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Merge pull request #1022 from hubmapconsortium/Derek-Furst/doi-forwarding
Derek furst/doi forwarding
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‎doi-pages/doi-redirect.tsv‎

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hubmap_id landing_page_to_register data_information_page doi
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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
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HBM522.KQLL.594 test_landing_page2 https://purl.humanatlas.io/asct-b/lymph-vasculature/v1.5 https://doi.org/10.35079/HBM522.KQLL.594
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HBM838.CHFF.356 test_landing_page3 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM528.GWLG.472 test_landing_page4 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM286.QFNP.554 test_landing_page4 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM846.LZCV.363 test_landing_page5 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM663.DHKQ.865 test_landing_page6 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM629.BDQB.527 test_landing_page7 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM676.GTXH.329 test_landing_page8 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM653.SJPF.374 test_landing_page9 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM656.ZKVH.979 test_landing_page10 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM957.HKNH.796 test_landing_page11 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM639.WWMD.883 test_landing_page12 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM683.KXSC.925 test_landing_page13 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM353.CWQW.535 test_landing_page14 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM425.GDQX.743 test_landing_page15 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM646.WTZK.555 test_landing_page16 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM722.FWCH.887 test_landing_page17 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM284.KHZR.923 test_landing_page18 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM999.RGNX.353 test_landing_page19 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM236.WBVX.927 test_landing_page20 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM387.GWMM.369 test_landing_page21 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM283.JWPZ.657 test_landing_page22 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM678.SJXK.375 test_landing_page23 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM744.HXCC.628 test_landing_page24 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM523.FTSL.294 test_landing_page25 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM428.VFLB.998 test_landing_page26 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM646.LHSJ.765 test_landing_page27 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM226.CSDM.832 test_landing_page28 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM673.QFPX.636 test_landing_page29 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM967.WHNN.233 test_landing_page30 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM638.XQKL.755 test_landing_page31 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM428.HCDN.258 test_landing_page32 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM765.TCFP.373 test_landing_page33 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM698.RZDG.587 test_landing_page34 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM974.DJSV.344 test_landing_page35 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM443.ZFRL.298 test_landing_page36 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM858.WBVC.362 test_landing_page37 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM298.LDDB.387 test_landing_page38 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM253.VXLN.367 test_landing_page39 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM556.VHXG.898 test_landing_page40 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM674.XVGG.736 test_landing_page41 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM749.SCVF.253 test_landing_page42 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM425.QWWF.933 test_landing_page43 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM837.HCJN.829 test_landing_page44 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM288.RSVK.723 test_landing_page45 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM346.DFPP.785 test_landing_page46 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM646.NHKK.829 test_landing_page47 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM577.XHHB.694 test_landing_page48 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM449.BMVS.455 test_landing_page49 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM737.CVZK.963 test_landing_page50 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM244.DLVB.376 test_landing_page51 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM589.XHFM.629 test_landing_page52 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM442.NPRG.337 test_landing_page53 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM769.WSLR.852 test_landing_page54 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM447.MXVB.286 test_landing_page55 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM585.JSKG.833 test_landing_page56 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM437.GKTS.458 test_landing_page57 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM965.PTTW.982 test_landing_page58 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759
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HBM854.FKSW.462 test_landing_page59 https://purl.humanatlas.io/asct-b/main-bronchus/v1.2 https://doi.org/10.35079/HBM467.LMBG.759

‎src/app.py‎

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@@ -265,29 +265,37 @@ def http_internal_server_error(e):
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## sets the reference_redirects dict which is used
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## by the /redirect method below
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try:
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csv_reader_list = []
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reference_redirects = {}
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url = app.config['REDIRECTION_INFO_URL']
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url2 = app.config['SECONDARY_REDIRECTION_INFO_URL']
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# Use Memcached to improve performance
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response = schema_manager.make_request_get(url)
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resp_txt = response.content.decode('utf-8')
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cr = csv.reader(resp_txt.splitlines(), delimiter='\t')
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first = True
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id_column = None
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redir_url_column = None
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for row in cr:
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if first:
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first = False
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header = row
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column = 0
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for label in header:
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if label == 'hubmap_id': id_column = column
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if label == 'data_information_page': redir_url_column = column
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column = column + 1
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if id_column is None: raise Exception(f"Column hubmap_id not found in {url}")
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if redir_url_column is None: raise Exception (f"Column data_information_page not found in {url}")
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else:
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reference_redirects[row[id_column].upper().strip()] = row[redir_url_column]
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csv_reader_list.append(cr)
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response2 = schema_manager.make_request_get(url2)
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resp_txt2 = response2.content.decode('utf-8')
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cr2 = csv.reader(resp_txt2.splitlines(), delimiter='\t')
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csv_reader_list.append(cr2)
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for csv_reader in csv_reader_list:
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first = True
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id_column = None
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redir_url_column = None
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for row in csv_reader:
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if first:
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first = False
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header = row
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column = 0
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for label in header:
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if label == 'hubmap_id': id_column = column
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if label == 'data_information_page': redir_url_column = column
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column = column + 1
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if id_column is None: raise Exception(f"Column hubmap_id not found in {url}")
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if redir_url_column is None: raise Exception (f"Column data_information_page not found in {url}")
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else:
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reference_redirects[row[id_column].upper().strip()] = row[redir_url_column]
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rr = redirect('abc', code = 307)
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print(rr)
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except Exception:

‎src/instance/app.cfg.example‎

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@@ -84,4 +84,6 @@ DOI_REDIRECT_URL = 'https://portal.hubmapconsortium.org/browse/<entity_type>/<id
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# OLD: https://raw.githubusercontent.com/hubmapconsortium/ccf-releases/main/reference-entity-ids.tsv
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# New URL in use since 7/2/2024 following the HRA 2.1 release
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REDIRECTION_INFO_URL = 'https://cdn.humanatlas.io/digital-objects/reference-entity-ids.tsv'
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#Replace with correct branch in the url for secondary redirection info url
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SECONDARY_REDIRECTION_INFO_URL = #'https://raw.githubusercontent.com/hubmapconsortium/entity-api/refs/heads/<branch>/doi-pages/doi-redirect.tsv'
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