GISAID blocking access #58

TKMarkCheng · 2024-11-09T18:46:42Z

I think GISAID has now blocked usage of GISAIDR? A friend of mine has told me that when they tried to download via GISAIDR::download()

they run into Error in matches[[1]][[2]] : subscript out of bounds. When running on debug mode, the error happens at extract_first_match("'(.{5,20})','DownloadSelectionComponent", download_page_text) which returns

<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">\n<html lang=\"en\" translate=\"no\">\n<head>\n<META http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\">\n<meta content=\"IE=EmulateIE8\" http-equiv=\"X-UA-Compatible\">\n<meta content=\"notranslate\" name=\"google\">\n<meta content=\"GISAID actively promotes the sharing of virus sequences, related clinical and epidemiological data associated with human isolates, and geographic and species-specific data associated with avian and other animal isolates.\" name=\"description\">\n<script type=\"text/javascript\">\nvar CKEDITOR_BASEPATH = 'entities/files/js/ckeditor/';\n</script>\n<meta content=\"GISAID, GISAID Initiative, COVID-19, EpiCoV, EpiFlu, EpiRSV, Global Health Security, Real-Time Disease Surveillance\" name=\"keywords\">\n<meta content=\"noindex\" name=\"robots\">\n<style type=\"text/css\">\nbody {\n    margin: 0;\n}\n#c_smn8xy_16n {\n    position: absolute;\n    width: 100%;\n    min-width: auto;\n    height: 100%;\n    margin: auto;\n}\n#c_smn8xy_16o {\n    position: absolute;\n    top: 0px;\n    right: 0px;\n    bottom: 50px;\n    left: 0px;\n    overflow: auto;\n    padding: 0px 0px 0px 0px;\n}\n#c_smn8xy_16q {\n    position: absolute;\n    bottom: 0;\n    left: 0;\n    right: 0;\n    height:  50px;\n}\n</style>\n<title>GISAID Initiative</title>\n<link type=\"text/css\" rel=\"stylesheet\" href=\"/epi3/entities/tmp//static/_smn8xy_be/combined_std.css\">\n<link type=\"text/css\" rel=\"stylesheet\" href=\"/epi3/entities/tmp//static/_smn8xy_bf/combined_std.css\">\n<link type=\"text/css\" rel=\"stylesheet\" href=\"/epi3/entities/tmp//static/_smn8xy_22g/combined_std.css\">\n<script language=\"JavaScript\" type=\"text/javascript\">\nfunction loadScript(u,c) {\n//alert(\"Loading \" + u)\n\tvar s=document.createElement(\"script\");\n\ts.type=\"text/javascript\";\n\tif (s.readyState) {\n\t\ts.onreadystatechange = function() {\n\t\t\tif (s.readyState == \"loaded\" || s.readyState == \"complete\") {\n\t\t\t\ts.onreadystatechange=null;\n\t\t\t\tc();\n\t\t\t}\n\t\t};\n\t} else {\n\t\ts.onload = function() {\n\t\t\tc()\n\t\t}\n\t};\n\ts.src = u;\n\tdocument.getElementsByTagName(\"head\")[0].appendChild(s)\n};\n\nvar full_page_load_responses = [];\n\nloadScript(\"/epi3/entities/files/js/sys.js?no_cache=1731089165.92\",function(){sys[\"SID\"] = \"36E666TGEBYM1BOTU3ZI1R2ACO6IVV9R\";sys[\"WID\"] = \"wid_smn8xy_qur\";sys[\"PID\"] = \"pid_smn8xy_qus\";sys[\"UID\"] = \"\";sys[\"is_development_mode\"] = false;sys[\"testrunner_active\"] = false;sys[\"page_name\"] = \"\";sys[\"msgs\"] = new Object({'txt_disable_popupblocker':' Please disable popup-blocker!'});loadScript(\"/epi3/entities/tmp//static/_smn8xy_bc/combined_std.js\",function(){loadScript(\"/epi3/entities/tmp//static/_smn8xy_1i7/combined_std.js\",function(){loadScript(\"/epi3/entities/tmp//static/_smn8xy_22f/combined_std.js\",function(){if(document.readyState=='loaded'||document.readyState=='complete'){sys.handleDomReady();}else{window.onload=sys.handleDomReady;}});});});sys.onPageInit(function(){sys.createComponent('c_smn8xy_16p','CaptchaComponent',new Object({'buttons':'c_smn8xy_16q-c_smn8xy_16p','__main__':'c_smn8xy_16p-c_smn8xy_16p'}),\"FormComponent\",\"\",function(){this.getForm().createFI('ce_smn8xy_mu','Fieldset100Widget','ce_smn8xy_mu',function(){this.getForm().createFI('ce_smn8xy_mv','InfoWidget','ce_smn8xy_mv',function(){this.setParams(new Object({'on_change':null,'has_help':false}));}); }); this.getForm().createFI('ce_smn8xy_mw','LinesetWidget','ce_smn8xy_mw',function(){this.getForm().createFI('ce_smn8xy_mx','CaptchaWidget','captcha',function(){this.setParams(new