[Loris-dev] Issues with landing page, data query and BrainBrowser

Tue Feb 2 09:49:47 EST 2021

Hi Alfredo,

Please let me know if your issue has been resolved.

Thank you

On Mon, Jan 25, 2021 at 8:35 AM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Dear Zia,
>
> The issue is when loading the landing page once a user had logged in into
> LORIS. The systems remains unresponsive until the graph is loaded. I am
> moving to the last version of LORIS right now, I will inform if the issues
> persists in the latests version.
>
> Thank you.
>
> Alfredo.
>
> On Jan 7, 2021, at 3:34 PM, Zia Mohades <zia.mohades at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hello,
>
> Regarding your first question. As Dave mentioned we haven't experienced
> any issues with loading when we click on the link/site under the graph. We
> did however noticed some formatting issues which should be fixed in the new
> version of LORIS but nothing related to the loading functionality.
>
>
> Thank you
>
>
> On Wed, Jan 6, 2021 at 12:51 PM Dave MacFarlane <dave.macfarlane at mcin.ca>
> wrote:
>
>> On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo <
>> AMORALESPINZON at bwh.harvard.edu> wrote:
>>
>>> Dear LorisDev team,
>>>
>>> We are experiencing the following issues in Loris. Could you please help
>>> me or guide me on how address them.
>>>
>>> 1. After login into LORIS, the webpage does not allow the user to go to
>>> any link until the graph under "Study Progression" is created. This is
>>> taking more than one minute to load. I guess this is because we have
>>> hundreds of centers. Is it possible to remove the graph from the landing
>>> page? (See attachment)
>>>
>>>
>> I don't believe it should take that long even with a large number of
>> sites. I'll let someone from CCNA handle this part of the question since
>> they also have hundreds of sites and might have more insight..
>>
>>
>>>
>>> 2. When using the Data Query Tool the front-end crashes with error 500.
>>>
>>> This is what I can see in the loris-error.log
>>>
>>> ===
>>> [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client
>>> 216.15.126.108:56023
>>> <http://secure-web.cisco.com/1WEkcMysyWStSVz7qKpBtYZtz-xrpp1mPaByBjiqSPA9SZmeKHvGSdf3rXamfd2uDcyk9mX81q9xtiBMKgVKyYR4W-1DBZqDKCk4UB2yFtZodmXth8cvg6mRuv8aZ2OY7zrD4ceY6Bes_NzGusndhEPxln-qfV2pPRZutvE8WIGrAkktkyqbT2932WsPmQrUJ7Aw_BNaLRnmyvD8kpuuzmVtIyfXe3WzGxt0DPppl0YkPeNvdZTlHVtv0OQkEgOOmfmxZjJnwbymbl6gNZCS4Aw/http%3A%2F%2F216.15.126.108%3A56023>]
>>> PHP Fatal error:  Uncaught ConfigurationException: NDB_Factory::CouchDB()
>>> requires all parameters to be supplied. in
>>> /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0
>>> /var/www/loris/modules/dataquery/php/dataquery.class.inc(59):
>>> NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0,
>>> '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1
>>> /var/www/loris/php/libraries/NDB_Form.class.inc(188):
>>> LORIS\\dataquery\\Dataquery->setup()\n#2
>>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171):
>>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3
>>> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49):
>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>> Object(LORIS\\dataquery\\Dataquery))\n#4
>>> /var/www/loris/php/libraries/NDB_Page.class.inc(659):
