Graphpad prism v8 - Githubissues

JamesYates commented 4 years ago

I've tried to read tables from graphpad prism version 8 using pzfx. I get and error that suggests the xml isn't interpretable. If I export the tables from prism into xml format then all is fine. Is there a fix for this?

Error in doc_parse_file(con, encoding = encoding, as_html = as_html, options = options) : Start tag expected, '<' not found [4]

Yue-Jiang commented 4 years ago

Hi! Thanks for reporting. I suspect it's more nuanced than an issue with version 8, since I just created a small file with 8.4.3 and it imports fine. Would you be able to share a small example file that fails to import to help me trouble shoot? Can email me privately if you don't want to attach it here.

JamesYates commented 4 years ago

Hello

Thanks for the prompt reply

Attached is an example file based upon the one I was having issues with. I have checked and it won’t import into R

Regards

James

From: Yue Jiang notifications@github.com Sent: 01 July 2020 15:36 To: Yue-Jiang/pzfx pzfx@noreply.github.com Cc: Yates, James James.Yates@astrazeneca.com; Author author@noreply.github.com Subject: Re: [Yue-Jiang/pzfx] Graphpad prism v8 (#8)

Hi! Thanks for reporting. I suspect it's more nuanced than an issue with version 8, since I just created a small file with 8.4.3 and it imports fine. Would you be able to share a small example file that fails to import to help me trouble shoot? Can email me privately if you don't want to attach it here.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Yue-Jiang/pzfx/issues/8#issuecomment-652456888, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN5BO65WKK52B52DBRUGJ7LRZNCWRANCNFSM4ONOTR7A.

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Yue-Jiang commented 4 years ago

Looking at the file you sent me, I suspect it's not a valid .pzfx file, but rather a .pzf file, even though the file extension suggests otherwise. .pzf is an older version of GraphPad Prism output format, which is not XML hence not really parsable, causing the error. However, the file can be opened with GraphPad Prism 8.4.3, and when I save it as .pzfx I'm able to import it into R using read_pzfx().

Yue-Jiang commented 4 years ago

This doc contains more info on the XML specification of .pzfx format. This R package assumes the input .pzfx file follows these specifications. https://www.graphpad.com/support/faq/prism-integrated-saves-prism-files-instruments/

JamesYates commented 4 years ago

Hello

So simple! Thanks for looking into this

James

From: Yue Jiang notifications@github.com Sent: 04 July 2020 03:37 To: Yue-Jiang/pzfx pzfx@noreply.github.com Cc: Yates, James James.Yates@astrazeneca.com; Author author@noreply.github.com Subject: Re: [Yue-Jiang/pzfx] Graphpad prism v8 (#8)

Looking at the file you sent me, I suspect it's not a valid .pzfx file, but rather a .pzf file, even though the file extension suggests otherwise. .pzf is an older version of GraphPad Prism output format, which is not XML hence not really parsable, causing the error. However, the file can be opened with GraphPad Prism 8.4.3, and when I save it as .pzfx I'm able to import it into R using read_pzfx().

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/Yue-Jiang/pzfx/issues/8#issuecomment-653710736, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AN5BO66M6DH47HJTKNSF33DRZ2IWFANCNFSM4ONOTR7A.

AstraZeneca UK Limited is a company incorporated in England and Wales with registered number:03674842 and its registered office at 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA.

This e-mail and its attachments are intended for the above named recipient only and may contain confidential and privileged information. If they have come to you in error, you must not copy or show them to anyone; instead, please reply to this e-mail, highlighting the error to the sender and then immediately delete the message. For information about how AstraZeneca UK Limited and its affiliates may process information, personal data and monitor communications, please see our privacy notice at www.astrazeneca.comhttps://www.astrazeneca.com

Yue-Jiang / pzfx

Graphpad prism v8 #8