Object({'on_change':null,'has_help':false}));}); this.getForm().createFI('ce_smn8xy_my','EntryWidget','solution',function(){this.setParams(new Object({'on_change':null,'on_exit':false,'has_help':false,'on_return':null}));}); }); this.getForm().createFI('ce_smn8xy_mz','Fieldset100Widget','ce_smn8xy_mz',function(){this.getForm().createFI('ce_smn8xy_n0','InfoWidget','ce_smn8xy_n0',function(){this.setParams(new Object({'on_change':null,'has_help':false}));}); }); this.getForm().createFI('ce_smn8xy_n1','ButtonsWidget','ce_smn8xy_n1',function(){this.getForm().createFI('ce_smn8xy_n2','ButtonWidget','ce_smn8xy_n2',function(){this.setParams(new Object({'on_change':null,'has_help':false,'cmd':'Solve'}));\n }); }); });});sys.onPageInit(function() {new sys.Packer(\"c_smn8xy_16n\", \"c_smn8xy_16o\");new LegacyHandler();\n        var resizeTimer;\n        $(window).resize(function() {\n           clearTimeout(resizeTimer);\n           resizeTimer = setTimeout(sys.handleAfterWindowResize, 100);\n        });\n        sys.showInitiallyHiddens();\n        \n        setTimeout(function() { sys.executeFullPageLoadResponses(); }, 500);\n\t});if(sys[\"testrunner_active\"]){sys.testrunner_activatePage();};\n});\n</script>\n</head>\n<body marginheight=\"0\" marginwidth=\"0\" topmargin=\"0\" leftmargin=\"0\" style=\"text-align:left;\" onbeforeunload=\"sys.handleUnloadPage()\" class=\"yui-skin-sam\">\n<form class=\"sys-form\">\n<input style=\"display:none\" name=\"dummy\" type=\"entry\"><button id=\"sys_focus_button\" type=\"button\"></button>\n<div id=\"sys_devmenu\">\n<img title=\"Clear caches and reload page\" onclick=\"sys.devmenu_reloadApplication(false, null, true)\" style=\"cursor:pointer\" align=\"absmiddle\" src=\"/epi3/entities/files/icons//sys_recache.gif\"><img title=\"Reload page\" onclick=\"sys.devmenu_reloadApplication(false)\" style=\"cursor:pointer\" align=\"absmiddle\" src=\"/epi3/entities/files/icons//sys_reload.gif\"><img title=\"Reload page and reset work setup\" onclick=\"sys.devmenu_reloadApplication(true)\" style=\"cursor:pointer\" align=\"absmiddle\" src=\"/epi3/entities/files/icons//sys_reset.png\"><span id=\"sys_devmenu_info\"></span><img title=\"Run tests\" onclick=\"sys.devmenu_startTestRunner()\" style=\"cursor:pointer;margin-left:5px\" align=\"absmiddle\" src=\"/epi3/entities/files/icons//testrunner_24.png\"></div>\n<div style=\"display:none\" id=\"testrunner_indicator\">\n<img style=\"position:absolute;top:30px;left:30px\" src=\"/epi3/entities/files/icons//testrunner_large.png\"></div>\n<div id=\"sys_curtain\" class=\"sys_curtain\" onclick=\"sys.handleCurtainClick()\"></div>\n<div id=\"sys_timer\" class=\"sys_timer\">\n<div class=\"sys_timer_inner\">\n<img class=\"sys_timer_img\" src=\"/epi3/entities/files/icons//sys_timer.gif\"><div id=\"sys_timer_message\" class=\"sys_timer_message\"></div>\n<div style=\"margin-top:20px\" id=\"sys_timer_gauge\" class=\"sys_timer_gauge\"></div>\n</div>\n</div>\n<div style=\"width: 100%; min-width: auto; margin-left: auto; margin-right: auto\" class=\"page\">\n        \n<div id=\"c_smn8xy_16n\" class=\"packer\">\n            \n<div style=\"top: 0px; right: 0px; bottom: 50px; left: 0px;\" scrollpositions=\",\" id=\"c_smn8xy_16o\" class=\"main container-slot\">\n                \n<div cid=\"c_smn8xy_16p\" class=\"sys-component-slot\" id=\"c_smn8xy_16p-c_smn8xy_16p\">\n<div id=\"ce_smn8xy_mu\">\n<div class=\"sys-form-label\" style=\";;text-align:center\">To confirm your request, please repeat the text to let us know you're human</div>\n<table class=\"sys-form-firow\" style=\"width:98%;\">\n<tr>\n<td colspan=\"2\" rowspan=\"1\">\n\t\t\t\n<div id=\"ce_smn8xy_mv\">\n<div class=\"sys-form-fi-info\" style=\"\">\n     \n</div>\n\n<div class=\"sys-form-fi-message-cnt\">\n<div class=\"sys-form-fi-message\" id=\"ce_smn8xy_mv_msg\"></div>\n</div>\n</div>\t\t\n</td>\n</tr>\n</table>\n</div>\n<div id=\"ce_smn8xy_mw\">\n<table