[Loris-dev] Imaging Uploader Failing File Verification

[Eli Johnson]

Thanks Nicolas,

It looks like the error was that the script was still pulling /tmp as the
directory. To resolve, I set upload_tmp_dir and sys_temp_dir to my custom
path and then set systemd PrivateTmp to false (specific to centos/rhel).

-Eli

Eli Johnson
Developer/Researcher
Institute of Child Development
University of Minnesota
joh17964 at umn.edu


On Fri, Jul 24, 2020 at 12:22 PM Nicolas Brossard <
nicolasbrossard.mni at gmail.com> wrote:

> Also, here are links for information regarding error code 7:
>
> https://www.php.net/manual/en/features.file-upload.post-method.php
> https://www.php.net/manual/en/features.file-upload.errors.php
>
> Hope this helps.
>
> Best,
> Nicolas
>
> On Fri, Jul 24, 2020 at 1:18 PM Nicolas Brossard <
> nicolasbrossard.mni at gmail.com> wrote:
>
>> Hi Eli,
>>
>> If you have specified a value for TMPDIR in your environment file, you
>> should also set the value of variable upload_tmp_dir in your php.ini
>> file, otherwise the uploader will still use the default system temporary
>> directory (usually /tmp, which most often than not has limited space).
>>
>> On Fri, Jul 24, 2020 at 12:26 PM Eli Johnson <joh17964 at umn.edu> wrote:
>>
>>> Hi Nicolas,
>>>
>>> I do have a custom path for TMPDIR set in the environment file and I
>>> have confirmed that the directory is writable (by user apache in this case
>>> since OS is RHEL) and has plenty of space.
>>>
>>> Where do I find what the upload error code number indicates? I saw that
>>> it was 7 but couldn't find where it was being set or what it meant.
>>>
>>> Any other recommendations for debugging this? The error log is sparse
>>> and not particularly helpful here. Should I still be looking in
>>> imaging_uploader.class.inc or is this an issue that begins in a parent
>>> library (ie File_Upload.class.inc)?
>>>
>>> Best,
>>> Eli
>>>
>>> Eli Johnson
>>> Developer/Researcher
>>> Institute of Child Development
>>> University of Minnesota
>>> joh17964 at umn.edu
>>>
>>>
>>> On Fri, Jul 24, 2020 at 11:03 AM Nicolas Brossard <
>>> nicolasbrossard.mni at gmail.com> wrote:
>>>
>>>> Hi Eli,
>>>>
>>>> Looking at what is being passed to $file->setHandlerArgs, I can see
>>>> that the upload error code is set to 7, which means that the system could
>>>> not copy your file in the temporary directory dedicated to uploading files
>>>> on the server. By default, uploaded files are written in /tmp, but you
>>>> can override this by setting variable TMPDIR in
>>>> <LORIS_MRI_ROOT>/environment. I would check that whichever directory
>>>> you are uploading to has enough free space to allow the upload and that
>>>> user www-data has write permission on that directory.
>>>>
>>>> Let me know if that fixes the issue.
>>>>
>>>> Best,
>>>> Nicolas
>>>>
>>>> On Thu, Jul 23, 2020 at 11:50 PM Eli Johnson <joh17964 at umn.edu> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Using LORIS v23.0 on RHEL 7, accessing LORIS front end from Chrome.
>>>>>
>>>>> I'm currently setting up the LORIS-MRI and imaging modules for LORIS.
>>>>> I am running into an issue with the Imaging Uploader on the front end where
>>>>> it is returning the error message "The
>>>>> file TEST111_986793_testing1.zip is not of type .tgz, .tar.gz or .zip."
>>>>> When checking the error-log from the back end I'm seeing...
>>>>>
>>>>> PHP Warning:  mime_content_type(): Empty filename or path in
>>>>> /<basepath>/modules/imaging_uploader/php/imaging_uploader.class.inc on line
>>>>> 646, referer: http://<site>/imaging_uploader
>>>>>
>>>>>
>>>>> Upon further investigation into imaging_uploader.class.inc, the
>>>>> function isCompressed() is being passed an empty string from isValid().
>>>>> IsValid is passing it $temp_file, defined in
>>>>> $temp_file=$file->fileInfo['tmp_name'], but this is also an
>>>>> empty string. So I'm trying to figure out at what stage 'tmp_name' should
>>>>> be defined for $file->fileInfo but I am struggling to track it down. I
>>>>> checked what was being passed in $file->setHandlerArgs and it contains this:
>>>>>
>>>>> Array
>>>>> (
>>>>>     [IsPhantom] => N
>>>>>     [candID] => 986793
>>>>>     [pSCID] => TEST111
>>>>>     [visitLabel] => testing1
>>>>>     [mriFile] => Array
>>>>>         (
>>>>>             [name] => TEST111_986793_testing1.zip
>>>>>             [type] =>
>>>>>             [tmp_name] =>
>>>>>             [error] => 7
>>>>>             [size] => 0
>>>>>         )
>>>>> )
>>>>>
>>>>>
>>>>> Any suggestions on how to get the uploader working? I have verified
>>>>> that the MRIUploadIncomingPath variable is set appropriately and is an
>>>>> existing, writable directory. I also am able to successfully upload the
>>>>> same zip file from the back end.
>>>>>
>>>>>
>>>>> Thanks,
>>>>> Eli
>>>>>
>>>>>
>>>>> Eli Johnson
>>>>> Developer/Researcher
>>>>> Institute of Child Development
>>>>> University of Minnesota
>>>>> joh17964 at umn.edu
>>>>> _______________________________________________
>>>>> Loris-dev mailing list
>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>
>>>>
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