>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest),
>>> Object(LORIS\\dataquery\\Dataquery))\n#5
>>> /var/www/loris/php/libraries/Module.class.inc(341):
>>> NDB_Page->process(Object(Zend\\ in
>>> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer:
>>>
>>> https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935
>>> <https://secure-web.cisco.com/1RSIugAJMQUGXvusoQetBHcf0j84JY0S6EgPaD1_LfdQpRlhPtrtNIEnrXDjYllpX2Okn2abcPbPraSpdkPmoEybMpPc-Km4z6MVi-cEQvYUmv2DORKXippBAeVsHB0tHs55X02iHpm3xNKlG5T2Zt2wCngYaxfNWxR4sC-mDMLsEIJzdQPZiyVJUPUNF5LVPRVKOnErvdPDgIPq3Ce3Y24ceSJTkt0CRJzTNusjrVm646V02S1_3iAdJswiSHhyaWSbCfXHWlwEigX-r1r7_FQ/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fimaging_browser%2FviewSession%2F%3FsessionID%3D85935>
>>> ===
>>>
>>>
>> The DQT currently requires a CouchDB backend with the data imported into
>> it. It looks like the CouchDB hostname/database/username/ password/etc
>> aren't set up. The Configurations section of the file
>> modules/dataquery/README.md should have more information about the setup
>> required. Is the `<CouchDB>` tag in project/config.xml setup as described
>> in step 3 of that document?
>>
>>
>>>
>>> 3. In the statistics section (Reports -> Statistics) I can see the
>>> following message at the bottom of the page:
>>>
>>> ===
>>> Oops
>>>
>>> It seems like the scan type selected does not have a corresponding
>>> column in the mri_parameter_form table in the database.
>>> In order to display the statistics for the scan type, make sure the
>>> mri_parameter_form table contains a column in the exact format
>>> SCANTYPE_Scan_done
>>> ===
>>>
>>>
>> The statistics page using an instrument named "mri_parameter_form" to
>> determine numbers for the scan done. For each scan type in the
>> mri_scan_types table* it expects there to be a column named
>> "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's
>> somewhere in the MRI documentation that goes into more depth but I'm not
>> entirely sure where, maybe Cecile can chime in..
>>
>> In the loris-error.log a see a large list of the following messages:
>>>
>>> ===
>>> [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client
>>> 216.15.126.108:56738
>>> <http://secure-web.cisco.com/194rpS3q9XNXxClvnkwJk3Z5TXDYQpXdnJTmjmtMl0rW6vlUQEBQ8jnizUEJXqsPLQZcrPYqfCmX2WJTnp3nbXr5cVnEgCU8VA2JkoAWYhp3kgMry9HCaKnqYtfk4JpPMefzKgVd51jBzXzOCuvJIFpJYxFjIcZKtr3exwshNEd_qp-CKLKgW6jrpJOdMJ1oi5p0T_OtI91aMZo_Jz2piFL5ozxblRcq0dwB8GHVUChwyf71wqsVzCO7DtSOwr8oum5QXdnAvSQRVRl8WFapVmg/http%3A%2F%2F216.15.126.108%3A56738>]
>>> PHP Notice:  Undefined index: Female in
>>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line
>>> 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/
>>> <https://secure-web.cisco.com/1aW5ReU5kAMfdryzMa60cZ7x3ix4DOm9RDXsWQ9OW63HzvgMvrO8HyVV3oMaPfYYwVqN6aeUrpnadfu93Z3s3G-LudGQUVVKEbi6NBbvaxNUzXFvgvnp3SSSeHMd5qZhvpFr2JV8Ve9jZDAP0rFkfXoPUT6SVoZ8xWd0Gsnxf1ADisP3ucBGZlwIpFb3lDNuEYdn2D48-jDWyMKRxSCPbuOlWgbyVYZ2xMsedRJPsi1OlNoNqBoR1Oy67jnvcSROGs3EYjfWI9bZ3juyNtOfZiA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fstatistics%2F>
>>> [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client
>>> 216.15.126.108:56738
