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

Mon Feb 8 09:47:18 EST 2021

Hi Zia,

The issue persists, see the times in the attached image (site_recruitment | jquery | 3.4 min). I am now running LORIS v23.

How can we check what is happening? We can a have a Zoom call where I can share my screen if needed.

Regards,
Alfredo.

 [cid:9491381B-A96A-43E2-93CC-CED1300E544D]

On Feb 2, 2021, at 9:49 AM, Zia Mohades <zia.mohades at mcin.ca<mailto:zia.mohades at mcin.ca>> wrote:

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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<mailto: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<mailto:zia.mohades at mcin.ca>> wrote:

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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<mailto:dave.macfarlane at mcin.ca>> wrote:
On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto: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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