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diegozea / MIToS.jl

A Julia package to analyze protein sequences, structures, and evolutionary information
https://diegozea.github.io/MIToS.jl/stable/
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404 error from function 'getpdbdescription' #59

Closed kool7d closed 3 years ago

kool7d commented 3 years ago

I am getting a 404 error from function 'getpdbdescription'.

` HTTP/1.1 404 Not Found X-Powered-By: Express Strict-Transport-Security: max-age=31536000000; includeSubDomains Cache-Control: private, no-cache, max-age=0, must-revalidate Content-Type: text/html; charset=utf-8 Content-Length: 39674 ETag: W/"9afa-t3cWyFWTs7aO0Iy60YWTWEN5EGo" Vary: Accept-Encoding Date: Thu, 31 Dec 2020 00:07:16 GMT X-Backend-Server: 10.100.50.12

""") in top-level scope at Scratch1.jl:302 in getpdbdescription at MIToS\IWuWP\src\PDB\PDBMLParser.jl:269 in #getpdbdescription#36 at MIToS\IWuWP\src\PDB\PDBMLParser.jl:269 in downloadpdbheader at MIToS\IWuWP\src\PDB\PDBMLParser.jl:244 in #downloadpdbheader#35 at MIToS\IWuWP\src\PDB\PDBMLParser.jl:248 in download_file at MIToS\IWuWP\src\Utils\Read.jl:28 in #download_file#3 at MIToS\IWuWP\src\Utils\Read.jl:28 in open at HTTP\IAI92\src\HTTP.jl:348 in #open#6 at HTTP\IAI92\src\HTTP.jl:348 in request##kw at HTTP\IAI92\src\HTTP.jl:314 in #request#4 at HTTP\IAI92\src\HTTP.jl:314 in at HTTP\IAI92\src\RedirectRequest.jl:21 in #request#1 at HTTP\IAI92\src\RedirectRequest.jl:24 in at HTTP\IAI92\src\BasicAuthRequest.jl:21 in #request#1 at HTTP\IAI92\src\BasicAuthRequest.jl:28 in request##kw at HTTP\IAI92\src\MessageRequest.jl:28 in #request#1 at HTTP\IAI92\src\MessageRequest.jl:51 in at HTTP\IAI92\src\RetryRequest.jl:31 in #request#1 at HTTP\IAI92\src\RetryRequest.jl:44 in 56#58##kw at base\error.jl:284 in at base\error.jl:288 in at HTTP\IAI92\src\ExceptionRequest.jl:19 in #request#1 at HTTP\IAI92\src\ExceptionRequest.jl:22`

diegozea commented 3 years ago

Hi! Thanks for pointing it out :) It looks like PDB has deprecated the old REST API: https://data.rcsb.org/migration-guide.html#pdb-file-description. I am looking up into updating it to the new one. I'll keep you posted.

diegozea commented 3 years ago

Hi! https://github.com/diegozea/MIToS.jl/commit/27f2c5b9fe66ae2bfb54a73679b5092529abdb11 should fix that. Note that the output structure has changed. I will publish a new version in a little with this update. Thanks again, Best