>>> <http://secure-web.cisco.com/194rpS3q9XNXxClvnkwJk3Z5TXDYQpXdnJTmjmtMl0rW6vlUQEBQ8jnizUEJXqsPLQZcrPYqfCmX2WJTnp3nbXr5cVnEgCU8VA2JkoAWYhp3kgMry9HCaKnqYtfk4JpPMefzKgVd51jBzXzOCuvJIFpJYxFjIcZKtr3exwshNEd_qp-CKLKgW6jrpJOdMJ1oi5p0T_OtI91aMZo_Jz2piFL5ozxblRcq0dwB8GHVUChwyf71wqsVzCO7DtSOwr8oum5QXdnAvSQRVRl8WFapVmg/http%3A%2F%2F216.15.126.108%3A56738>]
>>> PHP Notice:  Undefined index: OLYMPUS_CLINICAL_SCREENING in
>>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line
>>> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/
>>> <https://secure-web.cisco.com/1aW5ReU5kAMfdryzMa60cZ7x3ix4DOm9RDXsWQ9OW63HzvgMvrO8HyVV3oMaPfYYwVqN6aeUrpnadfu93Z3s3G-LudGQUVVKEbi6NBbvaxNUzXFvgvnp3SSSeHMd5qZhvpFr2JV8Ve9jZDAP0rFkfXoPUT6SVoZ8xWd0Gsnxf1ADisP3ucBGZlwIpFb3lDNuEYdn2D48-jDWyMKRxSCPbuOlWgbyVYZ2xMsedRJPsi1OlNoNqBoR1Oy67jnvcSROGs3EYjfWI9bZ3juyNtOfZiA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fstatistics%2F>
>>> [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client
>>> 216.15.126.108:56738
>>> <http://secure-web.cisco.com/194rpS3q9XNXxClvnkwJk3Z5TXDYQpXdnJTmjmtMl0rW6vlUQEBQ8jnizUEJXqsPLQZcrPYqfCmX2WJTnp3nbXr5cVnEgCU8VA2JkoAWYhp3kgMry9HCaKnqYtfk4JpPMefzKgVd51jBzXzOCuvJIFpJYxFjIcZKtr3exwshNEd_qp-CKLKgW6jrpJOdMJ1oi5p0T_OtI91aMZo_Jz2piFL5ozxblRcq0dwB8GHVUChwyf71wqsVzCO7DtSOwr8oum5QXdnAvSQRVRl8WFapVmg/http%3A%2F%2F216.15.126.108%3A56738>]
>>> PHP Notice:  Undefined index: Male in
>>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line
>>> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/
>>> <https://secure-web.cisco.com/1aW5ReU5kAMfdryzMa60cZ7x3ix4DOm9RDXsWQ9OW63HzvgMvrO8HyVV3oMaPfYYwVqN6aeUrpnadfu93Z3s3G-LudGQUVVKEbi6NBbvaxNUzXFvgvnp3SSSeHMd5qZhvpFr2JV8Ve9jZDAP0rFkfXoPUT6SVoZ8xWd0Gsnxf1ADisP3ucBGZlwIpFb3lDNuEYdn2D48-jDWyMKRxSCPbuOlWgbyVYZ2xMsedRJPsi1OlNoNqBoR1Oy67jnvcSROGs3EYjfWI9bZ3juyNtOfZiA/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fstatistics%2F>
>>> ===
>>>
>>>
>> What version of LORIS is this? I think the notices are unrelated and
>> probably harmless but should still be fixed if they haven't been yet.
>>
>>
>>> 4. I am not able to visualiza any image. A message “LOADING …” appears
>>> but nothing happens.
>>> Looking at the loris-error.log I can see that the path to the images is
>>> missing a ‘/‘
>>>
>>> ===
>>> PHP Warning:  readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc):
>>> failed to open stream: No such file or directory in
>>> /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer:
>>> https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603
>>> <https://secure-web.cisco.com/1qcnAyuV-itGYLsW-bvfnnZmMXgviJ0bIS9ewUeKT7Z2LHVxmN8AAU4UInV2oAgZB6NrfGeuQY9xvXYra4_NtFqwgjqKJCIX6ppgg2uhZuVWYnAS95VZLN5cW8-aU6C-xULojAnf3IticPcrom9I3-N4KMODp1Q9-weJyX26EQxaHXpoCXh9X9EcFZM_TM55umfEaItv8nQkF2DSbxHEuPylNfr__PRXLNppDHcJz2Bx1w5JBNctLW55U7asBDcXV1wJQuUeyyqWUIS4RbH7_tQ/https%3A%2F%2Fipmsa-loris.bic.mni.mcgill.ca%2Fbrainbrowser%2F%3Fminc_id%3D%5B112603>
>>> ]
>>> ===
>>>
>>> Do you know where can this missing ‘/‘ should be set?
>>>
>>>
>> It looks like that code is using the imagePath configuration variable
>> which should have a trailing /.  It should be the configuration option
>> labeled "Path to images for display in Imaging Browser (e.g.
>> /data/$project/data/)" in the Configuration module frontend.
>>
>> - Dave
>> _______________________________________________
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