var, fmt=None, **kwargs): To exclude `sequence` from the response, set to 0. For no limit, set to `None`. Defaults value set in instance variable, `rle_seq_limit`. + do_normalize (bool): `True` if fully justified normalization should be + performed. `False` otherwise. Defaults to `True` """ if fmt: try: @@ -225,10 +225,10 @@ class AlleleTranslator(Translator): """Class for translating formats to and from VRS Alleles""" def __init__( - self, data_proxy, default_assembly_name="GRCh38", normalize=True, identify=True + self, data_proxy, default_assembly_name="GRCh38", identify=True ): """Initialize AlleleTranslator class""" - super().__init__(data_proxy, default_assembly_name, normalize, identify) + super().__init__(data_proxy, default_assembly_name, identify) self.from_translators = { "beacon": self._from_beacon, @@ -253,6 +253,8 @@ def _from_beacon(self, beacon_expr, **kwargs): To exclude `sequence` from the response, set to 0. For no limit, set to `None`. Defaults value set in instance variable, `rle_seq_limit`. + do_normalize (bool): `True` if fully justified normalization should be + performed. `False` otherwise. Defaults to `True` #>>> a = tlr.from_beacon("19 : 44908822 C > T") #>>> a.model_dump() @@ -316,6 +318,8 @@ def _from_gnomad(self, gnomad_expr, **kwargs): To exclude `sequence` from the response, set to 0. For no limit, set to `None`. Defaults value set in instance variable, `rle_seq_limit`. + do_normalize (bool): `True` if fully justified normalization should be + performed. `False` otherwise. Defaults to `True` #>>> a = tlr.from_gnomad("1-55516888-G-GA") #>>> a.model_dump() @@ -378,6 +382,8 @@ def _from_hgvs(self, hgvs_expr: str, **kwargs): To exclude `sequence` from the response, set to 0. For no limit, set to `None`. Defaults value set in instance variable, `rle_seq_limit`. + do_normalize (bool): `True` if fully justified normalization should be + performed. `False` otherwise. Defaults to `True` #>>> a = tlr.from_hgvs("NC_000007.14:g.55181320A>T") #>>> a.model_dump() @@ -452,6 +458,8 @@ def _from_spdi(self, spdi_expr, **kwargs): To exclude `sequence` from the response, set to 0. For no limit, set to `None`. Defaults value set in instance variable, `rle_seq_limit`. + do_normalize (bool): `True` if fully justified normalization should be + performed. `False` otherwise. Defaults to `True` #>>> a = tlr.from_spdi("NC_000013.11:32936731:1:C") #>>> a.model_dump() @@ -626,8 +634,10 @@ def _post_process_imported_allele(self, allele, **kwargs): normalization, this sets the limit for the length of the `sequence`. To exclude `sequence` from the response, set to 0. For no limit, set to `None`. + do_normalize (bool): `True` if fully justified normalization should be + performed. `False` otherwise. Defaults to `True` """ - if self.normalize: + if kwargs.get("do_normalize", True): allele = normalize( allele, self.data_proxy, @@ -654,10 +664,10 @@ class CnvTranslator(Translator): """Class for translating formats from format to VRS Copy Number""" def __init__( - self, data_proxy, default_assembly_name="GRCh38", normalize=True, identify=True + self, data_proxy, default_assembly_name="GRCh38", identify=True ): """Initialize CnvTranslator class""" - super().__init__(data_proxy, default_assembly_name, normalize, identify) + super().__init__(data_proxy, default_assembly_name, identify) self.from_translators = { "hgvs": self._from_hgvs, } diff --git a/tests/extras/cassettes/test_from_spdi.yaml b/tests/extras/cassettes/test_from_spdi.yaml new file mode 100644 index 00000000..e864fe94 --- /dev/null +++ b/tests/extras/cassettes/test_from_spdi.yaml @@ -0,0 +1,86 @@ +interactions: +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + 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: + - Tue, 12 Mar 2024 12:34:06 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + 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, 12 Mar 2024 12:34:06 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +version: 1 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 6f18cf6d..9cde005a 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/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181220 response: @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:23 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181218&end=55181219 response: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:23 