On Sun, 16 Jun 2024 15:22:57 +0200 Lucas Nussbaum <lu...@debian.org> wrote: > Source: ncbi-acc-download > Version: 0.2.8-2 > Severity: serious > Justification: FTBFS > Tags: trixie sid ftbfs > User: lu...@debian.org > Usertags: ftbfs-20240615 ftbfs-trixie > > Hi, > > During a rebuild of all packages in sid, your package failed to build > on amd64.
I fixed the failure in Ubuntu with the attached patch and forwarded the patch upstream: https://github.com/kblin/ncbi-acc-download/pull/27 -- Benjamin Drung Debian & Ubuntu Developer
From: Benjamin Drung <benjamin.dr...@canonical.com> Date: Wed, 31 Jul 2024 14:14:16 +0200 Subject: test: set Content-Type header in request mock requests 2.31 requires the `Content-Type` header to be set for `request.iter_content(4096, decode_unicode=True)` to decode the response. Bug-Debian: https://bugs.debian.org/1073450 Bug-Ubuntu: https://launchpad.net/bugs/2075177 Forwarded: https://github.com/kblin/ncbi-acc-download/pull/27 Signed-off-by: Benjamin Drung <benjamin.dr...@canonical.com> --- tests/test_wgs.py | 22 ++++++++++++++++++---- 1 file changed, 18 insertions(+), 4 deletions(-) diff --git a/tests/test_wgs.py b/tests/test_wgs.py index a2ea541..c07310d 100644 --- a/tests/test_wgs.py +++ b/tests/test_wgs.py @@ -84,7 +84,11 @@ def test_download_wgs_parts_no_biopython(): def test_download_wgs_parts_wgs(req): cfg = Config(format="genbank") wgs_contig = open(full_path('wgs.gbk'), 'rt') - req.get(ENTREZ_URL, body=open(full_path('wgs_full.gbk'), 'rt')) + req.get( + ENTREZ_URL, + body=open(full_path('wgs_full.gbk'), 'rb'), + headers={"Content-Type": "text/plain; charset=UTF-8"}, + ) outhandle = wgs.download_wgs_parts(wgs_contig, cfg) wgs_full = open(full_path('wgs_full.gbk'), 'rt') @@ -98,7 +102,10 @@ def test_download_wgs_parts_wgs_retry(req): wgs_contig = open(full_path('wgs.gbk'), 'rt') req.get(ENTREZ_URL, response_list=[ {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, - {"body": open(full_path('wgs_full.gbk'), 'rt')}, + { + "body": open(full_path('wgs_full.gbk'), 'rb'), + "headers": {"Content-Type": "text/plain; charset=UTF-8"}, + }, ]) outhandle = wgs.download_wgs_parts(wgs_contig, cfg) @@ -123,7 +130,11 @@ def test_download_wgs_parts_wgs_scafld(req): def test_download_wgs_parts_supercontig(req): cfg = Config(format="genbank") supercontig = open(full_path('supercontig.gbk'), 'rt') - req.get(ENTREZ_URL, body=open(full_path('supercontig_full.gbk'), 'rt')) + req.get( + ENTREZ_URL, + body=open(full_path('supercontig_full.gbk'), 'rb'), + headers={"Content-Type": "text/plain; charset=UTF-8"}, + ) outhandle = wgs.download_wgs_parts(supercontig, cfg) supercontig_full = open(full_path('supercontig_full.gbk'), 'rt') @@ -137,7 +148,10 @@ def test_download_wgs_parts_supercontig_retry(req): supercontig = open(full_path('supercontig.gbk'), 'rt') req.get(ENTREZ_URL, response_list=[ {"text": u'Whoa, slow down', "status_code": 429, "headers": {"Retry-After": "0"}}, - {"body": open(full_path('supercontig_full.gbk'), 'rt')} + { + "body": open(full_path('supercontig_full.gbk'), 'rb'), + "headers": {"Content-Type": "text/plain; charset=UTF-8"}, + }, ]) outhandle = wgs.download_wgs_parts(supercontig, cfg)
