[Loris-dev] Troubleshooting Imaging Browser not loading for 22.0.0 release
Blake Fitch
blake.fitch at tuebingen.mpg.de
Tue Feb 25 07:33:36 EST 2020
Hi Ling Ma,
That made that page work. Thank you.
Best,
Blake
On 25.02.20 13:27, Ling Ma wrote:
> Correction: That part of code is not a PHP command line, it is a whole
> SQL query command separated in several lines. The SQL doesn't accept
> "//" as a comment
>
> On Tue, Feb 25, 2020 at 7:22 AM Ling Ma <lingyun.ma at mcin.ca
> <mailto:lingyun.ma at mcin.ca>> wrote:
>
> Hi Blake,
>
> I just rechecked the image your shared, I saw the problem: you
> should not add "//" in front of the several lines in your code, I
> saw three of them, which will make the syntax totally invalid,
> because it is not a command line, they are a whole command wrapped
> in several lines.
>
>
> Best regards,
> Ling Ma
>
> On Tue, Feb 25, 2020 at 7:19 AM Ling Ma <lingyun.ma at mcin.ca
> <mailto:lingyun.ma at mcin.ca>> wrote:
>
> Hi Blake,
>
> The $modalities_subquery seems to be the only place where it
> is possible to create a wrong SQL when this variable is empty
> and when the Loris-MRI is not installed, which will create a
> favorite environment for image_browser. I am wondering what
> your MySQL server version is, version 5.7 or above? If yes,
> what is the step you have taken to install Loris? If you have
> followed the exact installation instructions, then I am
> wondering whether you could share your zipped database dump,
> which should not be big since this is a new installation, so
> that we could investigate what has happened. Thanks a lot and
> sorry for the trouble.
>
> Another possibility is to check the MySQL parameters used in
> sql_mode? Which could be checked via "SELECT@@sql_mode;",
> could you also check that value? What is the value you see?
> Since image_browser uses a relatively complicated query, it is
> possible that a parameter might make the syntax not valid.
>
> Best regards,
> Ling Ma
> Dev consultant.
>
> On Tue, Feb 25, 2020 at 4:32 AM Blake Fitch
> <blake.fitch at tuebingen.mpg.de
> <mailto:blake.fitch at tuebingen.mpg.de>> wrote:
>
> Hi Christine,
>
> I have ensured that he code matches the link you sent. I
> did the edit, ran make in /var/www/loris, and restarted
> apache. I still get:
> "An error occured while loading the page."
>
> Here is a snapshot of the code in that area of the file:
>
> Best,
> Blake
>
> On 24.02.20 19:33, Christine Rogers, Ms. wrote:
>> Hi Blake,
>> First/next troubleshooting question --
>>
>> Could you verify you're using the latest update from this
>> bugfix:
>> https://github.com/aces/Loris/pull/6089/commits/c78af4ebc97d354b6820c51c8bb746e0e0e554f5
>>
>> This may resolve it, let us know --
>> Thanks,
>> Christine
>>
>> On Mon, Feb 24, 2020 at 1:23 PM Christine Rogers, Ms.
>> <christine.rogers at mcgill.ca
>> <mailto:christine.rogers at mcgill.ca>> wrote:
>>
>> Hi Loris team and community,
>> i'm forwarding a question from Blake (below) from Max
>> Planck in Tuebingen --he's encountering a (known) bug
>> in the 22.0.0 Imaging Browser where the module
>> doesn't load (issue #6088)
>>
>> His apache error log output is below.
>> Blake is running Ubuntu and has installed 22.0.0, and
>> uploaded some test DICOMs. He's applied the proposed
>> bugfix #6089, without success (see below).
>>
>> Could someone help resolve / share a solution for this ?
>> Thanks,
>> Christine
>>
>> ---------- Forwarded message ---------
>> From: *Blake Fitch* <blake.fitch at tuebingen.mpg.de
>> <mailto:blake.fitch at tuebingen.mpg.de>>
>> Date: Fri, Feb 21, 2020 at 11:11 AM
>> Subject: Re: Fix for Imaging Browser not loading
>> To: Christine Rogers, Ms. <christine.rogers at mcgill.ca
>> <mailto:christine.rogers at mcgill.ca>>
>>
>>
>> Hi Christine,
>>
>> I did the new patch. Looks the same. here's there
>> error log entry that pops out.
>>
>> [Fri Feb 21 16:09:51.361760 2020] [php7:warn] [pid
>> 25261] [client 10.38.124.254:55712
>> <http://10.38.124.254:55712>] PHP Warning:
>> PDOStatement::execute(): SQLSTATE[42000]: Syntax
>> error or access violation: 1064 You have an error in
>> your SQL syntax; check the manual that corresponds to
>> your MySQL server version for the right syntax to use
>> near '// \n CASE \n WHEN
>> s.MRIQCPending='Y' THEN ' at line 30 in
>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php
>> on line 81, referer: http://10.38.133.3/imaging_browser/
>> [Fri Feb 21 16:09:51.361873 2020] [php7:error] [pid
>> 25261] [client 10.38.124.254:55712
>> <http://10.38.124.254:55712>] PHP Fatal error:
>> Uncaught Exception: Invalid SQL statement: SELECT
>> \n p.Name as Site,\n
>> c.PSCID as PSCID,\n c.CandID as DCCID,\n Project.Name
>> as project,\n s.Visit_label as visitLabel,\n
>> \n CASE s.MRIQCStatus\n WHEN 'Fail' THEN\n
>> IF(s.MRIQCPending='Y', 'Pending Fail', 'Fail')\n WHEN
>> 'Pass' THEN\n IF(s.MRIQCPending='Y', 'Pending Pass',
>> 'Pass') \n ELSE s.MRIQCStatus\n END
>> \n as Visit_QC_Status,\n
>> DATE_FORMAT(MIN(pf.Value), "%Y-%m-%d") as
>> First_Acquisition,\n FROM_UNIXTIME(MIN(f.InsertTime))
>> as First_Insertion,\n
>> FROM_UNIXTIME(MAX(fqc.QCLastChangeTime)) as
>> Last_QC,\n \n CASE \n
>> COALESCE(Max(fqc.QCLastChangeTime),
>> 'new')\n WHEN 'new' THEN
>> 'new'\n WHEN '' THEN
>> 'new'\n WHEN NULL THEN
>> 'new'\n ELSE ''\n END as
>> New_Da in
>> /var/www/loris/src/Data/Provisioners/DBRowProvisioner.php
>> on line 84, referer: http://10.38.133.3/imaging_browser/
>>
>> Best,
>> Blake
>>
>>
>>
>> --
>>
>> christine.rogers at mcgill.ca
>> <mailto:christine.rogers at mcgill.ca>
>> McGill Centre for Integrative Neuroscience | MCIN.ca
>> Montreal Neurological Institute
>> McGill University | Montreal | Canada
>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> <mailto:Loris-dev at bic.mni.mcgill.ca>
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>>
>>
>> --
>>
>> christine.rogers at mcgill.ca
>> <mailto:christine.rogers at mcgill.ca>
>> McGill Centre for Integrative Neuroscience | MCIN.ca
>> Montreal Neurological Institute
>> McGill University | Montreal | Canada
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