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petermr / CEVOpen

Contentmining of Open phytochemical literature for medicinal activities
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Unable to pull the latest commits due to file name error #59

Closed deadlyvices closed 4 years ago

deadlyvices commented 4 years ago

I get this when I try to pull down the most recent changes using git: E:\source\repos\CEVOpen [master ↓59 ↑1]> git pull fatal: cannot create directory at 'articleAnalysis/oil186/raw/Example_Table_Images/APA/Anti-Bacterial — MIC, DD:IZ': Invalid argument

Can someone please change the name of the offending folder so it works on Windows? it's the ':' that's causing the problem: Windows interprets this as a file stream. Until this is done, I'm unable to do any commits.

deadlyvices commented 4 years ago

I also think that leaving commas and other punctuation characters out of filenames would greatly help portability!

MikeWilliams-UK commented 4 years ago

It's probably wise to follow the rules listed here https://docs.microsoft.com/en-us/windows/win32/fileio/naming-a-file

MikeWilliams-UK commented 4 years ago

This article has a simpler to read list, but I think it equates to the same thing https://stackoverflow.com/questions/1976007/what-characters-are-forbidden-in-windows-and-linux-directory-names I think the second answer (with 433 votes at present) i easiest to read

ambarishK commented 4 years ago

Hello manny sir!

It needs to rename the files which you have committed. There is an issue while git pull. For example - ./articleAnalysis/oil186/raw/Example_Table_Images/APA/Anti-Bacterial — MIC, DD:IZ/Anti-bacterial — MEO, DEO, .textClipping

petermr commented 4 years ago

Please be specific if possible. Which files?

On Wed, Nov 20, 2019 at 4:38 PM Ambarish Kumar notifications@github.com wrote:

Hello many sir!

It needs to rename the files which you have committed. There is an issue while git pull.

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petermr commented 4 years ago

filenames

The filenames have to work on a variety of Operating systems. The main problems (to avoid) are:

Recommended characters: a-z0-9_

Use '.' only for suffix

I think the current problems are caused by Manny's commits - @mannyrules you will have to change your filenames and recommit.

MikeWilliams-UK commented 4 years ago

I would say do NOT use file names or folders which differ only by case.

MikeWilliams-UK commented 4 years ago

It will also be wise to keep the total path to less than 260 characters (including path separator) as some parts of the Windows OS still have this limit.

Also cloning your repo to C:\Dev\Project also helps to shorten file paths.

deadlyvices commented 4 years ago

Can I suggest a simple rule? Stick to:

So any filename that matches the regex [a-z0-9._-]+ should be right as rain

MikeWilliams-UK commented 4 years ago

A bit more complex that filenames that begin with a single dot should be avoided. Filenames with two consecutive dots next to a path separator are not permitted.

petermr commented 4 years ago

I think we have all said essentially the same thing. Good

EmanuelFaria commented 4 years ago

Hello manny sir!

It needs to rename the files which you have committed. There is an issue while git pull. For example - ./articleAnalysis/oil186/raw/Example_Table_Images/APA/Anti-Bacterial — MIC, DD:IZ/Anti-bacterial — MEO, DEO, .textClipping

Thanks for letting me know. I'll clean these up and repost as soon as possible. That text clipping was not meant to be in there. I just deleted it. Sorry for any confusion.

deadlyvices commented 4 years ago

I'm still getting these issues, and it's now stopping me from working: fatal: cannot create directory at 'articleAnalysis/oil186/raw/Example_Table_Images/GRID/Anti-MICRO?ORGANISM': Invalid argument I use git as much for sharing my work between my home and my work PC, so this is stopping me from doing that.

petermr commented 4 years ago

I will revisit this in 2 hours

On Sun, 24 Nov 2019, 11:42 Clyde Davies, notifications@github.com wrote:

I'm still getting these issues, and it's now stopping me from working: fatal: cannot create directory at 'articleAnalysis/oil186/raw/Example_Table_Images/GRID/Anti-MICRO?ORGANISM': Invalid argument

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/petermr/CEVOpen/issues/59?email_source=notifications&email_token=AAFTCS6RP3YGIHZLKMOFLODQVJSD7A5CNFSM4JPQXZ62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAJLOI#issuecomment-557880761, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFTCS2VJMJGXO4AZ5PMKSLQVJSD7ANCNFSM4JPQXZ6Q .

deadlyvices commented 4 years ago

Thanks.

petermr commented 4 years ago

working on it right now.

On Sun, Nov 24, 2019 at 2:30 PM Clyde Davies notifications@github.com wrote:

Thanks.

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-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

petermr commented 4 years ago

Have now committed a new version. Please check . I think, I have flattened the filenames to minimal character set b ut cannot be absolutely sure as my Mac doesnt complain

On Sun, Nov 24, 2019 at 3:52 PM Peter Murray-Rust < peter.murray.rust@googlemail.com> wrote:

working on it right now.

On Sun, Nov 24, 2019 at 2:30 PM Clyde Davies notifications@github.com wrote:

Thanks.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/petermr/CEVOpen/issues/59?email_source=notifications&email_token=AAFTCS5E2IU5MI5T6CNQWB3QVKFX7A5CNFSM4JPQXZ62YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAMSSA#issuecomment-557893960, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFTCSYGSJKPF77YRMFOTOTQVKFX7ANCNFSM4JPQXZ6Q .

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

-- Peter Murray-Rust Founder ContentMine.org and Reader Emeritus in Molecular Informatics Dept. Of Chemistry, University of Cambridge, CB2 1EW, UK

MikeWilliams-UK commented 4 years ago

Just created a fresh folder on my pc C:\Temp\test git clone https://github.com/petermr/CEVOpen.git worked without a hitch

Well done @petermr