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -69,7 +69,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181220&end=55181221 response: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:23 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -99,7 +99,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181219&end=55181219 response: @@ -113,7 +113,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:23 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -129,7 +129,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181220&end=55181220 response: @@ -143,7 +143,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:23 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -159,7 +159,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -183,20 +183,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:23 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A500004E8953DC8714.1.1.m_5 + - 322CFCD26EC09885000045491929D908.1.1.m_5 NCBI-SID: - - F908C0590198759C_1297SID + - CC70304937911EDE_9EBESID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=F908C0590198759C_1297SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:18 GMT + - ncbi_sid=CC70304937911EDE_9EBESID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:23 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -224,7 +224,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -249,20 +249,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:18 GMT + - Mon, 11 Mar 2024 21:21:24 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A500003B8959035020.1.1.m_5 + - 322CFCD26EC09885000059491D137F58.1.1.m_5 NCBI-SID: - - 0FA55D02B01B7AFC_8F66SID + - 11F6059A8AEDFE53_CBBESID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=0FA55D02B01B7AFC_8F66SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:19 GMT + - ncbi_sid=11F6059A8AEDFE53_CBBESID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:24 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 09748095..86e7d5a9 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/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181230 response: @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:20 GMT + - Mon, 11 Mar 2024 21:21:25 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181229&end=55181230 response: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:20 GMT + - Mon, 11 Mar 2024 21:21:25 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -69,7 +69,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181230&end=55181231 response: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:20 GMT + - Mon, 11 Mar 2024 21:21:25 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -99,7 +99,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -123,20 +123,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:20 GMT + - Mon, 11 Mar 2024 21:21:25 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5673E54A8BE5000063882725ADF6.1.1.m_5 + - D0BD851AC14C189500002C313D4FD5D0.1.1.m_5 NCBI-SID: - - F7C03B5CCF0884C3_8C08SID + - 71199B9F013A4D28_29E9SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=F7C03B5CCF0884C3_8C08SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:19 GMT + - ncbi_sid=71199B9F013A4D28_29E9SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:25 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -164,7 +164,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -189,20 +189,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:20 GMT + - Mon, 11 Mar 2024 21:21:26 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A500003C89622340FC.1.1.m_5 + - D0BD851AC14C1895000028314069F8AE.1.1.m_5 NCBI-SID: - - BD11D769E840C2B7_657ESID + - 452BF474A62AD4D4_8223SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=BD11D769E840C2B7_657ESID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:20 GMT + - ncbi_sid=452BF474A62AD4D4_8223SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:26 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -230,7 +230,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -254,20 +254,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:20 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A50000368965BD192F.1.1.m_5 + - 322CFCD26EC09885000052492B99F28C.1.1.m_5 NCBI-SID: - - BA7AA08372DBFA5B_13E4SID + - 3CBEA9D58E5CB1D2_9D51SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=BA7AA08372DBFA5B_13E4SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:21 GMT + - ncbi_sid=3CBEA9D58E5CB1D2_9D51SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:26 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 93b305ae..88d2888f 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/2.28.2 + - python-requests/2.31.0 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 Feb 2024 07:31:17 GMT + - Mon, 11 Mar 2024 21:21:22 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -50,7 +50,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul?start=55181319&end=55181320 response: @@ -64,7 +64,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:17 GMT + - Mon, 11 Mar 2024 21:21:22 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -80,7 +80,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -104,20 +104,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:16 GMT + - Mon, 11 Mar 2024 21:21:22 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A50000628949718316.1.1.m_5 + - D0BD851AC14C1895000025312F867227.1.1.m_5 NCBI-SID: - - 2F921A653A749DFD_6EE3SID + - FDDE2744782CFB95_7232SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=2F921A653A749DFD_6EE3SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:17 GMT + - ncbi_sid=FDDE2744782CFB95_7232SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:22 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -145,7 +145,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -170,20 +170,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:17 GMT + - Mon, 11 Mar 2024 21:21:22 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A5000062894EE9424B.1.1.m_5 + - 939BB8C393EB3495000051352B0274C2.1.1.m_5 NCBI-SID: - - 70A997EB67A84453_801ESID + - BD57D6E9DECB71A1_68D7SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=70A997EB67A84453_801ESID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:18 GMT + - ncbi_sid=BD57D6E9DECB71A1_68D7SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:23 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 4be419e6..b6ff17d9 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/2.28.2 + - python-requests/2.31.0 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 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316466&end=32316467 response: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -69,7 +69,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316467&end=32316467 response: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -99,7 +99,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316465&end=32316466 response: @@ -113,7 +113,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -129,7 +129,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32316467&end=32316468 response: @@ -143,7 +143,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -159,7 +159,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -183,20 +183,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5673E54A8BE50000428839BFCD43.1.1.m_5 + - 322CFCD26EC0988500003C494447D8A5.1.1.m_5 NCBI-SID: - - 67AAAD8049161044_5118SID + - 6B966A414785074D_5D23SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=67AAAD8049161044_5118SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:24 GMT + - ncbi_sid=6B966A414785074D_5D23SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:31 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -224,7 +224,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -249,20 +249,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:24 GMT + - Mon, 11 Mar 2024 21:21:31 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5673E54A8BE500002E883BE24A8B.1.1.m_5 + - D0BD851AC14C189500003231556FB088.1.1.m_5 NCBI-SID: - - 494214AB6C2024F6_B661SID + - 871F39FE5D993665_56C5SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=494214AB6C2024F6_B661SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:25 GMT + - ncbi_sid=871F39FE5D993665_56C5SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:32 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 2ceb71e5..97105a88 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/2.28.2 + - python-requests/2.31.0 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 Feb 2024 07:31:21 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331092&end=32331094 response: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:21 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -69,7 +69,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331094&end=32331094 