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Moving a manuscript from Review --> Copyediting

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Re: Moving a manuscript from Review --> Copyediting

Postby Dan » Wed Jul 09, 2014 11:58 am

I just directly copied and pasted it.
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Re: Moving a manuscript from Review --> Copyediting

Postby asmecher » Wed Jul 09, 2014 12:16 pm

Hi Dan,

OK -- unfortunately as you're finding out this can be really time-consuming to debug remotely. I'd like to figure out definitively where there have been any relevant modifications here. To do this, use the standard "diff" tool. It should already be available on your server. You'll need a "stock" copy of OJS 2.4.4; download the .tar.gz file from the download page and unpack it somewhere in your home directory.

If your stock copy of OJS 2.4.4 is in ~/ojs-2.4.4, and your live version of OJS 2.4.4 is in /var/www/html/ojs, then you can use the following command to generate a .diff file (called "mods.diff"):
Code: Select all
diff -u -r ~/ojs-2.4.4 /var/www/html/ojs > mods.diff
If you're not familiar with how to read .diff files, PM me with the file and I'll take a quick look at it. It's probably the fastest way.

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Tue Jul 29, 2014 6:35 pm

Greetings, Alec --

I'm wondering, when you have a moment, if we should be thinking of a Plan B if we're not able to fix this.

There's the nuclear option, where we just delete the OJS site and start over -- scary but doable -- but I also wanted to ask if it's possible for us to bypass the accept manuscript, copyediting, and proofreading functions that no longer function and upload PDF files of articles somewhere before we "Publish Issue" so that subscribers and readers can access them? Currently we are storing 13 articles in a Dropbox, prior to publication.

Thanks --

Best,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby asmecher » Tue Jul 29, 2014 9:06 pm

Hi Michael,

I sent Dan a message about this yesterday -- it's a file permission problem. He has the details. Otherwise your installation is fine; no need for anything rash.

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Wed Jul 30, 2014 4:07 am

Thank you so much, Alec!

Best,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Fri Sep 05, 2014 10:20 am

Hello, Alec!

We've had no luck on this end -- we haven't been able to upload files since April -- and I'm going to contact our Computer Science Dept. to see if they can help. But one piece of information would help in my request to them: when you and Dan were problem-solving on this forum -- for which, thank you! -- you were focusing on a PHP file. Then, the next I heard, Dan was changing the permissions on a folder, with some help from our ISP. That process led to the site being wiped out, which we were able to restore via a month-old backup.

But when I contact our CS colleagues, I'd like to point them to this forum and tell them how we got from examining the PHP to changing folder permissions. Do you recall how that happened? What led to that problem-solving strategy? That's help me describe the problem to them.

As always, thank you very much, in advance --

Best,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby asmecher » Fri Sep 05, 2014 10:31 am

Hi Michael,

A problem with file permissions was one of my first suspicions. Dan responded that file permissions were already set wide open, so we were forced to dive deeper into the code. When I finally gave up debugging remotely and logged in for myself, the problem did turn out to be file permissions; the foray into PHP code was based on a false assumption.

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Fri Sep 05, 2014 10:41 am

That's perfect. Thanks, Alec -- I can work with that, at least in my request for help to the CS Dept.

What's curious is why it worked fine -- nary a problem -- from 2006 until April of this year.

I'll report back if you like.

Best,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Fri Sep 05, 2014 12:01 pm

Alec, one more thing real quick as I prepare these materials for the CS folks. I asked Dan what the permissions *should* be set at, and he replied:

... some subdirectories are set to 777, others to 755. I don’t really know what the appropriate setting should be… Alec said 755 wouldn’t work, but 777 wasn’t secure enough. My plan was to set it to 777, see how that worked, and figure out security second, but changing ownership to do that made the site spasm.

Do you happen to know what the files directory permissions *should* be set at?

Thanks,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby asmecher » Fri Sep 05, 2014 12:04 pm

Hi Michael,

The numerical permissions are only part of the picture -- you'll also need to know who owns the files and how your server is configured to run PHP scripts. There are gory details in this FAQ entry. Unfortunately there is no one-size-fits-all answer.

Regards,
Alec Smecher
Public Knowledge Project Team
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Fri Sep 05, 2014 12:08 pm

Got it - -thanks, Alec!

You are very patient.
I hope you can stay that way for another week or so!

Best,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby michael_clj » Sun Sep 14, 2014 5:46 pm

Hello, Alec -- a quick update and a question:

I asked our web-hosting company to look at the permissions problems and they responded:

I have changed all the folders to 755 and files to 644 which is what php requires for functioning properly. Persmissions and ownership should not be a problem now.

The issue may be that their site is not compatible with the newer php. You are running php 5.3.28 and it is configured to run as suphp. When running like this, php runs as the user so since the files are owned by the same user, they have full write access to all folders and files.


That seemed to solve to uploading problem right away. I was able to go into OJS and test it, accepting a submission and moving it to copyediting -- the problem we first encountered in April.

But then, when we tried click on any file within the OJS -- a submission, say, or a file selected for copyediting, the server responded with 404 errors and our IP addresses blocked for too many attempts. (Havoc.) We identified an example file that is causing the 404 and blocking problem
http://www.communityliteracy.org/index. ... 239/1221/1. The file exists — we uploaded it and put it there and can see it — http://composing.org/iws-help/file-exists-404-error.jpg.

On that problem, the web-hosting company reports:

This would mean that there needs to be a folder in their public_html called index.php because the url contains /index.php/. Now, in some cases, this could be functional via some kind of rewrite, but that would be uncommon. Also that url doesn't really have a file attached to it unless they uploaded a file named simply 1.

It sounds like they have a problem with their OJS software application. This is a code related problem from what I can see and not a server or hosting issue.


Does this additional information shed any light on the existing issue?

Thank you so much!

Best,
Michael
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Re: Moving a manuscript from Review --> Copyediting

Postby asmecher » Sun Sep 14, 2014 8:25 pm

Hi Michael,

Your hosting company is misreading this -- you can see elsewhere in your OJS that URLs containing ".../index.php/..." are present and working fine (every URL OJS uses will contain this). Technically speaking, this works using a CGI variable called PATH_INFO. All requests to OJS are sent to the main index.php script in your installation directory, and the remainder is used by that script to figure out what part of the system to load.

Regards,
Alec Smecher
Public Knowledge Project Team
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