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

[Dave MacFarlane]

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] 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
> ===
>
>
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] 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/
> [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client
> 216.15.126.108:56738] 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/
> [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client
> 216.15.126.108:56738] 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/
> ===
>
>
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]
> ===
>
> 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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