response: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:21 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -99,7 +99,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331093&end=32331094 response: @@ -113,7 +113,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:21 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -129,7 +129,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331092&end=32331093 response: @@ -143,7 +143,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:21 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -159,7 +159,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331091&end=32331092 response: @@ -173,7 +173,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -189,7 +189,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331090&end=32331091 response: @@ -203,7 +203,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -219,7 +219,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331089&end=32331090 response: @@ -233,7 +233,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -249,7 +249,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331088&end=32331089 response: @@ -263,7 +263,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -279,7 +279,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331087&end=32331088 response: @@ -293,7 +293,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -309,7 +309,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331086&end=32331087 response: @@ -323,7 +323,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -339,7 +339,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331085&end=32331086 response: @@ -353,7 +353,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -369,7 +369,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331084&end=32331085 response: @@ -383,7 +383,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -399,7 +399,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331083&end=32331084 response: @@ -413,7 +413,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -429,7 +429,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331083 response: @@ -443,7 +443,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -459,7 +459,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331081&end=32331082 response: @@ -473,7 +473,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -489,7 +489,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331094&end=32331095 response: @@ -503,7 +503,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -519,7 +519,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 method: GET uri: http://localhost:5000/seqrepo/1/sequence/ga4gh:SQ._0wi-qoDrvram155UmcSC-zA5ZK4fpLT?start=32331082&end=32331094 response: @@ -533,7 +533,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -549,7 +549,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -573,20 +573,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:21 GMT + - Mon, 11 Mar 2024 21:21:27 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A500005E896ACACF1F.1.1.m_5 + - D0BD851AC14C18950000393147BE4CE2.1.1.m_5 NCBI-SID: - - 97ACF1D2D5A114F9_1396SID + - 5853A8146278684D_2189SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=97ACF1D2D5A114F9_1396SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:21 GMT + - ncbi_sid=5853A8146278684D_2189SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:28 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -594,7 +594,7 @@ interactions: X-RateLimit-Limit: - '3' X-RateLimit-Remaining: - - '1' + - '2' X-UA-Compatible: - IE=Edge X-XSS-Protection: @@ -614,7 +614,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -638,20 +638,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:22 GMT + - Mon, 11 Mar 2024 21:21:28 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - D0BD5673E54A8BE500004D88316ED359.1.1.m_5 + - D0BD851AC14C18950000413149C0245C.1.1.m_5 NCBI-SID: - - 860499C848FAF975_EF3FSID + - 02EFD13408F7159A_FFF2SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=860499C848FAF975_EF3FSID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:22 GMT + - ncbi_sid=02EFD13408F7159A_FFF2SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:28 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -679,7 +679,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -704,20 +704,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:23 GMT + - Mon, 11 Mar 2024 21:21:29 