Problem documents

[CathyHajo]

I am still having trouble with a handful of documents. They are appearing in the digital edition, but I cannot upload corrected versions of them to the site. I edit the files and commit the changes and sync it without problems, but when I try to update the site using Digital Ocean console, I get an error message: "The following untracked working tree files would be overwritten by the merge. Please move or remove them before you can merge."

I've checked the files over and over and there is nothing wrong with them that I can see. Every once in a while a few of them make it through a merge, but generally those same files keep getting bounced.

Right now: 302933.xml 320098.xml 421086.xml 421962.xml 422010.xml 422026.xml

[JonathanReeve]

Git is trying to tell you that there are untracked files in the server not registered with git with git add. It doesn't want to pull in changes that would overwrite those files, because it doesn't like to overwrite files that aren't registered with git, since there's no way to undo the changes. This could be because the app has moved the files from xml_queue to xml_added, and git doesn't recognize those files in xml_added, because they're in a different directory. This is another point for consolidating these directories somehow, since version controlling them all across two directories is a bit of a nightmare. I'll have to think about this a lot more.

You can safely delete any untracked files, since you already have the canonical versions tracked in git. In fact, one thing you can do is delete all the XML files on the server prior to running git reset --hard HEAD and git pull. You can do this by running rm -rf /var/www/html/sanger/xml_*. This will make sure that it doesn't complain about changed files, since you'll just be making a copy of the repository exactly as it exists on GitHub.

On Fri, Jul 17, 2015 at 3:30 PM Cathy Moran Hajo notifications@github.com wrote:

I am still having trouble with a handful of documents. They are appearing in the digital edition, but I cannot upload corrected versions of them to the site. I edit the files and commit the changes and sync it without problems, but when I try to update the site using Digital Ocean console, I get an error message: "The following untracked working tree files would be overwritten by the merge. Please move or remove them before you can merge."

I've checked the files over and over and there is nothing wrong with them that I can see. Every once in a while a few of them make it through a merge, but generally those same files keep getting bounced.

Right now: 302933.xml 320098.xml 421086.xml 421962.xml 422010.xml 422026.xml

— Reply to this email directly or view it on GitHub https://github.com/JonathanReeve/sanger/issues/92.

[CathyHajo]

Hi Jon,

I just tried to delete the files on the server, but got a long string of file names with "cannot remove" "Permission denied" It is not all of them, but I can't really make any sense about which ones it is.

Cathy

Cathy Moran Hajo, Ph.D. Associate Editor/Assistant Director The Margaret Sanger Papers Project New York University, Division of Libraries 838 Broadway, Suite 504 New York, NY 10003-4218 (212) 998-8666 cathy.hajo@nyu.edu

Visit our website at: http://www.nyu.edu/projects/sanger

On Mon, Jul 20, 2015 at 1:26 PM, Jonathan Reeve notifications@github.com wrote:

Git is trying to tell you that there are untracked files in the server not registered with git with git add. It doesn't want to pull in changes that would overwrite those files, because it doesn't like to overwrite files that aren't registered with git, since there's no way to undo the changes. This could be because the app has moved the files from xml_queue to xml_added, and git doesn't recognize those files in xml_added, because they're in a different directory. This is another point for consolidating these directories somehow, since version controlling them all across two directories is a bit of a nightmare. I'll have to think about this a lot more.

You can safely delete any untracked files, since you already have the canonical versions tracked in git. In fact, one thing you can do is delete all the XML files on the server prior to running git reset --hard HEAD and git pull. You can do this by running rm -rf /var/www/html/sanger/xml_*. This will make sure that it doesn't complain about changed files, since you'll just be making a copy of the repository exactly as it exists on GitHub.

On Fri, Jul 17, 2015 at 3:30 PM Cathy Moran Hajo <notifications@github.com

wrote:

I am still having trouble with a handful of documents. They are appearing in the digital edition, but I cannot upload corrected versions of them to the site. I edit the files and commit the changes and sync it without problems, but when I try to update the site using Digital Ocean console, I get an error message: "The following untracked working tree files would be overwritten by the merge. Please move or remove them before you can merge."

I've checked the files over and over and there is nothing wrong with them that I can see. Every once in a while a few of them make it through a merge, but generally those same files keep getting bounced.