class=\"sys-form-firow\" style=\"width:98%;\">\n<tr>\n<td class=\"sys-form-cfilabel\" colspan=\"1\" rowspan=\"1\" style=\"width:60px\">\n\t\t\n<div class=\"sys-form-filabel sys-form-filabel\"></div>\n\t\n</td><td colspan=\"1\" rowspan=\"1\" style=\"\">\n\t\t\n<table class=\"sys-form-filine\">\n<tr>\n<td class=\"sys-form-filine-td\" colspan=\"1\" rowspan=\"1\" style=\";vertical-align:middle\">\n\t\t\n<div class=\"sys-form-lsfilabel sys-form-filabel\">Repeat</div>\n\t\n</td><td class=\"sys-form-filine-td\" colspan=\"1\" rowspan=\"1\" style=\";vertical-align:middle\">\n\t\t\n<div id=\"ce_smn8xy_mx\">\n<div class=\"sys-form-fi-captcha sys-event-hook\">\n\t\n<img src=\"/epi3/entities/tmp//tmp_2024_11_10_01_52_smn8xy_qut/captcha\">\n</div>\n\n<div class=\"sys-form-fi-message-cnt\">\n<div class=\"sys-form-fi-message\" id=\"ce_smn8xy_mx_msg\"></div>\n</div>\n</div>\t\n</td><td class=\"sys-form-filine-td\" colspan=\"1\" rowspan=\"1\" style=\";vertical-align:middle\">\n\t\t\n<div class=\"sys-form-lsfilabel sys-form-filabel\">here:</div>\n\t\n</td><td class=\"sys-form-filine-td\" colspan=\"1\" rowspan=\"1\" style=\";vertical-align:middle\">\n\t\t\n<div id=\"ce_smn8xy_my\">        \n<div class=\"sys-form-fi-entry\" style=\";width:100px\">\n       \n<div style=\"float:right;padding-left:3px\">\n                       \n</div>\n        \t\n<input class=\"sys-event-hook sys-fi-mark\" id=\"ce_smn8xy_my_entry\" maxlength=\"64\" placeholder=\"\" style=\";\" type=\"text\" value=\"\">\n            \n<div class=\"\" id=\"ce_smn8xy_my_acomplc\"></div>            \n</div>\n    \n<div class=\"sys-form-fi-message-cnt\">\n<div class=\"sys-form-fi-message\" id=\"ce_smn8xy_my_msg\"></div>\n</div>\n    \n</div>\t\n</td>\n</tr>\n</table>\t\n</td>\n</tr>\n</table>\n</div>\n<div id=\"ce_smn8xy_mz\">\n<table class=\"sys-form-firow\" style=\"width:98%;\">\n<tr>\n<td colspan=\"2\" rowspan=\"1\">\n\t\t\t\n<div id=\"ce_smn8xy_n0\">\n<div class=\"sys-form-fi-info\" style=\"\">\n    \n<center>GISAID is committed to an equitable user experience:<br clear=\"none\">Sorry, no robots allowed</center>\n</div>\n\n<div class=\"sys-form-fi-message-cnt\">\n<div class=\"sys-form-fi-message\" id=\"ce_smn8xy_n0_msg\"></div>\n</div>\n</div>\t\t\n</td>\n</tr>\n</table>\n</div>\n</div>\n            \n</div>\n            \n<div style=\"width: 100%; height: 50px;\" id=\"c_smn8xy_16q\" class=\"buttons container-slot\">\n<div cid=\"c_smn8xy_16p\" class=\"sys-component-slot\" id=\"c_smn8xy_16q-c_smn8xy_16p\">\n<div id=\"ce_smn8xy_n1\">\n<div id=\"ce_smn8xy_n2\">\n<div style=\"float: right\">\n\t\n<button class=\"sys-event-hook sys-form-button\" style=\"\" title=\"\" type=\"button\"><img align=\"absmiddle\" class=\"sys-form-button-icon\" src=\"/epi3/entities/files/icons/gnome-icon-theme-2.18.0.jar/gnome-icon-theme-2.18.0/24x24/stock/generic/stock_calc-accept.png\">Continue</button>\n\n</div>\n</div>\n</div>\n</div>\n</div>\n        \n</div>\n    \n</div>\n</form>\n</body>\n</html>\n

keywords being To confirm your request, please repeat the text to let us know you're human which is part of the newly introduced captcha check.

The text was updated successfully, but these errors were encountered:

Wytamma · 2024-11-10T13:08:43Z

Hi @TKMarkCheng - yes GISAID seems to be blocking programmatic access. I’ll try to push some changes to get around this but haven’t had much luck. I think if you log in through the web site you can enter the text into the captcha manually and rerun the GISAIDR script.

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GISAID blocking access #58

GISAID blocking access #58

TKMarkCheng commented Nov 9, 2024

Wytamma commented Nov 10, 2024 •

edited

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GISAID blocking access #58

GISAID blocking access #58

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TKMarkCheng commented Nov 9, 2024

Wytamma commented Nov 10, 2024 • edited Loading

Wytamma commented Nov 10, 2024 •

edited

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