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A50000558971255303.1.1.m_5 + - 322CFCD26EC09885000058493B468457.1.1.m_5 NCBI-SID: - - 675FB4D79FE04D06_FE55SID + - 139990C564E81E74_BE4FSID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=675FB4D79FE04D06_FE55SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:23 GMT + - ncbi_sid=139990C564E81E74_BE4FSID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:29 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -745,7 +745,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -769,20 +769,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:23 GMT + - Mon, 11 Mar 2024 21:21:30 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A500005A8973EEEAC9.1.1.m_5 + - 322CFCD26EC098850000354940E77BC7.1.1.m_5 NCBI-SID: - - 77ED135DEA0F9216_C267SID + - CD04062346A2F11F_DF44SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=77ED135DEA0F9216_C267SID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:23 GMT + - ncbi_sid=CD04062346A2F11F_DF44SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:30 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 3676030a..dc0baf82 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/2.28.2 + - python-requests/2.31.0 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 Feb 2024 07:31:14 GMT + - Mon, 11 Mar 2024 21:21:17 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -39,7 +39,7 @@ interactions: Connection: - keep-alive User-Agent: - - python-requests/2.28.2 + - python-requests/2.31.0 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: @@ -63,20 +63,20 @@ interactions: Content-Type: - text/plain Date: - - Mon, 19 Feb 2024 07:31:16 GMT + - Mon, 11 Mar 2024 21:21:21 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 322CF705C067C1A50000158944465C93.1.1.m_5 + - 939BB8C393EB349500002A352803F722.1.1.m_5 NCBI-SID: - - 04E0C48AA9C209F7_3DDESID + - 639F2F2ECDBC5B06_3AC1SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=04E0C48AA9C209F7_3DDESID; domain=.nih.gov; path=/; expires=Wed, 19 - Feb 2025 07:31:16 GMT + - ncbi_sid=639F2F2ECDBC5B06_3AC1SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:21 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 f9ad64ff..c37d8e4b 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 @@ -1,88 +1,4 @@ interactions: -- request: - body: null - headers: - Accept: - - '*/*' - Accept-Encoding: - - gzip, deflate - Connection: - - keep-alive - User-Agent: - - python-requests/2.31.0 - 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 - 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text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 17:17:56 GMT + - Mon, 11 Mar 2024 21:21:36 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -137,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 17:17:56 GMT + - Mon, 11 Mar 2024 21:21:36 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -167,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 17:17:56 GMT + - Mon, 11 Mar 2024 21:21:36 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -197,7 +113,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 17:17:56 GMT + - Mon, 11 Mar 2024 21:21:36 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -227,7 +143,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 17:17:56 GMT + - Mon, 11 Mar 2024 21:21:36 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -257,7 +173,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - 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text/plain Date: - - Thu, 22 Feb 2024 17:17:59 GMT + - Mon, 11 Mar 2024 21:21:37 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B247C4D7BE0F500005AC9A142192D.1.1.m_5 + - 322CFCD26EC09885000062496D69004E.1.1.m_5 NCBI-SID: - - DD7E32BFC75A3A29_2025SID + - 83659F4CFCC93AC3_72C0SID Referrer-Policy: - origin-when-cross-origin Server: - Finatra Set-Cookie: - - ncbi_sid=DD7E32BFC75A3A29_2025SID; domain=.nih.gov; path=/; expires=Sat, 22 - Feb 2025 17:18:00 GMT + - ncbi_sid=83659F4CFCC93AC3_72C0SID; domain=.nih.gov; path=/; expires=Tue, 11 + Mar 2025 21:21:37 GMT Strict-Transport-Security: - max-age=31536000; includeSubDomains; preload Transfer-Encoding: @@ -428,20 +344,20 @@ interactions: Content-Type: - text/plain Date: - - Thu, 22 Feb 2024 17:18:00 GMT + - Mon, 11 Mar 2024 21:21:38 GMT Keep-Alive: - timeout=4, max=40 NCBI-PHID: - - 939B247C4D7BE0F5000044C9A8CCAD75.1.1.m_5 + - 