Help, cannot make backups any more (security)

roland · November 5, 2018, 6:01pm

Situation
I can’t make a backup any more via Administration -> backup, the backup program will not run. And worse: the page displays an error message with the Mysql password in plain text for anyone to see !!

OpenEMR Version
I’m using OpenEMR version 5.0.1(6)

Browser:
I’m using: Firefox 63

Operating System
I’m using: FreeBSD 11.1

Error message: Dumping OpenEMR database... "/usr/bin/mysqldump -u 'openvemr' -p'xxxxxxxxxxxxxxx' -h 'localhost' --port='3306' --opt --quote-names -r /tmp/openemr_web_backup/emr_backup/openemr.sql 'openvemr'" returned 127:

(replaced the mysql password with x’s obviously…)
What went wrong?
Roland

stephenwaite · November 5, 2018, 6:20pm

hi @roland, can you check to see if this directory exists on your freebsd box?

roland · November 5, 2018, 6:59pm

hi @stephenwaite,
yes it does exist (owner www) but it is empty

stephenwaite · November 5, 2018, 9:04pm

and does mysqldump live here on freebsd?

roland · November 5, 2018, 9:31pm

no, it is at /usr/local/bin/mysqldump

stephenwaite · November 5, 2018, 9:31pm

ok @roland, maybe a symlink to /usr/bin then?

roland · November 5, 2018, 9:50pm

ok, I did that, but it still doesn’t work. It starts copying the database but then stalls again with another error:
Dumping OpenEMR database... Dumping OpenEMR web directory tree... "tar --same-owner --ignore-failed-read -zcphf /tmp/openemr_web_backup/emr_backup/openemr.tar.gz "version.php" "repositories" "contrib" "CODE_OF_CONDUCT.md" "vendor" "services" "patients" "controller.php" "custom" "ci" "templates" "composer.lock" "portal" "interface" ".bowerrc" "controllers" "ccdaservice" "images" ".env.example" ".editorconfig" "config" "CONTRIBUTING.md" "cloud" "myportal" "entities" "phpfhir" "composer.json" "ccr" "index.php" "library" "modules" "gacl" ".travis.yml" "public" "acknowledge_license_cert.html" "sql" "build.xml" "Documentation" "docker-compose.yml" "README.md" ".github" "common" ".gitignore" "LICENSE" "sites/default" "bower.json"" returned 1:

now what?

stephenwaite · November 5, 2018, 11:04pm

must be due to bsd’s implementation of tar
try cd ing to your www document root, like /var/www/html/openemr and issuing the following at the command line to see more error details

roland:

tar --same-owner --ignore-failed-read -zcphf /tmp/openemr_web_backup/emr_backup/openemr.tar.gz “version.php” “repositories” “contrib” “CODE_OF_CONDUCT.md” “vendor” “services” “patients” “controller.php” “custom” “ci” “templates” “composer.lock” “portal” “interface” “.bowerrc” “controllers” “ccdaservice” “images” “.env.example” “.editorconfig” “config” “CONTRIBUTING.md” “cloud” “myportal” “entities” “phpfhir” “composer.json” “ccr” “index.php” “library” “modules” “gacl” “.travis.yml” “public” “acknowledge_license_cert.html” “sql” “build.xml” “Documentation” “docker-compose.yml” “README.md” “.github” “common” “.gitignore” “LICENSE” “sites/default” “bower.json”

roland · November 5, 2018, 11:54pm

it seems to be only part of the problem: did that too and it said:

tar: Option --ignore-failed-read is not supported

then I ran it again without that option, it then starts to copy the directories but after a while still hangs, now it seems to be unable to handle a patient file name:
Can't translate pathname 'sites/default/documents/38/Linus_Bl��ser.jpg' to UTF-8

The (cat) patiënt’s name is Linus Bläser. We have many patients with é,Ö,ǘ or c-cedilla’s in their name. Is this backup script specific? The rest of OpenEMR runs fine; it never was a problem except in the ACL list which does not accept these characters (see one of my other posts that was unanswered unfortunately).

stephenwaite · November 6, 2018, 12:28am

hi @roland, what locale is your environment?

https://www.freebsd.org/doc/en_US.ISO8859-1/books/handbook/using-localization.html

also, are you sure it hangs from the command line and it’s not writing the tar file? you could open another terminal and ls -lrt the file to see if it’s growing in size, it may take a little while to finish it’s work

forgot that instead of the symlink you could have changed the path to mysql binaries in Admin->Globals->Miscellaneous

roland · November 6, 2018, 10:44am

hi,
ok, I forgot about the path to the mysql binaries in globals too and changed it, symlink removed. You were right about it taking some time, it took a while before it had completed tarring the directories. However, it still stops, leaving two gz files in tmp, it’s not combined into one file and not presented for download in the browser like it used to.
I doubt the locale (en_dk, which has the proper time/decimal/money format) has anything to do with it, since it always ran without problems in all versions, and the locale hasn’t changed.
I’ll forget the backup script for now and do manual backups…
Am I wrong or could this be a problem of OpenEMR’s inconsistent internationalization support? Forgive me if that sounds a bit harsh, it is frustration with past unanswered issues, and still present shortcomings with time entry, decimal separators and diacritical characters e.g. in the ACL.
thanks,
Roland

stephenwaite · November 6, 2018, 11:08am

hi @roland, this is mostly a freebsd issue since openemr is using the native operating system binaries and it seems like the locale prevents the filename completion

now that you’ve fixed the path you just need to edit the backup script to remove the --ignore-failed-read in openemr/backup.php at rel-501 · openemr/openemr · GitHub and it should work minus the patient file names mentioned previously

roland · November 6, 2018, 5:01pm

Well, I tried everything, but I still feel that a backup “minus some patient file names” is not a real backup. The locale hasn’t changed, as I said I never had this problem in 5.00 or earlier versions. No other software on the Freebsd box does this, just the OEMR 5.01 backup script. But I’ll use manual copying, that works.

stephenwaite · November 6, 2018, 6:05pm

it’s only those documents like the .jpg you mentioned previously that are not captured so you could rename those few

and we could work on escaping those special characters here

github.com

openemr/openemr/blob/rel-501/interface/main/backup.php#L717


if ($newBackupMethod) {
   // Create a tar object using the pear library
   //  (this is the preferred method)
    $tar = new Archive_Tar($archiveName, $compressMethod);
    if ($tar->create($itemArray)) {
        return true;
    }
} else {
   // Create the tar files via command line tools
   //  (this method used when the tar pear library is not available)
    $files = '"' . implode('" "', $itemArray) . '"';
    if ($compressMethod == "gz") {
        $command = "tar --same-owner --ignore-failed-read -zcphf $archiveName $files";
    } else {
        $command = "tar -cpf $archiveName $files";
    }


    $temp0 = exec($command, $temp1, $temp2);
    if ($temp2) {
        die("\"$command\" returned $temp2: $temp0");
    }

roland · November 6, 2018, 10:57pm

hi @stephenwaite,
thanks. Although the console complained about those document titles with ä and ü etc., and the script seemed to stall, I was surprised to find them in the tar archive with the filenames intact. It’s not an option to rename all the documents that have diacritical characters in them, too many and we never had to. But thanks for diving into the script code. I don’t understand, it’s not clear what you mean by we; should I change the lines in red in the code or are you working on some fix?
thanks for your time
Roland

stephenwaite · November 6, 2018, 11:53pm

hi @roland, sounds like we don’t need to fix it so you should be all set to run the backup inside openemr if you remove the --ignore-failed-read mentioned above

Help, cannot make backups any more (**security**)

Help, cannot make backups any more (security)