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Derek furst/doi forwarding #1022

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0ad0f8b
Merge pull request #1019 from hubmapconsortium/Derek-Furst/retracted-…
yuanzhou Jun 11, 2026
3e2f6f2
Update VERSION
yuanzhou Jun 11, 2026
190dc15
pushing dummy doi-redirects.tsv for testing
DerekFurstPitt Jun 29, 2026
94d0951
wip, testing redirect with a valid url
DerekFurstPitt Jul 1, 2026
985b42f
updated test tsv file to have real hubmap_ids and redirect links that…
DerekFurstPitt Jul 1, 2026
f254656
fixed redirect urls in test tsv
DerekFurstPitt Jul 1, 2026
f8993c4
moved placeholder tsv file and renamed. added 57 new hubmap ids that …
DerekFurstPitt Jul 13, 2026
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2 changes: 1 addition & 1 deletion VERSION
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Original file line number Diff line number Diff line change
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2.6.17
2.6.18
61 changes: 61 additions & 0 deletions doi-pages/doi-redirect.tsv
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Original file line number Diff line number Diff line change
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hubmap_id landing_page_to_register data_information_page doi
HBM377.WFSM.936 test_landing_page1 https://purl.humanatlas.io/omap/1-human-lymph-node-ibex/v1. https://doi.org/10.35079/HBM377.WFSM.936
HBM522.KQLL.594 test_landing_page2 https://purl.humanatlas.io/asct-b/lymph-vasculature/v1.5 https://doi.org/10.35079/HBM522.KQLL.594
HBM838.CHFF.356 test_landing_page3 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM528.GWLG.472 test_landing_page4 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM286.QFNP.554 test_landing_page4 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM846.LZCV.363 test_landing_page5 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM663.DHKQ.865 test_landing_page6 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM629.BDQB.527 test_landing_page7 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM676.GTXH.329 test_landing_page8 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM653.SJPF.374 test_landing_page9 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM656.ZKVH.979 test_landing_page10 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM957.HKNH.796 test_landing_page11 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM639.WWMD.883 test_landing_page12 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM683.KXSC.925 test_landing_page13 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM353.CWQW.535 test_landing_page14 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM425.GDQX.743 test_landing_page15 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM646.WTZK.555 test_landing_page16 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM722.FWCH.887 test_landing_page17 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM284.KHZR.923 test_landing_page18 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM999.RGNX.353 test_landing_page19 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM236.WBVX.927 test_landing_page20 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM387.GWMM.369 test_landing_page21 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM283.JWPZ.657 test_landing_page22 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM678.SJXK.375 test_landing_page23 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM744.HXCC.628 test_landing_page24 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM523.FTSL.294 test_landing_page25 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM428.VFLB.998 test_landing_page26 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM646.LHSJ.765 test_landing_page27 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM226.CSDM.832 test_landing_page28 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM673.QFPX.636 test_landing_page29 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM967.WHNN.233 test_landing_page30 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM638.XQKL.755 test_landing_page31 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM428.HCDN.258 test_landing_page32 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM765.TCFP.373 test_landing_page33 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM698.RZDG.587 test_landing_page34 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM974.DJSV.344 test_landing_page35 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM443.ZFRL.298 test_landing_page36 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM858.WBVC.362 test_landing_page37 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM298.LDDB.387 test_landing_page38 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM253.VXLN.367 test_landing_page39 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM556.VHXG.898 test_landing_page40 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM674.XVGG.736 test_landing_page41 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM749.SCVF.253 test_landing_page42 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM425.QWWF.933 test_landing_page43 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM837.HCJN.829 test_landing_page44 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM288.RSVK.723 test_landing_page45 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM346.DFPP.785 test_landing_page46 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM646.NHKK.829 test_landing_page47 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM577.XHHB.694 test_landing_page48 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM449.BMVS.455 test_landing_page49 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM737.CVZK.963 test_landing_page50 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM244.DLVB.376 test_landing_page51 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM589.XHFM.629 test_landing_page52 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM442.NPRG.337 test_landing_page53 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM769.WSLR.852 test_landing_page54 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM447.MXVB.286 test_landing_page55 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM585.JSKG.833 test_landing_page56 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM437.GKTS.458 test_landing_page57 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM965.PTTW.982 test_landing_page58 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
HBM854.FKSW.462 test_landing_page59 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
42 changes: 25 additions & 17 deletions src/app.py
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Expand Up @@ -265,29 +265,37 @@ def http_internal_server_error(e):
## sets the reference_redirects dict which is used
## by the /redirect method below
try:
csv_reader_list = []
reference_redirects = {}
url = app.config['REDIRECTION_INFO_URL']
url2 = app.config['SECONDARY_REDIRECTION_INFO_URL']
# Use Memcached to improve performance
response = schema_manager.make_request_get(url)
resp_txt = response.content.decode('utf-8')
cr = csv.reader(resp_txt.splitlines(), delimiter='\t')

first = True
id_column = None
redir_url_column = None
for row in cr:
if first:
first = False
header = row
column = 0
for label in header:
if label == 'hubmap_id': id_column = column
if label == 'data_information_page': redir_url_column = column
column = column + 1
if id_column is None: raise Exception(f"Column hubmap_id not found in {url}")
if redir_url_column is None: raise Exception (f"Column data_information_page not found in {url}")
else:
reference_redirects[row[id_column].upper().strip()] = row[redir_url_column]
csv_reader_list.append(cr)
response2 = schema_manager.make_request_get(url2)
resp_txt2 = response2.content.decode('utf-8')
cr2 = csv.reader(resp_txt2.splitlines(), delimiter='\t')
csv_reader_list.append(cr2)

for csv_reader in csv_reader_list:
first = True
id_column = None
redir_url_column = None
for row in csv_reader:
if first:
first = False
header = row
column = 0
for label in header:
if label == 'hubmap_id': id_column = column
if label == 'data_information_page': redir_url_column = column
column = column + 1
if id_column is None: raise Exception(f"Column hubmap_id not found in {url}")
if redir_url_column is None: raise Exception (f"Column data_information_page not found in {url}")
else:
reference_redirects[row[id_column].upper().strip()] = row[redir_url_column]
rr = redirect('abc', code = 307)
print(rr)
except Exception:
Expand Down
2 changes: 2 additions & 0 deletions src/instance/app.cfg.example
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Expand Up @@ -84,4 +84,6 @@ DOI_REDIRECT_URL = 'https://portal.hubmapconsortium.org/browse/<entity_type>/<id
# OLD: https://raw.githubusercontent.com/hubmapconsortium/ccf-releases/main/reference-entity-ids.tsv
# New URL in use since 7/2/2024 following the HRA 2.1 release
REDIRECTION_INFO_URL = 'https://cdn.humanatlas.io/digital-objects/reference-entity-ids.tsv'
#Replace with correct branch in the url for secondary redirection info url
SECONDARY_REDIRECTION_INFO_URL = #'https://raw.githubusercontent.com/hubmapconsortium/entity-api/refs/heads/<branch>/doi-pages/doi-redirect.tsv'

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