322CFCD26EC098850000444971137956.1.1.m_5 NCBI-SID: - - C12E8A945D8F2E08_3217SID + - C9FD64A84A1A879F_95E6SID Referrer-Policy: - 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max-age=31536000; includeSubDomains; preload Transfer-Encoding: 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 e4d48088..d3800f36 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 @@ -23,7 +23,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 19:17:58 GMT + - Mon, 11 Mar 2024 21:21:39 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -53,7 +53,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 19:17:58 GMT + - Mon, 11 Mar 2024 21:21:39 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -83,7 +83,7 @@ interactions: Content-Type: - text/plain; charset=utf-8 Date: - - Thu, 22 Feb 2024 19:17:58 GMT + - Mon, 11 Mar 2024 21:21:39 GMT Server: - Werkzeug/2.2.2 Python/3.10.4 status: @@ -113,7 +113,7 @@ interactions: Content-Type: - 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close + Content-Length: + - '1035' + Content-Type: + - application/json + Date: + - Thu, 22 Feb 2024 15:20:08 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +- request: + body: null + headers: + Accept: + - '*/*' + Accept-Encoding: + - gzip, deflate + Connection: + - keep-alive + User-Agent: + - python-requests/2.31.0 + 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: + - Thu, 22 Feb 2024 15:20:08 GMT + Server: + - Werkzeug/2.2.2 Python/3.10.4 + status: + code: 200 + message: OK +version: 1 diff --git a/tests/extras/test_allele_translator.py b/tests/extras/test_allele_translator.py index a7b93b8e..9c1c67b9 100644 --- a/tests/extras/test_allele_translator.py +++ b/tests/extras/test_allele_translator.py @@ -10,7 +10,6 @@ def tlr(rest_dataproxy): data_proxy=rest_dataproxy, default_assembly_name="GRCh38", identify=False, - normalize=False, ) @@ -185,19 +184,18 @@ def tlr(rest_dataproxy): @pytest.mark.vcr def test_from_beacon(tlr): - tlr.normalize = False - assert tlr._from_beacon(snv_inputs["beacon"]).model_dump(exclude_none=True) == snv_output + assert tlr._from_beacon(snv_inputs["beacon"], do_normalize=False).model_dump(exclude_none=True) == snv_output @pytest.mark.vcr def test_from_gnomad(tlr): - tlr.normalize = False - assert tlr._from_gnomad(snv_inputs["gnomad"]).model_dump(exclude_none=True) == snv_output - assert tlr._from_gnomad(deletion_inputs["gnomad"]).model_dump(exclude_none=True) == gnomad_deletion_output - assert tlr._from_gnomad(insertion_inputs["gnomad"]).model_dump(exclude_none=True) == gnomad_insertion_output - assert tlr._from_gnomad(duplication_inputs["gnomad"]).model_dump(exclude_none=True) == duplication_output + do_normalize = False + assert tlr._from_gnomad(snv_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output + assert tlr._from_gnomad(deletion_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == gnomad_deletion_output + assert tlr._from_gnomad(insertion_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == gnomad_insertion_output + assert tlr._from_gnomad(duplication_inputs["gnomad"], do_normalize=do_normalize).model_dump(exclude_none=True) == duplication_output - tlr.normalize = True + # do_normalize defaults to true assert tlr._from_gnomad(snv_inputs["gnomad"]).model_dump(exclude_none=True) == snv_output assert tlr._from_gnomad(deletion_inputs["gnomad"]).model_dump(exclude_none=True) == deletion_output_normalized assert tlr._from_gnomad(insertion_inputs["gnomad"]).model_dump(exclude_none=True) == insertion_output @@ -232,27 +230,27 @@ def test_from_gnomad(tlr): @pytest.mark.vcr def test_from_hgvs(tlr): - tlr.normalize = False - assert tlr._from_hgvs(snv_inputs["hgvs"]).model_dump(exclude_none=True) == snv_output - assert tlr._from_hgvs(deletion_inputs["hgvs"]).model_dump(exclude_none=True) == deletion_output - assert tlr._from_hgvs(insertion_inputs["hgvs"]).model_dump(exclude_none=True) == insertion_output - assert tlr._from_hgvs(duplication_inputs["hgvs"]).model_dump(exclude_none=True) == duplication_output + do_normalize = False + assert tlr._from_hgvs(snv_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output + assert tlr._from_hgvs(deletion_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == deletion_output + assert tlr._from_hgvs(insertion_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == insertion_output + assert tlr._from_hgvs(duplication_inputs["hgvs"], do_normalize=do_normalize).model_dump(exclude_none=True) == duplication_output @pytest.mark.vcr def test_from_spdi(tlr): - tlr.normalize = False - assert tlr._from_spdi(snv_inputs["spdi"]).model_dump(exclude_none=True) == snv_output + do_normalize = False + assert tlr._from_spdi(snv_inputs["spdi"], do_normalize=do_normalize).model_dump(exclude_none=True) == snv_output for spdi_del_expr in deletion_inputs["spdi"]: - assert tlr._from_spdi(spdi_del_expr).model_dump(exclude_none=True) == deletion_output, spdi_del_expr + assert tlr._from_spdi(spdi_del_expr, do_normalize=do_normalize).model_dump(exclude_none=True) == deletion_output, spdi_del_expr for spdi_ins_expr in insertion_inputs["spdi"]: - assert tlr._from_spdi(spdi_ins_expr).model_dump(exclude_none=True) == insertion_output, spdi_ins_expr - assert tlr._from_spdi(duplication_inputs["spdi"]).model_dump(exclude_none=True) == duplication_output + assert tlr._from_spdi(spdi_ins_expr, do_normalize=do_normalize).model_dump(exclude_none=True) == insertion_output, spdi_ins_expr + assert tlr._from_spdi(duplication_inputs["spdi"], do_normalize=do_normalize).model_dump(exclude_none=True) == duplication_output @pytest.mark.vcr def test_to_spdi(tlr): - tlr.normalize = True + # do_normalize defaults to true spdiexpr = snv_inputs["spdi"] allele = tlr.translate_from(spdiexpr, "spdi") to_spdi = tlr.translate_to(allele, "spdi") @@ -369,33 +367,33 @@ def test_to_spdi(tlr): 'type': 'Allele'}), ("NC_000019.10:g.289464_289465insCACA", {'digest': 'YFUR4oR_84b-rRFf0UzOjfI4eE5FTKAP', - 'id': 'ga4gh:VA.YFUR4oR_84b-rRFf0UzOjfI4eE5FTKAP', - 'type': 'Allele', - 'location': {'digest': 'L145KFLJeJ334YnOVm59pPlbdqfHhgXZ', - 'end': 289466, - 'id': 'ga4gh:SL.L145KFLJeJ334YnOVm59pPlbdqfHhgXZ', - 'sequenceReference': {'refgetAccession': 'SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl', - 'type': 'SequenceReference'}, - 'start': 289464, - 'type': 'SequenceLocation'}, - 'state': {'length': 6, - 'repeatSubunitLength': 2, - 'sequence': 'CACACA', + 'id': 'ga4gh:VA.YFUR4oR_84b-rRFf0UzOjfI4eE5FTKAP', + 'type': 'Allele', + 'location': {'digest': 'L145KFLJeJ334YnOVm59pPlbdqfHhgXZ', + 'end': 289466, + 'id': 'ga4gh:SL.L145KFLJeJ334YnOVm59pPlbdqfHhgXZ', + 'sequenceReference': {'refgetAccession': 'SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl', + 'type': 'SequenceReference'}, + 'start': 289464, + 'type': 'SequenceLocation'}, + 'state': {'length': 6, + 'repeatSubunitLength': 2, + 'sequence': 'CACACA', 'type': 'ReferenceLengthExpression'}}), ("NC_000019.10:g.289485_289500del", {'digest': 'Djc_SwVDFunsArqwUM00PciVaF70VTcU', - 'id': 'ga4gh:VA.Djc_SwVDFunsArqwUM00PciVaF70VTcU', - 'type': 'Allele', - 'location': {'digest': 'WTE7jyihK4qvRRzEqM7u5nSD4iS2k3xp', - 'end': 289501, - 'id': 'ga4gh:SL.WTE7jyihK4qvRRzEqM7u5nSD4iS2k3xp', - 'sequenceReference': {'refgetAccession': 'SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl', - 'type': 'SequenceReference'}, - 'start': 289480, - 'type': 'SequenceLocation'}, - 'state': {'length': 5, - 'repeatSubunitLength': 16, - 'sequence': 'CGAGG', + 'id': 'ga4gh:VA.Djc_SwVDFunsArqwUM00PciVaF70VTcU', + 'type': 'Allele', + 'location': {'digest': 'WTE7jyihK4qvRRzEqM7u5nSD4iS2k3xp', + 'end': 289501, + 'id': 'ga4gh:SL.WTE7jyihK4qvRRzEqM7u5nSD4iS2k3xp', + 'sequenceReference': {'refgetAccession': 'SQ.IIB53T8CNeJJdUqzn9V_JnRtQadwWCbl', + 'type': 'SequenceReference'}, + 'start': 289480, + 'type': 'SequenceLocation'}, + 'state': {'length': 5, + 'repeatSubunitLength': 16, + 'sequence': 'CGAGG', 'type': 'ReferenceLengthExpression'}}), ) @@ -408,7 +406,7 @@ def test_to_spdi(tlr): @pytest.mark.parametrize("hgvsexpr,expected", hgvs_tests) @pytest.mark.vcr def test_hgvs(tlr, hgvsexpr, expected): - tlr.normalize = True + # do_normalize defaults to true tlr.identify = True allele = tlr.translate_from(hgvsexpr, "hgvs") assert allele.model_dump(exclude_none=True) == expected @@ -420,7 +418,7 @@ def test_hgvs(tlr, hgvsexpr, expected): @pytest.mark.vcr def test_rle_seq_limit(tlr): - tlr.normalize = True + # do_normalize defaults to true tlr.identify = True a_dict = { diff --git a/tests/extras/test_cnv_translator.py b/tests/extras/test_cnv_translator.py index 4793058e..edb553d7 100644 --- a/tests/extras/test_cnv_translator.py +++ b/tests/extras/test_cnv_translator.py @@ -10,7 +10,6 @@ def tlr(rest_dataproxy): data_proxy=rest_dataproxy, default_assembly_name="GRCh38", identify=True, - normalize=False, )