Trouble viewing interval files in UCSC with Apache+XSendFile
Hello, I've encountered a strange combination of factors that results in file access problems. Perhaps I'm doing something wrong - any advice will be appreciated. I'm using Apache + XSendFile. when viewing a strict BED file, everything works, because the actual dataset filename is passed on to Apache/XSendFile. When viewing any other kind of interval file, Galaxy first creates a temporary file in strict BED format ( in "Interval::as_ucsc_display_file()" ). This method uses "tempfile.mkstemp()", which is documented to create a temporary file with user-only read/write access (no group or world access). So when the file name is passed on to apache/XsendFile - apache can't read the file and returns 404. I'm wondering if anyone else encountered such problem, or is my configuration is somehow wrong. Thanks, -gordon
Until a better solution comes along, this tiny patch makes the temp files world-readable: http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.p... Assaf Gordon wrote, On 04/05/2011 11:14 AM:
Hello,
I've encountered a strange combination of factors that results in file access problems. Perhaps I'm doing something wrong - any advice will be appreciated.
I'm using Apache + XSendFile.
when viewing a strict BED file, everything works, because the actual dataset filename is passed on to Apache/XSendFile.
When viewing any other kind of interval file, Galaxy first creates a temporary file in strict BED format ( in "Interval::as_ucsc_display_file()" ). This method uses "tempfile.mkstemp()", which is documented to create a temporary file with user-only read/write access (no group or world access). So when the file name is passed on to apache/XsendFile - apache can't read the file and returns 404.
I'm wondering if anyone else encountered such problem, or is my configuration is somehow wrong.
Thanks, -gordon ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Assaf Gordon wrote:
Until a better solution comes along, this tiny patch makes the temp files world-readable:
http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.p...
We avoid this by running our webserver as the Galaxy user. Obviously not a solution for everyone (i.e. multiple sites under the same server).
Assaf Gordon wrote, On 04/05/2011 11:14 AM:
Hello,
I've encountered a strange combination of factors that results in file access problems. Perhaps I'm doing something wrong - any advice will be appreciated.
I'm using Apache + XSendFile.
when viewing a strict BED file, everything works, because the actual dataset filename is passed on to Apache/XSendFile.
When viewing any other kind of interval file, Galaxy first creates a temporary file in strict BED format ( in "Interval::as_ucsc_display_file()" ). This method uses "tempfile.mkstemp()", which is documented to create a temporary file with user-only read/write access (no group or world access). So when the file name is passed on to apache/XsendFile - apache can't read the file and returns 404.
I'm wondering if anyone else encountered such problem, or is my configuration is somehow wrong.
Thanks, -gordon ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Do you mean as the same user the galaxy python daemons run as? But not as the same user who has write permissions to those python scripts, right? Mike. On Thu, Apr 7, 2011 at 5:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Assaf Gordon wrote:
Until a better solution comes along, this tiny patch makes the temp files world-readable:
http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.p...
We avoid this by running our webserver as the Galaxy user. Obviously not a solution for everyone (i.e. multiple sites under the same server).
Assaf Gordon wrote, On 04/05/2011 11:14 AM:
Hello,
I've encountered a strange combination of factors that results in file
access problems.
Perhaps I'm doing something wrong - any advice will be appreciated.
I'm using Apache + XSendFile.
when viewing a strict BED file, everything works, because the actual dataset filename is passed on to Apache/XSendFile.
When viewing any other kind of interval file, Galaxy first creates a temporary file in strict BED format ( in "Interval::as_ucsc_display_file()" ). This method uses "tempfile.mkstemp()", which is documented to create a temporary file with user-only read/write access (no group or world access). So when the file name is passed on to apache/XsendFile - apache can't read the file and returns 404.
I'm wondering if anyone else encountered such problem, or is my configuration is somehow wrong.
Thanks, -gordon ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Michael Pheasant wrote:
Do you mean as the same user the galaxy python daemons run as? But not as the same user who has write permissions to those python scripts, right?
To be more specific, it's done by group, and that group only has read-access, yes. --nate
Mike.
On Thu, Apr 7, 2011 at 5:43 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Assaf Gordon wrote:
Until a better solution comes along, this tiny patch makes the temp files world-readable:
http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.p...
We avoid this by running our webserver as the Galaxy user. Obviously not a solution for everyone (i.e. multiple sites under the same server).
Assaf Gordon wrote, On 04/05/2011 11:14 AM:
Hello,
I've encountered a strange combination of factors that results in file
access problems.
Perhaps I'm doing something wrong - any advice will be appreciated.
I'm using Apache + XSendFile.
when viewing a strict BED file, everything works, because the actual dataset filename is passed on to Apache/XSendFile.
When viewing any other kind of interval file, Galaxy first creates a temporary file in strict BED format ( in "Interval::as_ucsc_display_file()" ). This method uses "tempfile.mkstemp()", which is documented to create a temporary file with user-only read/write access (no group or world access). So when the file name is passed on to apache/XsendFile - apache can't read the file and returns 404.
I'm wondering if anyone else encountered such problem, or is my configuration is somehow wrong.
Thanks, -gordon ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (3)
-
Assaf Gordon -
Michael Pheasant -
Nate Coraor