Right now: 302933.xml 320098.xml 421086.xml 421962.xml 422010.xml 422026.xml

— Reply to this email directly or view it on GitHub https://github.com/JonathanReeve/sanger/issues/92.

— Reply to this email directly or view it on GitHub https://github.com/JonathanReeve/sanger/issues/92#issuecomment-122960919 .

[CathyHajo]

It looks like the files in the directory are write protected. When I tried to delete some using the console that had *.bak extensions it told me they were write protected and I did not have permission.

Cathy

Cathy Moran Hajo, Ph.D. Associate Editor/Assistant Director The Margaret Sanger Papers Project New York University, Division of Libraries 838 Broadway, Suite 504 New York, NY 10003-4218 (212) 998-8666 cathy.hajo@nyu.edu

Visit our website at: http://www.nyu.edu/projects/sanger

On Tue, Jul 21, 2015 at 11:17 AM, Cathy Moran Hajo cathy.hajo@nyu.edu wrote:

Hi Jon,

I just tried to delete the files on the server, but got a long string of file names with "cannot remove" "Permission denied" It is not all of them, but I can't really make any sense about which ones it is.

Cathy

Cathy Moran Hajo, Ph.D. Associate Editor/Assistant Director The Margaret Sanger Papers Project New York University, Division of Libraries 838 Broadway, Suite 504 New York, NY 10003-4218 (212) 998-8666 cathy.hajo@nyu.edu

Visit our website at: http://www.nyu.edu/projects/sanger

On Mon, Jul 20, 2015 at 1:26 PM, Jonathan Reeve notifications@github.com wrote:

Git is trying to tell you that there are untracked files in the server not registered with git with git add. It doesn't want to pull in changes that would overwrite those files, because it doesn't like to overwrite files that aren't registered with git, since there's no way to undo the changes. This could be because the app has moved the files from xml_queue to xml_added, and git doesn't recognize those files in xml_added, because they're in a different directory. This is another point for consolidating these directories somehow, since version controlling them all across two directories is a bit of a nightmare. I'll have to think about this a lot more.

You can safely delete any untracked files, since you already have the canonical versions tracked in git. In fact, one thing you can do is delete all the XML files on the server prior to running git reset --hard HEAD and git pull. You can do this by running rm -rf /var/www/html/sanger/xml_*. This will make sure that it doesn't complain about changed files, since you'll just be making a copy of the repository exactly as it exists on GitHub.

On Fri, Jul 17, 2015 at 3:30 PM Cathy Moran Hajo < notifications@github.com> wrote:

I am still having trouble with a handful of documents. They are appearing in the digital edition, but I cannot upload corrected versions of them to the site. I edit the files and commit the changes and sync it without problems, but when I try to update the site using Digital Ocean console, I get an error message: "The following untracked working tree files would be overwritten by the merge. Please move or remove them before you can merge."

I've checked the files over and over and there is nothing wrong with them that I can see. Every once in a while a few of them make it through a merge, but generally those same files keep getting bounced.

Right now: 302933.xml 320098.xml 421086.xml 421962.xml 422010.xml 422026.xml

— Reply to this email directly or view it on GitHub https://github.com/JonathanReeve/sanger/issues/92.

— Reply to this email directly or view it on GitHub https://github.com/JonathanReeve/sanger/issues/92#issuecomment-122960919 .

[JonathanReeve]

Oh they might be owned by www-data, in which case it'd be sudo -u www-data before the rm command above.

[CathyHajo]

Hi Jon,

I tried that and still got a list of permission denied errors from both xml_added and xml_queue.

Cathy

Cathy Moran Hajo, Ph.D. Associate Editor/Assistant Director The Margaret Sanger Papers Project New York University, Division of Libraries 838 Broadway, Suite 504 New York, NY 10003-4218 (212) 998-8666 cathy.hajo@nyu.edu

Visit our website at: http://www.nyu.edu/projects/sanger

On Sat, Aug 1, 2015 at 8:42 PM, Jonathan Reeve notifications@github.com wrote:

Oh they might be owned by www-data, in which case it'd be sudo -u www-data before the rm command above.

— Reply to this email directly or view it on GitHub https://github.com/JonathanReeve/sanger/issues/92#issuecomment-126966879 .